Research

For the most recent panorama, please see our 2022 highlights:

Inventing a New Discipline: SoHP and MHAAM Annual Bulletin

Archive of previous Annual Bulletins

______________________________

MHAAM Publications 2016 - 2024

2024

"Solar storms, ice cores and nuns’ teeth: the new science of history" The Guardian 20 February (2024)

Mikanowski, Jacob

2023

"A genetic history of the Balkans from Roman frontier to Slavic migrations" Cell 186:25 (2023)

I. Olalde, P. Carrion, I. Mikić, N. Rohland, S. Mallick, I. Lazaridis, M. Mah, M. Korać, S. Golubović, S. Petković, N. Miladinović-Radmilović, D. Vulović, T. Alihodžić, A. Ash, M. Baeta, J. Bartík, Ž. Bedić, M. Bilić, C. Bonsall, M. Bunčić, D. Bužanić, M. Carić, L. Čataj, M. Cvetko, I. Drnić, A. Dugonjić, A. Đukić, K. Đukić, Z. Farkaš, P. Jelínek, M. Jovanovic, I. Kaić, H. Kalafatić, M. Krmpotić, S. Krznar, T. Leleković, M.M. de Pancorbo, V. Matijević, Z.B. Milošević, A. Osterholtz, J.M. Paige, D.T. Pavičić, Z. Premužić, P. Rajić Šikanjić, A. Rapan Papeša, L. Paraman, M. Sanader, I. Radovanović, M. Roksandic, A. Šefčáková, S. Stefanović, M. Teschler-Nicola, D. Tončinić, B. Zagorc, K. Callan, F. Cnadilio, O. Cheronet, D. Fernandes, A. Kearns, A.M. Lawson, K. Mandl, A. Wagner, F. Zalzala, A. Zettl, Ž. Tomanović, D. Keckarević, M. Novak, K. Harper, M. McCormick, R. Pinhasi, M. Grbić C. Lalueza-Fox, D. Reich.

The rise and fall of the Roman Empire was a socio-political process with enormous ramifications for human history. The Middle Danube was a crucial frontier and a crossroads for population and cultural movement. Here, we present genome-wide data from 136 Balkan individuals dated to the 1st millennium CE. Despite extensive militarization and cultural influence, we find little ancestry contribution from peoples of Italic descent. However, we trace a large-scale influx of people of Anatolian ancestry during the Imperial period. Between ∼250 and 550 CE, we detect migrants with ancestry from Central/Northern Europe and the Steppe, confirming that “barbarian” migrations were propelled by ethnically diverse confederations. Following the end of Roman control, we detect the large-scale arrival of individuals who were genetically similar to modern Eastern European Slavic-speaking populations, who contributed 30%–60% of the ancestry of Balkan people, representing one of the largest permanent demographic changes anywhere in Europe during the Migration Period.

“The Genetic Legacy of African Americans from Catoctin Furnace.” Science 381:1-13 (2023).

É. Harney, S. Micheletti, K.S. Bruwelheide, W.A. Freyman, K. Bryc, A. Akbari, E. Jewett, E. Comer, H.L. Gates, L. Heywood, J. Thornton, R. Curry, S.A. Esselmann, K.G. Barca, J. Sedig, K. Sirak, I. Olalde, N. Adamski, R. Bernardos, N. Broomandkhoshbacht, M. Ferry, L. Qiu, K. Stewardson, J.N. Workman, F. Zalzala, S. Mallick, A. Micco, M. Mah, Z. Zhang, 23andMe Research Team, N. Rohland, J.L. Mountain, D.W. Owsley, D. Reich.

Few African Americans have been able to trace family lineages back to ancestors who died before the 1870 United States Census, the first in which all Black people were listed by name. We analyzed 27 individuals from Maryland’s Catoctin Furnace African American Cemetery (1774–1850), identifying 41,799 genetic relatives among consenting research participants in 23andMe, Inc.’s genetic database. One of the highest concentrations of close relatives is in Maryland, suggesting that descendants of the Catoctin individuals remain in the area. We find that many of the Catoctin individuals derived African ancestry from the Wolof or Kongo groups and European ancestry from Great Britain and Ireland. This study demonstrates the power of joint analysis of historical DNA and large datasets generated through direct-to-consumer ancestry testing.

“Early contact between late farming and pastoralist societies in southeastern Europe.” Nature 620: 358-365 (2023).

S. Penske, A. B. Rohrlach, A. Childebayeva, G. Gnecchi-Ruscone, C. Schmid, M.A. Spyrou, G.U. Neumann, N. Atanassova, K. Beutler, K. Boyadzhiev, Y. Boyadzhiev, I. Bruyako, A. Chohadzhiev, B. Govedarica, M. Karaucak, R. Krauss, M. Leppek, I. Manzura, K. Privat, S. Ross, V. Slavchev, A. Sobotkova, M. Toderaş, T. Valchev, H. Ringbauer, P.W. Stockhammer, S. Hansen, J. Krause, W. Haak.

Archaeogenetic studies have described two main genetic turnover events in prehistoric western Eurasia: one associated with the spread of farming and a sedentary lifestyle starting around 7000–6000 BC and a second with the expansion of pastoralist groups from the Eurasian steppes starting around 3300 BC. The period between these events saw new economies emerging on the basis of key innovations, including metallurgy, wheel and wagon and horse domestication. However, what happened between the demise of the Copper Age settlements around 4250 BC and the expansion of pastoralists remains poorly understood. To address this question, we analysed genome-wide data from 135 ancient individuals from the contact zone between southeastern Europe and the northwestern Black Sea region spanning this critical time period. While we observe genetic continuity between Neolithic and Copper Age groups from major sites in the same region, from around 4500 BC on, groups from the northwestern Black Sea region carried varying amounts of mixed ancestries derived from Copper Age groups and those from the forest/steppe zones, indicating genetic and cultural contact over a period of around 1,000 years earlier than anticipated. We propose that the transfer of critical innovations between farmers and transitional foragers/herders from different ecogeographic zones during this early contact was integral to the formation, rise and expansion of pastoralist groups around 3300 BC.

“Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.” F1000Research (2023).

M. Borry, A. Forsythe, A. Andrades Valtueña, A. Hübner, A. Ibrahim, A. Quagliariello, A.E. White, A. Kocher, A. Vågene, B.J. Bartholdy, D. Spurite, G. Yaxal Ponce-Soto, G. Neumann, I-T Huang, I. Light, I.M. Velsko, I. Jackson, J. Frangenberg, J.G. Serrano, J. Fumey, K.T. Özdogan, K.E. Blevins, K.G. Daly, M. Lolopolo, M. Moraitou, M. Michel, M. van Os, M. Bravo-Lopez, M.S. Sarhan, N.D. Dagtas, N. Oskolkov, O.S. Smith, O. Lebrasseur, P. Rozwalak, R. Eisenhofer, S. Wasef, S.L. Ramachandran, V. Vanghi, C. Warinner, J. Fellows Yates. (2023)

Background: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.github.io) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications. Methods: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate automated metadata curation and data validation, as well as rapid data filtering and downloading. Results: AncientMetagenomeDir was extended to include standardised metadata of over 5000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community. Conclusions: Together, both standardised metadata and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.

“Isotopic and proteomic evidence for communal stability at Pre-Pottery Neolithic Jericho in the Southern Levant.” Scientific Reports 13, 16360 (2023).

X. Wang, B. Zhang, Y. Sun, T. Ingman, S. Eisenmann, M. Lucas, E. Scott, J. Ilgner, G. Wu, P. le Roux, X. Wu, X. Zhang, A. Fan, P. Roberts, P.W. Stockhammer.

As one of the key, long-term occupied sites in the Southern Levant, Jericho was one of the most important early Neolithic centres to witness social and economic changes associated with the domestication of plants and animals. This study applies strontium (⁸⁷Sr/⁸⁶Sr), oxygen (δ¹⁸O) and carbon (δ¹³C) isotope analyses to the enamel of 52 human teeth from Pre-Pottery Neolithic (PPN) layers of Jericho to directly study human diet and mobility and investigate the degree of consolidation and the flexibility of social organization of Jericho society in the PPN period. The results indicate only two non-local individuals out of the 44 sampled inhabitants identified by strontium isotope analysis and are consistent with the presence of a largely sedentary community at PPN Jericho with no evidence for large-scale migration. We also construct strontium spatial baselines (⁸⁷Sr/⁸⁶Sr map) with local ⁸⁷Sr/⁸⁶Sr signatures for the sites across the Southern Levant based on systematic compilation and analysis of available data. In addition, we apply proteomic analysis of sex-specific amelogenin peptides in tooth enamel for sex estimation of the sampled individuals (n = 44), the results of which showed a sex-biased ratio (more male than female detected in this sample pool) in Jericho society during the PPN period, which may be due to the limited sample size or selective ritual practices like particular burial zones used for specific groups. We also pretreated a batch of human bone samples recovered from PPNB Jericho for stable carbon and nitrogen isotope analyses for dietary investigations. However, the extracted collagen showed poor preservation and no valid δ¹³C or δ¹⁵N data were obtained.

“Yersinia pestis in the Early Bronze Age Cemetery of Drasenhofen. The Currently Oldest Plague Deaths in Austria in their Cultural-Historical Context.” Archaeologica Austriaca 107: I–XXII (2023).

G.U. Neumann, F. Kanz, A. Furtwängler, K. Fiebig, D. Verdianu, P.W. Stockhammer, K. Rebay-Salisbury.

Within the framework of an interdisciplinary analysis of the Early Bronze Age burials from Drasenhofen, evidence was found for what are currently the oldest plague victims in Austria. The male individuals, who died at the age of 23–30 and 22–27 years, respectively, were buried not far from each other in the north-easternmost and south-easternmost grave of the row cemetery comprising a total of 22 graves. Despite the spatial and temporal proximity, the genetic pathogen analyses detected two different strains of plague bacteria (Yersinia pestis). Thus, it was not one infection that was transmitted within the Bronze Age group, but two independent infection events. In this article, we present the phylogenetic positions of these two Yersinia pestis strains together with other prehistoric, historic and modern plague genomes known so far, discuss biological basics of transmission and possible transmission routes, and attempt a cultural-historical interpretation in comparison with similar anthropological and archaeological contexts.

“Should we give the bones a name? (De-)personalization and objectification of prehistoric people.” In: M. Renger/S. Schreiber/A. Veling (Hrsg.) Theorie | Archäologie | Reflexion 1. Kontroversen und Ansätze im deutschsprachigen Diskurs. Theoriedenken in der Archäologie 1. Propylaeum, 423–452 (2023).

K. Hofmann, C. Sanchez-Stockhammer, P.W. Stockhammer.

“What is your name?” is not a question that prehistoric archaeologists can ask a person they have excavated. Rather, the ‘human remains’ are carefully documented, numbered, identified, and archived as objects. In rare cases, however, the archaeological context confronts us with an individual who seems to be looking at us from the past, because of his or her special preservation (e.g. as a bog or an ice corpse). In such cases, the finders sometimes feel compelled to give that individual a name – a new name due to their lack of knowledge of the original name, if there ever was one. Ultimately, however, most of the deceased are and remain objects for the current researchers, depersonalised remains that are desubjectivised even further in the context of archaeological documentation practices. For a few years now, bioarchaeological approaches have made it possible to shed a completely new light on the lives of these anonymous bones, allowing us to learn about the lives of these individuals in an unprecedented way. A human being with individual traits begins to emerge from the bones – a human being, however, whom we continue to list under a catalogue number and objectively refer to in the accompanying publication as “find site, grave number” (or using similar codes). But does this do justice to the deceased? Shouldn’t the new potential for gaining knowledge about past individual lives force us to consider giving a name to these individuals? Or would that pose the danger of nostrification (i.e. of making the other from a distant and alien past too much our own)? Where does the appreciation of the remains as human beings begin and where do we cross the thin line to appropriation? In our contribution we discuss current naming practices, their consequences on the perception of human remains, the results of an online survey, and future developments resulting from novel approaches to gaining knowledge. We hope to raise awareness for a reflective approach toward naming practices in archaeology and the descriptions and narratives that commonly accompany these naming practices.

“Fostering Women and Mobile Children in Final Neolithic and Early Bronze Age Central Europe.” In: K. Kristiansen/G. Kroonen/E. Willerslev (Hrsg.), The Indo-European Puzzle Revisited. Integrating Archaeology, Genetics, and Linguistics. Cambridge University Press, 303–307 (2023).

P.W. Stockhammer.

Over the last several years, it has become clear that Central and Western Europe witnessed an enormous transformation during the third millennium – not only in cultural terms, as has long been clear from the appearance of the Corded Ware Complex (CWC) and the Bell Beaker Complex (BBC), but also from a genetic point of view: archaeogenetic analyses from Central Europe to the British Isles and the Iberian Peninsula have revealed genetic signatures with an origin in the western Eurasian steppe regions (Haak et al. 2015; Allentoft et al. 2015; Olalde et al. 2018; Olalde et al. 2019; Fernandes et al. 2020). Whereas early publications on this topic employed dubious vocabulary, like “Yamnaya migration,” there is no doubt that the spread of genes from east to west in prehistoric times could only take place through mobile individuals. Archaeogenetic studies have also suggested a sex bias in these mobile people and that the migration process was predominantly related to male mobility (Goldberg et al. 2017). Since the publication of the scientific results for the Iberian Peninsula (Olalde et al. 2019), newspapers have even interpreted this as evidence of male hoards invading Spain and committing genocide of the local male population. There is no doubt that such simplified narratives do justice neither to archaeological theory nor to the aim of narrating a complex past in a comprehensible manner.

“Rethinking Migrations in Late Prehistoric Eurasia: An Introduction.” In: M. Fernández-Götz, C. Nimura, P.W. Stockhammer, R. Cartwright (Hrsg.) Rethinking Migrations in Late Prehistoric Eurasia. Proceedings of the British Academy 254. Oxford: Oxford University Press, 1–20 (2023).

M. Fernández-Götz, C. Nimura, P.W. Stockhammer, R. Cartwright.

Mobility has always been a defining feature of the human journey, from prehistory to the present. This chapter serves as an introduction to our volume on population movements in late prehistoric Eurasia, outlining the background, scope, and aims of the book. It provides definitions for key terms such as mobility, migration, colonisation, and diaspora, as well as a discussion of specific modalities such as forced migration and return migration. The history of research is outlined in order to understand the main trends, methodologies, and shifts over time, and their interconnection with the wider intellectual and political context. Finally, the chapter offers insights into the current state of research, and concludes by summarising the different contributions contained in the volume.

“Mobility at the Onset of the Bronze Age: A Bioarchaeological Perspective.” In: M. Fernández-Götz, C. Nimura, P.W. Stockhammer, R. Cartwright (Hrsg.) (2022), Rethinking Migrations in Late Prehistoric Eurasia. Proceedings of the British Academy 254. Oxford: Oxford University Press, 170–188 (2023).

P.W. Stockhammer, K. Massy.

This paper presents the results of a long-term interdisciplinary research project in the micro-region of the Lech Valley in southern Germany. The comprehensive bioarchaeological study of burials from the Late Neolithic until the early Middle Bronze Age brought to light a strict patrilocal system, where each farmstead was populated by a biologically related core family. In addition to that, women from afar – c. 400–600 km – came into the Lech Valley, lived in the different farmsteads, possessed a high status, but never had any offspring visible in local burial grounds. Finally, we identified the biologically non-related, local, and poor burials as the remains of menial staff living together with the nuclear family and the women from afar in each of the farmsteads, thus shedding completely new light on the complexity and social inequality of farmsteads in the Early Bronze Age.

“Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic.” Science 380: 619-624 (2023).

M. Klapper, A. Hübner, A. Ibrahim, M. Borry, S. Chowdhury, J. Frangenberg, V. Hänsch, R. Herbst, H. Suma, I.M. Velsko, I. Wasmuth, J.A. Fellows Yates, S. Zhang, W.K. Al-Jammal, E.V. Bratovanov, H.M. Dahse, T. Horch, C. Hertweck, M.R. Gonzalez Morales, L.G. Straus, I. Vilotijevic, C. Warinner, P. Stallforth.

Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. We investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans ranging from 100,000 years ago to the present and reconstructed 459 bacterial metagenome-assembled genomes. We identified a biosynthetic gene cluster shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites that we name “paleofurans.” This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.

Top of Form

“Ethical considerations when co-analyzing ancient DNA and data from private genetic databases.” The American Journal of Human Genetics 110: 1-7 (2023).

É. Harney, K. Sirak, J. Sedig, S. Micheletti, R. Curry, S.A. Esselmann, D. Reich.

Ancient DNA studies have begun to explore the possibility of identifying identical DNA segments shared between historical and living people. This research requires access to large genetic datasets to maximize the likelihood of identifying previously unknown, close genetic connections. Direct-to-consumer genetic testing companies, such as 23andMe, Inc., manage by far the largest and most diverse genetic databases that can be used for this purpose. It is therefore important to think carefully about guidelines for carrying out collaborations between researchers and such companies. Such collaborations require consideration of ethical issues, including policies for sharing ancient DNA datasets, and ensuring reproducibility of research findings when access to privately controlled genetic datasets is limited. At the same time, they introduce unique possibilities for returning results to the research participants whose data are analyzed, including those who are identified as close genetic relatives of historical individuals, thereby enabling ancient DNA research to contribute to the restoration of information about ancestral connections that were lost over time, which can be particularly meaningful for families and groups where such history has not been well documented. We explore these issues by describing our experience designing and carrying out a study searching for genetic connections between 18th- and 19th-century enslaved and free African Americans who labored at Catoctin Furnace, Maryland, and 23andMe research participants. We share our experience in the hope of helping future researchers navigate similar ethical considerations, recognizing that our perspective is part of a larger conversation about best ethical practices.

“Interactions between Trypillian farmers and North Pontic forager-pastoralists in Eneolithic central Ukraine.” PLoS ONE 18, e0285449 (2023).

A.G. Nikitin, M. Videiko, N. Patterson, V. Renson, D. Reich.

The establishment of agrarian economy in Eneolithic East Europe is associated with the Pre-Cucuteni-Cucuteni-Trypillia complex (PCCTC). PCCTC farmers interacted with Eneolithic forager-pastoralist groups of the North Pontic steppe as PCCTC extended from the Carpathian foothills to the Dnipro Valley beginning in the late 5^th millennium BCE. While the cultural interaction between the two groups is evident through the Cucuteni C pottery style that carries steppe influence, the extent of biological interactions between Trypillian farmers and the steppe remains unclear. Here we report the analysis of artefacts from the late 5^th millennium Trypillian settlement at the Kolomiytsiv Yar Tract (KYT) archaeological complex in central Ukraine, focusing on a human bone fragment found in the Trypillian context at KYT. Diet stable isotope ratios obtained from the bone fragment suggest the diet of the KYT individual to be within the range of forager-pastoralists of the North Pontic area. Strontium isotope ratios of the KYT individual are consistent with having originated from contexts of the Serednii Stih (Sredny Stog) culture sites of the Middle Dnipro Valley. Genetic analysis of the KYT individual indicates ancestry derived from a proto-Yamna population such as Serednii Stih. Overall, the KYT archaeological site presents evidence of interactions between Trypillians and Eneolithic Pontic steppe inhabitants of the Serednii Stih horizon and suggests a potential for gene flow between the two groups as early as the beginning of the 4^th millennium BCE.

“High conservation of the dental plaque microbiome community across populations with differing subsistence strategies.” Molecular Biology and Evolution (2023).

I.M. Velsko, S. Gallois, R. Stahl, A. Henry, C. Warinner.

Industrialization—including urbanization, participation in the global food chain and consumption of heavily processed foods—is thought to drive substantial shifts in the human microbiome. While diet strongly influences stool microbiome composition, the influence of diet on the oral microbiome is largely speculative. Multiple ecologically distinct surfaces in the mouth, each harbouring a unique microbial community, pose a challenge to assessing changes in the oral microbiome in the context of industrialization, as the results depend on the oral site under study. Here, we investigated whether microbial communities of dental plaque, the dense biofilm on non-shedding tooth surfaces, are distinctly different across populations with dissimilar subsistence strategies and degree of industrialized market integration. Using a metagenomic approach, we compared the dental plaque microbiomes of Baka foragers and Nzime subsistence agriculturalists in Cameroon (n = 46) with the dental plaque and calculus microbiomes of highly industrialized populations in North America and Europe (n = 38). We found that differences in microbial taxonomic composition between populations were minimal, with high conservation of abundant microbial taxa and no significant differences in microbial diversity related to dietary practices. Instead, we find that the major source of variation in dental plaque microbial species composition is related to tooth location and oxygen availability, which may be influenced by toothbrushing or other dental hygiene measures. Our results support that dental plaque, in contrast to the stool microbiome, maintains an inherent stability against ecological perturbations in the oral environment.

“Density separation of petrous bone powders for optimized ancient DNA yields.” Genome Research 33, 622-31 (2023).

D.M. Fernandes, K.A. Sirak, O. Cheronet, M. Novak, F. Bruck, E. Zelger, A. Llanos-Lizcano, A. Wagner, A. Zettl, K. Mandl, K.S.D. Carlson, V. Oberreiter, K.T. Ozdogan, S. Sawyer, F. La Pastina, E. Borgia, A. Coppa, M. Dobes, P. Veleminsky, D. Reich, L.S. Bell, R. Pinhasi.

Density separation is a process routinely used to segregate minerals, organic matter, and even microplastics, from soils and sediments. Here we apply density separation to archaeological bone powders before DNA extraction to increase endogenous DNA recovery relative to a standard control extraction of the same powders. Using nontoxic heavy liquid solutions, we separated powders from the petrous bones of 10 individuals of similar archaeological preservation into eight density intervals (2.15 to 2.45 g/cm³, in 0.05 increments). We found that the 2.30 to 2.35 g/cm³ and 2.35 to 2.40 g/cm³ intervals yielded up to 5.28-fold more endogenous unique DNA than the corresponding standard extraction (and up to 8.53-fold before duplicate read removal), while maintaining signals of ancient DNA authenticity and not reducing library complexity. Although small 0.05 g/cm³ intervals may maximally optimize yields, a single separation to remove materials with a density above 2.40 g/cm³ yielded up to 2.57-fold more endogenous DNA on average, which enables the simultaneous separation of samples that vary in preservation or in the type of material analyzed. While requiring no new ancient DNA laboratory equipment and fewer than 30 min of extra laboratory work, the implementation of density separation before DNA extraction can substantially boost endogenous DNA yields without decreasing library complexity. Although subsequent studies are required, we present theoretical and practical foundations that may prove useful when applied to other ancient DNA substrates such as teeth, other bones, and sediments.

“Genetic population structure of the Xiongnu Empire at imperial and local scales.” Science Advances 9, eadf3904 (2023).

J.H. Lee, B.K. Miller, J. Bayarsaikhan, E. Johannesson, A. Ventresca Miller, C. Warinner, C. Jeong.

The Xiongnu established the first nomadic imperial power, controlling the Eastern Eurasian steppe from ca. 200 BCE to 100 CE. Recent archaeogenetic studies identified extreme levels of genetic diversity across the empire, corroborating historical records of the Xiongnu Empire being multiethnic. However, it has remained unknown how this diversity was structured at the local community level or by sociopolitical status. To address this, we investigated aristocratic and local elite cemeteries at the western frontier of the empire. Analyzing genome-wide data from 18 individuals, we show that genetic diversity within these communities was comparable to the empire as a whole, and that high diversity was also observed within extended families. Genetic heterogeneity was highest among the lowest-status individuals, implying diverse origins, while higher-status individuals harbored less genetic diversity, suggesting that elite status and power was concentrated within specific subsets of the broader Xiongnu population.

“Entwined African and Asian genetic roots of medieval peoples of the Swahili coast.” Nature 615, 866-73 (2023).

E.S. Brielle, J. Fleisher, S. Wynne-Jones, K. Sirak, N. Broomandkhoshbacht, K. Callan, E. Curtis, L. Iliev, A.M. Lawson, J. Oppenheimer, L. Qiu, K. Stewardson, J.N. Workman, F. Zalzala, G. Ayodo, A.O. Gidna, A. Kabiru, A. Kwekason, A.Z.P. Mabulla, F.K. Manthi, E. Ndiema, C. Ogola, E. Sawchuk, L. Al-Gazali, S. Ben-Salem, T. Letellier, D. Pierron, C. Radimilahy, J.A. Rakotoarisoa, R.L. Raaum, B.J. Culleton, S. Mallick, N. Rohland, N. Patterson, M.A. Mwenie, K.B. Ahmed, M.M. Mohamed, S.R. Williams, J. Monge, S. Kusimba, M.E. Prendergast, D. Reich, C.M. Kusimba.

The urban peoples of the Swahili coast traded across eastern Africa and the Indian Ocean and were among the first practitioners of Islam among sub-Saharan people. The extent to which these early interactions between Africans and non-Africans were accompanied by genetic exchange remains unknown. Here we report ancient DNA data for 80 individuals from 6 medieval and early modern (AD 1250–1800) coastal towns and an inland town after AD 1650. More than half of the DNA of many of the individuals from coastal towns originates from primarily female ancestors from Africa, with a large proportion—and occasionally more than half—of the DNA coming from Asian ancestors. The Asian ancestry includes components associated with Persia and India, with 80–90% of the Asian DNA originating from Persian men. Peoples of African and Asian origins began to mix by about AD 1000, coinciding with the large-scale adoption of Islam. Before about AD 1500, the Southwest Asian ancestry was mainly Persian-related, consistent with the narrative of the Kilwa Chronicle, the oldest history told by people of the Swahili coast. After this time, the sources of DNA became increasingly Arabian, consistent with evidence of growing interactions with southern Arabia. Subsequent interactions with Asian and African people further changed the ancestry of present-day people of the Swahili coast in relation to the medieval individuals whose DNA we sequenced.

“On the limits of fitting complex models of population history to f-statistics.” eLife 12:e85492 (2023).

R. Maier, P. Flegontov, O. Flegontova, U. Isildak, P. Changmai, D. Reich.

Our understanding of population history in deep time has been assisted by fitting admixture graphs ('AGs') to data: models that specify the ordering of population splits and mixtures, which along with the amount of genetic drift on each lineage and the proportions of mixture, is the only information needed to predict the patterns of allele frequency correlation among populations. Not needing to specify population size changes, split times, or whether admixture events were sudden or drawn out simplifies the space of models that need to be searched. However, the space of possible AGs relating populations is vast and cannot be sampled fully, and thus most published studies have identified fitting AGs through a manual process driven by prior hypotheses, leaving the vast majority of alternative models unexplored. Here, we develop a method for systematically searching the space of all AGs that can incorporate non-genetic information in the form of topology constraints. We implement this findGraphs tool within a software package, ADMIXTOOLS 2, which is a reimplementation of the ADMIXTOOLS software with new features and large performance gains. We apply this methodology to identify alternative models to AGs that played key roles in eight published studies and find that graphs modeling more than six populations and two or three admixture events are often not unique, with many alternative models fitting nominally or significantly better than the published one. Our results suggest that strong claims about population history from AGs should only be made when all well-fitting and temporally plausible models share common topological features. Our re-evaluation of published data also provides insight into the population histories of humans, dogs, and horses, identifying features that are stable across the models we explored, as well as scenarios of populations relationships that differ in important ways from models that have been highlighted in the literature, that fit the allele frequency correlation data, and that are not obviously wrong.

“Ancient mitogenomes from the Southern Pampas of Argentina reflect local differentiation and limited extra-regional linkages after rapid initial colonization.” American Journal of Biological Anthropology. Advance online publication (2023).

J.M.B. Motti, M. Pauro, C. Scabuzzo, A. Garcia, V. Aldazabal, R. Vecchi, C. Bayon, V. Pastor, D.A. Demarchi, C.M. Bravi, D. Reich, G.S. Cabana, R. Nores.

This study aims to contribute to the recovery of Indigenous evolutionary history in the Southern Pampas region of Argentina through an analysis of ancient complete mitochondrial genomes. We generated DNA data for nine complete mitogenomes from the Southern Pampas, dated to between 2531 and 723 cal BP. In combination with previously published ancient mitogenomes from the region and from throughout South America, we documented instances of extra-regional lineage-sharing, and estimated coalescent ages for local lineages using a Bayesian method with tip calibrations in a phylogenetic analysis. We identified a novel mitochondrial haplogroup, B2b16, and two recently defined haplogroups, A2ay and B2ak1, as well as three local haplotypes within founder haplogroups C1b and C1d. We detected lineage-sharing with ancient and contemporary individuals from Central Argentina, but not with ancient or contemporary samples from North Patagonian or Littoral regions of Argentina, despite archeological evidence of cultural interactions with the latter regions. The estimated coalescent age of these shared lineages is ~10,000 years BP.

“Kinship practices in Early Iron Age South-east Europe: Genetic and isotopic analysis of burials from the Dolge njive barrow cemetery, Dolenjska, Slovenia.” Antiquity. Advance online publication (2023).

I. Armit, C.E. Fischer, H. Koon, R. Nicholls, I. Olalde, N. Rohland, J. Buckberry, J. Montgomery, P. Mason, M. Črešnar, L. Büster, D. Reich.

The burial of multiple individuals within a single funerary monument invites speculation about the relationships between the deceased: were they chosen on the basis of status, gender or relatedness, for example? Here, the authors present the results of aDNA and isotope analyses conducted on seven individuals from an Early Iron Age barrow at Dolge njive, south-eastern Slovenia. All seven individuals are close biological relatives. While the group composition suggests strict adherence to neither patrilineal nor matrilineal structures, the funerary tradition appears highly gendered, and family links through both the male and female lines seem important in structuring of the community. The results have implications for understanding of kinship and funerary practices in late prehistoric Europe.

“Biomolecular analyses enable new insights into ancient Egyptian embalming.” Nature 614, 287–293 (2023).

M. Rageot, R.B. Hussein, S. Beck, V. Altmann-Wendling, M.I.M. Ibrahim, M.M. Bahgat, A.M. Yousef, K. Mittelstaedt, J-J. Filippi, S. Buckley, C. Spiteri, P.W. Stockhammer.

The ability of the ancient Egyptians to preserve the human body through embalming has not only fascinated people since antiquity, but also has always raised the question of how this outstanding chemical and ritual process was practically achieved. Here we integrate archaeological, philological and organic residue analyses, shedding new light on the practice and economy of embalming in ancient Egypt. We analysed the organic contents of 31 ceramic vessels recovered from a 26th Dynasty embalming workshop at Saqqara. These vessels were labelled according to their content and/or use, enabling us to correlate organic substances with their Egyptian names and specific embalming practices. We identified specific mixtures of fragrant or antiseptic oils, tars and resins that were used to embalm the head and treat the wrappings using gas chromatography–mass spectrometry analyses. Our study of the Saqqara workshop extends interpretations from a micro-level analysis highlighting the socio-economic status of a tomb owner to macro-level interpretations of the society. The identification of non-local organic substances enables the reconstruction of trade networks that provided ancient Egyptian embalmers with the substances required for mummification. This extensive demand for foreign products promoted trade both within the Mediterranean (for example, Pistacia and conifer by-products) and with tropical forest regions (for example, dammar and elemi). Additionally, we show that at Saqqara, antiu and sefet—well known from ancient texts and usually translated as ‘myrrh’ or ‘incense’ and ‘a sacred oil’—refer to a coniferous oils-or-tars-based mixture and an unguent with plant additives, respectively.

“Dental calculus.” Handbook of Archaeological Sciences, 2^nd Edition. John Wiley & Sons, Ltd, eds. M. Pollard, C. Makarewicz, and R. Armitage (2023).

Z. Fagernäs, C. Warinner.

Dental calculus, also known as tooth tartar, is a mineralized form of dental plaque, a bacterial biofilm that naturally forms on teeth. Dental calculus forms through the calcification of dental plaque, a bacterial biofilm that forms naturally on the surface of teeth. Dental calculus is ubiquitous in the archaeological record, found in all areas of the world and in populations from all time periods. Because multiple types of biomolecules and micro-remains are preserved over long time periods in dental calculus, studies of dental calculus have many different applications. This chapter discusses how studies of dental calculus have been used to investigate the oral microbiome, the host, diet, and craft activities in the past. In addition to genetic studies of the oral microbiome, proteins and metabolites within archaeological dental calculus can also be highly informative about the microorganisms inhabiting the oral cavity, as well as host immunological response.

“Ancient DNA reveals admixture history and endogamy in the prehistoric Aegean.” Nature Ecology & Evolution 7, 290-303 (2023).

E. Skourtanioti, H. Ringbauer, G.A.Gnecchi Ruscone, R.A. Bianco, M. Burri, C. Freund, A. Furtwängler, N.F. Gomes Martins, F. Knolle, G.U. Neumann, A. Tiliakou, A. Agelarakis, M. Andreadaki-Vlazaki, P. Betancourt, B.P. Hallager, O.A. Jones, O. Kakavogianni, A. Kanta, P. Karkanas, E. Kataki, K. Kissas, R. Koehl, L. Kvapil, J. Maran, P.J.P. McGeorge, A. Papadimitriou, A. Papathanasiou, L. Papazoglou-Manioudaki, K. Paschalidis, N. Polychronakou-Sgouritsa, S. Preve, E. Prevedorou, G. Price, E. Protopapadaki, T. Schmidt-Schultz, M. Schultz, K. Shelton, M.H. Wiener, J. Krause, C. Jeong and P.W. Stockhammer.

The Neolithic and Bronze Ages were highly transformative periods for the genetic history of Europe but for the Aegean—a region fundamental to Europe’s prehistory—the biological dimensions of cultural transitions have been elucidated only to a limited extent so far. We have analysed newly generated genome-wide data from 102 ancient individuals from Crete, the Greek mainland and the Aegean Islands, spanning from the Neolithic to the Iron Age. We found that the early farmers from Crete shared the same ancestry as other contemporaneous Neolithic Aegeans. In contrast, the end of the Neolithic period and the following Early Bronze Age were marked by ‘eastern’ gene flow, which was predominantly of Anatolian origin in Crete. Confirming previous findings for additional Central/Eastern European ancestry in the Greek mainland by the Middle Bronze Age, we additionally show that such genetic signatures appeared in Crete gradually from the seventeenth to twelfth centuries BC, a period when the influence of the mainland over the island intensified. Biological and cultural connectedness within the Aegean is also supported by the finding of consanguineous endogamy practiced at high frequencies, unprecedented in the global ancient DNA record. Our results highlight the potential of archaeogenomic approaches in the Aegean for unravelling the interplay of genetic admixture, marital and other cultural practices.

“Isotopic and DNA analyses reveal multiscale PPNB mobility and migration across Southeastern Anatolia and the Southern Levant.” PNAS 120 (4) e2210611120 (2023).

X. Wang, E. Skourtanioti, M. Benz, J. Gresky, J. Ilgner, M. Lucas, M. Morsch, J. Peters, N. Pöllath, H.Ringbauer, P.le Roux, M. Schultz, J. Krause, P. Roberts, and P.W. Stockhammer.

Growing reliance on animal and plant domestication in the Near East and beyond during the Pre-Pottery Neolithic B (PPNB) (the ninth to eighth millennium BC) has often been associated with a “revolutionary” social transformation from mobility toward more sedentary lifestyles. We are able to yield nuanced insights into the process of the Neolithization in the Near East based on a bioarchaeological approach integrating isotopic and archaeogenetic analyses on the bone remains recovered from Nevalı Çori, a site occupied from the early PPNB in Turkey where some of the earliest evidence of animal and plant domestication emerged, and from Ba'ja, a typical late PPNB site in Jordan. In addition, we present the archaeological sequence of Nevalı Çori together with newly generated radiocarbon dates. Our results are based on strontium (⁸⁷Sr/⁸⁶Sr), carbon, and oxygen (δ¹⁸O and δ¹³C_carb) isotopic analyses conducted on 28 human and 29 animal individuals from the site of Nevalı Çori. ⁸⁷Sr/⁸⁶Sr results indicate mobility and connection with the contemporaneous surrounding sites during the earlier PPNB prior to an apparent decline in this mobility at a time of growing reliance on domesticates. Genome-wide data from six human individuals from Nevalı Çori and Ba'ja demonstrate a diverse gene pool at Nevalı Çori that supports connectedness within the Fertile Crescent during the earlier phases of Neolithization and evidence of consanguineous union in the PPNB Ba'ja and the Iron Age Nevalı Çori.

2022

“An Archaeology of Microbes.” Journal of Anthropological Research, 78 (4), 420-458 (2022).

C. Warinner.

Humans have a deep and complex relationship with microbes. Beyond disease, microbes also profoundly shape human health and behavior through their activity in the microbiome and their diverse roles in food and cuisine. And yet we know very little about the origin, evolution, or ecology of the trillions of microorganisms that call us home. Recent advances in genomic and proteomic technologies are opening up dramatic new opportunities in the field of microbial archaeology, enabling us to investigate the complex and diverse microbial communities that have long inhabited our human bodies and our food systems—both in sickness and in health. From epidemic disease to alcoholic beverages, microbes are the invisible and often overlooked figures that have profoundly shaped human culture and influenced the course of human history. Emerging research on microbes is impacting how we investigate the human past and changing how we understand human and microbial cultures today. Here the developing field of microbial archaeology is discussed, including its current practice and future outlook.

“The Anglo-Saxon migration and the formation of the early English gene pool.” Nature 610, 112-119 (2022).

J. Gretzinger, D. Sayer, P. Justeau, E. Altena, M. Pala, K. Dulias, C.J. Edwards, S. Jodoin, L. Lacher, S. Sabin, Å.J Vågene, W. Haak, S.S. Ebenesersdóttir, K.H.S. Moore, R. Radzeviciute, K. Schmidt, S. Brace, M.A. Bager, N. Patterson, L. Papac, N. Broomandkhoshbacht, K. Callan, É. Harney, L. Iliev, A.M. Lawson, M. Michel, K. Stewardson, F. Zalzala, N. Rohland, S. Kappelhoff-Beckmann, F. Both, D. Winger, D. Neumann, L. Saalow, S. Krabath, S. Beckett, M. Van Twest, N. Faulkner, C. Read, T. Barton, J. Caruth, J. Hines, B. Krause-Kyora, U. Warnke, V.J. Schuenemann, I. Barnes, H. Dahlström, J.J. Clausen, A. Richardson, E. Popescu, N. Dodwell, S. Ladd, T. Phillips, R. Mortimer, F. Sayer, D. Swales, A. Stewart, D. Powlesland, R. Kenyon, L. Ladle, C. Peek, S. Grefen-Peters, P. Ponce, R. Daniels, C. Spall, J. Woolcock, A.M. Jones, A.V. Roberts, R. Symmons, A.C. Rawden, A. Cooper, K.I. Bos, T. Booth, H. Schroeder, M.G. Thomas, A. Helgason, M.B. Richards, D. Reich, J. Krause, S. Schiffels.

The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture. The extent to which migration from continental Europe mediated these transitions is a matter of long-standing debate. Here we study genome-wide ancient DNA from 460 medieval northwestern Europeans—including 278 individuals from England—alongside archaeological data, to infer contemporary population dynamics. We identify a substantial increase of continental northern European ancestry in early medieval England, which is closely related to the early medieval and present-day inhabitants of Germany and Denmark, implying large-scale substantial migration across the North Sea into Britain during the Early Middle Ages. As a result, the individuals who we analysed from eastern England derived up to 76% of their ancestry from the continental North Sea zone, albeit with substantial regional variation and heterogeneity within sites. We show that women with immigrant ancestry were more often furnished with grave goods than women with local ancestry, whereas men with weapons were as likely not to be of immigrant ancestry. A comparison with present-day Britain indicates that subsequent demographic events reduced the fraction of continental northern European ancestry while introducing further ancestry components into the English gene pool, including substantial southwestern European ancestry most closely related to that seen in Iron Age France.

“Genome-wide data from medieval German Jews show that the Ashkenazi founder event pre-dated the 14^th century.” Cell 185 (25), 4703-4716 (2022).

S. Waldman, D. Backenroth, E. Harney, S. Flohr, N.C. Neff, G.M. Buckley, H. Fridman, A. Akbari, N. Rohland, S. Mallick, I. Olalde, L. Cooper, A. Lomes, J. Lipson, J.C. Nistal, J. Yu, N. Barzilai, I. Peter, G. Atzmon, H. Ostrer, T. Lencz, Y.E. Maruvka, M. Lammerhirt, A. Beider, L.V. Rutgers, V. Renson, K.M. Prufer, S. Schiffels, H. Ringbauer, K. Sczech, S. Carmi, D. Reich.

We report genome-wide data from 33 Ashkenazi Jews (AJ), dated to the 14^th century, obtained following a salvage excavation at the medieval Jewish cemetery of Erfurt, Germany. The Erfurt individuals are genetically similar to modern AJ, but they show more variability in Eastern European-related ancestry than modern AJ. A third of the Erfurt individuals carried a mitochondrial lineage common in modern AJ and eight carried pathogenic variants known to affect AJ today. These observations, together with high levels of runs of homozygosity, suggest that the Erfurt community had already experienced the major reduction in size that affected modern AJ. The Erfurt bottleneck was more severe, implying substructure in medieval AJ. Overall, our results suggest that the AJ founder event and the acquisition of the main sources of ancestry pre-dated the 14^th century and highlight late medieval genetic heterogeneity no longer present in modern AJ.

“The diverse genetic origins of a Classical period Greek army.” PNAS 119 (41) e2205272119 (2022).

L.J. Reitsema, A. Mittnik, B. Kyle, G. Catalano, P.F. Fabbri, A.C.S. Kazmi, K.L. Reinberger, L. Sineo, S. Vassallo, R. Bernardos, N. Broomandkhoshbacht, K. Callan, F. Candilio, O. Cheronet, E. Curtis, D. Fernandes, M. Lari, A.M. Lawson, M. Mah, S. Mallick, K. Mandl, A. Micco, A. Modi, J. Oppenheimer, K.T. Özdogan, N. Rohland, K. Stewardson, S. Vai, C. Vergata, J.N. Workman, F. Zalzala, V. Zaro, A. Achilli, A. Anagnostopoulos, C. Capelli, V. Constantinou, H. Lancioni, A. Olivieri, A. Papadopoulou, N. Psatha, O. Semino, J. Stamatoyannopoulos, I. Valliannou, E. Yannaki, I. Lazaridis, N. Patterson, H. Ringbauer, D. Caramelli, R. Pinhasi, D. Reich.

Trade and colonization caused an unprecedented increase in Mediterranean human mobility in the first millennium BCE. Often seen as a dividing force, warfare is in fact another catalyst of culture contact. We provide insight into the demographic dynamics of ancient warfare by reporting genome-wide data from fifth-century soldiers who fought for the army of the Greek Sicilian colony of Himera, along with representatives of the civilian population, nearby indigenous settlements, and 96 present-day individuals from Italy and Greece. Unlike the rest of the sample, many soldiers had ancestral origins in northern Europe, the Steppe, and the Caucasus. Integrating genetic, archaeological, isotopic, and historical data, these results illustrate the significant role mercenaries played in ancient Greek armies and highlight how participation in war contributed to continental-scale human mobility in the Classical world.

“Finding Mycenaeans in Minoan Crete? Isotope and DNA analysis of human mobility in Bronze Age Crete.” PLOS ONE 17(8): e0272144 (2022).

M. Richards, C. Smith, O. Nehlich, V. Grimes, D. Weston, A. Mittnik, J. Krause, K. Dobney, Y. Tzedakis, H. Martlew.

We undertook a large-scale study of Neolithic and Bronze Age human mobility on Crete using biomolecular methods (isotope analysis, DNA), with a particular focus on sites dating to the Late Bronze Age (‘Late Minoan’) period. We measured the strontium and sulphur isotope values of animal remains from archaeological sites around the island of Crete to determine the local baseline values. We then measured the strontium and sulphur values of humans from Late Neolithic and Bronze Age sites. Our results indicate that most of the humans have sulphur and strontium isotope values consistent with being local to Crete, showing no evidence for a wide-scale movement of people from the Greek mainland or other areas away from Crete in these time periods. However, we found four individuals from the late Bronze Age (Late Minoan III) cemetery of Armenoi with sulphur isotope values not typically found in Crete and are instead consistent with an origin elsewhere. This cemetery at Armenoi also has one of only a few examples of the newly adopted Mycenaean Linear B script on Crete found outside of the palace sites, pointing to an influence (trade and possible migration) from the mainland, which may then be the place of origin of these four individuals. DNA (mtDNA) studies of eight Late Bronze Age individuals from Armenoi have results consistent with people living in Aegean region at this time and cannot be used to distinguish between individuals from Crete (‘Minoans’) and the Greek mainland [‘Mycenaeans’]).

“Ancient DNA from Protohistoric Period Cambodia indicates that South Asians admixed with local populations as early as 1st–3rd centuries CE.” Nature Scientific Reports 12, 22507 (2022).

P. Changmai, R. Pinhasi, M. Pietrusewsky, M.T. Stark, R.M. Ikehara‐Quebral, D. Reich, P. Flegontov.

Indian cultural influence is remarkable in present-day Mainland Southeast Asia (MSEA), and it may have stimulated early state formation in the region. Various present-day populations in MSEA harbor a low level of South Asian ancestry, but previous studies failed to detect such ancestry in any ancient individual from MSEA. In this study, we discovered a substantial level of South Asian admixture (ca. 40–50%) in a Protohistoric individual from the Vat Komnou cemetery at the Angkor Borei site in Cambodia. The location and direct radiocarbon dating result on the human bone (95% confidence interval is 78–234 calCE) indicate that this individual lived during the early period of Funan, one of the earliest states in MSEA, which shows that the South Asian gene flow to Cambodia started about a millennium earlier than indicated by previous published results of genetic dating relying on present-day populations. Plausible proxies for the South Asian ancestry source in this individual are present-day populations in Southern India, and the individual shares more genetic drift with present-day Cambodians than with most present-day East and Southeast Asian populations.

“A Bioarchaeological Investigation of Fraternal Stillborn Twins from Tell el-Hesi.” Near Eastern Archaeology 85, 228-37 (2022).

J. Ullinger, L. Gregoricka, R. Bernardos, D. Reich, A. Langston, P. Ferreri, B. Ingram.

A double nonadult burial excavated at the Ottoman period (1600–1800 CE) cemetery at Tell el-Hesi was hypothesized to belong to a set of stillborn twins. This study incorporated the use of multiple bioarchaeological techniques in order to assess both the age and survival of the perinates. Cranial and long-bone measurements were undertaken to determine age at death, while stable carbon and nitrogen isotopes were considered alongside microCT assessments of bacterial bioerosion in the cortices of long bones to identify whether these infants were born alive and had breastfed. Ancient DNA analysis can now identify twins with greater certainty and was also employed to confirm the sex and biological relationship between these two individuals. Using these various lines of evidence, we test two hypotheses, ultimately finding support for both: (1) the two perinates buried together from Tell el-Hesi were fraternal female twins; and (2) these perinates were likely stillborn.

“Life and death in early colonial Campeche: new insights from ancient DNA.” Antiquity 96 (388): 937-54 (2022).

V. Tiesler, J. Sedig, N. Nakatsuka, S. Mallick, I. Lazaridis, R. Bernardos, N. Broomandkhoshbacht, J. Oppenheimer, A.M. Lawson, K. Stewardson, N. Rohland, D.J. Kennett, T.D. Price, D. Reich.

Campeche, one of the Spanish Empire's main Mexican ports, was a place where previously distinct cultures and populations intermingled during the colonial era (AD 1540–1680). Investigation of the town's central plaza revealed a Hispanic cemetery of multi-ethnic burials. The authors combine previous analyses with newly generated genome-wide data from 10 individuals to trace detailed life histories of the mostly young, local Indigenous Americans and first-generation European and African immigrants, none of whom show evidence of genetic admixture. These results provide insights into the individual lives and social divides of the town's founder communities and demonstrate how ancient DNA analyses can contribute to understanding early colonial encounters.

“Pedigree-based Bayesian modelling of radiocarbon dates.” PloS ONE 17 (6), e0270374 (2022).

K. Massy, R. Friedrich, A. Mittnik, P.W Stockhammer.

Within the last decade, archaeogenetic analysis has revolutionized archaeological research and enabled novel insights into mobility, relatedness and health of past societies. Now, it is possible to develop these results further and integrate archaeogenetic insights into biological relatedness with radiocarbon dates as means of chronologically sequenced information. In our article, we demonstrate the potential of combining relative chronological information with absolute radiocarbon dates by Bayesian interpretation in order to improve age determinations. Using artificial pedigrees with four sets of simulated radiocarbon dates we show that the combination of relationship information with radiocarbon dates improves the age determination in many cases at least between 20 to 50%. Calibrated age ranges are more constrained than simply calibrating radiocarbon ages independently from each other. Thereby, the precision of modelled ages depends on the precision of the single radiocarbon dates, the number of modelled generations, the shape of the calibration curve and the availability of samples that can be precisely fixed in time due to specific patterns in the calibration curve ("anchor points"). Ambiguous calibrated radiocarbon dates, which are caused by inversions of the calibration curve, can be partly or almost entirely resolved through Bayesian modelling based upon information from pedigrees. Finally, we discuss selected case studies of biological pedigrees achieved for Early Bronze Age Southern Germany by recent archaeogenetic analysis, whereby the sites and pedigrees differ with regard to the quality of information, which can be used for a Bayesian model of the radiocarbon dates. In accordance with the abstract models, radiocarbon dates can again be better constrained and are therefore more applicable for archaeological interpretation and chronological placement of the dated individuals.

“HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data.” PLoS Computational Biology 18(9): e1010493 (2022).

E.A. Dimopouls, A. Carmagnini, I.M. Velsko, C. Warinner, G. Larson, L.A. Frantz, E. Irving-Pease.

Identification of specific species in metagenomic samples is critical for several key applications, yet many tools available require large computational power and are often prone to false positive identifications. Here we describe High-AccuracY and Scalable Taxonomic Assignment of MetagenomiC data (HAYSTAC), which can estimate the probability that a specific taxon is present in a metagenome. HAYSTAC provides a user-friendly tool to construct databases, based on publicly available genomes, that are used for competitive read mapping. It then uses a novel Bayesian framework to infer the abundance and statistical support for each species identification and provide per-read species classification. Unlike other methods, HAYSTAC is specifically designed to efficiently handle both ancient and modern DNA data, as well as incomplete reference databases, making it possible to run highly accurate hypothesis-driven analyses (i.e., assessing the presence of a specific species) on variably sized reference databases while dramatically improving processing speeds. We tested the performance and accuracy of HAYSTAC using simulated Illumina libraries, both with and without ancient DNA damage, and compared the results to other currently available methods (i.e., Kraken2/Bracken, KrakenUniq, MALT/HOPS, and Sigma). HAYSTAC identified fewer false positives than both Kraken2/Bracken, KrakenUniq and MALT in all simulations, and fewer than Sigma in simulations of ancient data. It uses less memory than Kraken2/Bracken, KrakenUniq as well as MALT both during database construction and sample analysis. Lastly, we used HAYSTAC to search for specific pathogens in two published ancient metagenomic datasets, demonstrating how it can be applied to empirical datasets. HAYSTAC is available from https://github.com/antonisdim/HAYSTAC.

“Ecology, not host phylogeny, shapes the oral microbiome in closely related species.” Molecular Biology and Evolution 39:12 (2022).

M. Moraitou, A. Forsythe, J.A. Fellows Yates, J.C. Brealey, C. Warinner, K. Guschanski.

Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here, we investigate the roles of host evolutionary relationships and ecology in shaping the oral microbiome in three closely related gorilla subspecies (mountain, Grauer's, and western lowland gorillas) using shotgun metagenomics of 46 museum-preserved dental calculus samples. We find that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauer's gorillas. Grauer's gorillas show intermediate bacterial taxonomic and functional, and dietary profiles. Altitudinal differences in gorilla subspecies ranges appear to explain these patterns, suggesting a close connection between dental calculus microbiomes and the environment, likely mediated through diet. This is further supported by the presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa in the oral microbiome. Mountain gorillas show a high abundance of nitrate-reducing oral taxa, which may promote adaptation to a high-altitude lifestyle by modulating blood pressure. Our results suggest that ecology, rather than evolutionary relationships and geographic distribution, shape the oral microbiome in these closely related species.

“Your horse is a donkey! Identifying domesticated equids from Western Iberia using collagen fingerprinting.” Journal of Archaeological Science 149:105696 (2022).

R. Paladugu, K. Korzow-Richter, M.J. Valente, S. Gabriel, C. Detry, C. Warinner, C. Barrocas Dias.

Skeletal remains of two equid species, Equus caballus (horse) and Equus asinus (donkey), have been found in archaeological contexts throughout Iberia since the Palaeolithic and Chalcolithic periods, respectively. These two species play different economic and cultural roles, and therefore it is important to be able to distinguish between the two species to better understand their relative importance in the past human societies. The most reliable morphological features for distinguishing between the two domesticated equids are based on cranial measurements and tooth enamel folds, leading to only a small percentage of archaeological remains that can be identified to species. Ancient DNA (aDNA) analysis can be used to reliably distinguish the two equids, but it can be cost prohibitive to apply to large assemblages, and aDNA preservation of non-cranial elements is often low. Collagen peptide mass fingerprinting by matrix-assisted laser desorption time-of-flight (MALDI-TOF) mass spectrometry, also known as zooarchaeology by mass spectrometry (ZooMS), is a minimally destructive and cost-effective alternative to aDNA analysis for taxonomic determination. However, current ZooMS markers lack resolution below the genus level Equus. In this paper, we report a novel ZooMS peptide marker that reliably distinguishes between horses and donkeys using the enzyme chymotrypsin. We apply this peptide marker to taxonomically identify bones from the Iberian Peninsula ranging from the Iron Age to the Late Modern Period. The peptide biomarker has the potential to facilitate the collection of morphological data for zooarchaeological studies of equids in Iberia and throughout Eurasia and Africa.

“Ancient dental calculus preserves signatures of biofilm succession and inter-individual variation independent of dental pathology.” PNAS Nexus 1: 1-14 (2022).

I. Velsko, L. Semerau, S.A. Inskip, M.I. García-Collado, K. Ziesemer, M. Serrano Ruber, L. Benítez de Lugo Enrich, J.M. Molero-García, D. Gallego Valle, A.C. Peña Ruiz, D.C. Salazar Garcia, M.L.P. Hoogland, C. Warinner.

Dental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here, we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals from the 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets from European populations before and after the introduction of tobacco were also analyzed. Calculus species profiles were compared with oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health, with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition, were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed interindividual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque.

“Remembering St. Louis Individual: Structural violence and acute bacterial infections in a historical anatomical collection.” Communications Biology 5:1050 (2022).

R.M. Austin, M. Zuckerman, T.P. Honap, H. Lee, G.K. Ward, C. Warinner, K. Sankaranarayanan, C.A. Hofman.

Incomplete documentary evidence, variable biomolecular preservation, and limited skeletal responses have hindered assessment of acute infections in the past. This study was initially developed to explore the diagnostic potential of dental calculus to identify infectious diseases, however, the breadth and depth of information gained from a particular individual, St. Louis Individual (St.LI), enabled an individualized assessment and demanded broader disciplinary introspection of ethical research conduct. Here, we document the embodiment of structural violence in a 23-year-old Black and/or African American male, who died of lobar pneumonia in 1930s St. Louis, Missouri. St.LI exhibits evidence of systemic poor health, including chronic oral infections and a probable tuberculosis infection. Metagenomic sequencing of dental calculus recovered three pre-antibiotic era pathogen genomes, which likely contributed to the lobar pneumonia cause of death (CoD): Klebsiella pneumoniae (13.8X); Acinetobacter nosocomialis (28.4X); and Acinetobacter junii (30.1X). Ante- and perimortem evidence of St.LI’s lived experiences chronicle the poverty, systemic racism, and race-based structural violence experienced by marginalized communities in St. Louis, which contributed to St.LI’s poor health, CoD, anatomization, and inclusion in the Robert J. Terry Anatomical Collection. These same embodied inequalities continue to manifest as health disparities affecting many contemporary communities in the United States.

“Plastic Purity and Sacred Dairy: Microbes, Vitality and Standardisation in Mongolian Dairying.” Copenhagen Journal of Asian Studies 40(1): 66-90 (2022).

B. Reichhardt, S. Abrahms-Kavunenko.

By investigating the growing use of plastics within Mongolian dairying, this paper explores emerging microbial/social assemblages as they relate to local and imported ideas of purity and hygiene. Although many Mongolian herders prefer to use dairy equipment made from materials such as wood and hide, these items are increasingly being replaced by plastic ones. As new infrastructure connects northern herders to more extensive markets, it presents challenges for herders and for the microbial communities with whom they co-exist, placing herders under increasing pressures to compete with large-scale dairy enterprises that brand, package and distribute standardized dairy products. Looking at the changing material culture of Mongolian dairying and its relationships with microbial communities, this paper examines two emergent notions of purity: the first in which sterility is generated and contained and the second in which living dairy is harnessed and grown.

“The genetic history of the Southern Arc: a bridge between West Asia and Europe.” Science 377: 6609 eabm4247 (2022).

I. Lazaridis, S. Alpaslan-Roodenberg, A. Acar, A. Açıkkol, A. Agelarakis, L. Aghikyan, U. Akyüz, D. Andreeva, G. Andrijasevic, D. Antonović, I. Armit, A. Atmaca, P. Avetisyan, A. İhsan Aytek, K. Bacvarov, R. Badalyan, S. Bakardzhiev, J. Balen, L. Bejko, R. Bernardos, A. Bertsatos, H. Biber, A. Bilir, M. Bodružić, M. Bonogofsky, C. Bonsall, D. Borić, N. Borovinić, G. Bravo Morante, K. Buttinger, K. Callan, F. Candilio, M. Carić, O. Cheronet, S. Chohadzhiev, M. Chovalopoulou, S. Chryssoulaki, I. Ciobanu, N. Čondić, M. Constantinescu, E. Cristiani, B.J. Culleton, E. Curtis, J. Davis, T.I. Demcenco, V. Dergachev, Z. Derin, S. Deskaj, S. Devejyan, R. Davtyan, V. Djordjević, K.S. Duffett Carlson, L.R. Eccles, N. Elenski, A. Engin, N. Erdoğan, S. Erir-Pazarcı, D.M. Fernandes, M. Ferry, S. Freilich, A. Frînculeasa, M.L. Galaty, B. Gamarra, B. Gasparyan, B. Gaydarska, E. Genç, T. Gültekin, S. Gündüz, T. Hajdu, V. Heyd, S. Hobosyan, N. Hovhannisyan, I. Iliev, L. Iliev, S. Iliev, İ. İvgin, I. Janković, L. Jovanova, P. Karkanas, B. Kavaz-Kındığılı, E. Hilal Kaya, D. Keating, D. Kennett, S. Deniz Kesici, A. Khudaverdyan, K. Kiss, S. Kılıç, P. Klostermann, S. Kostak Boca Negra Valdes, S. Kovačević, M. Krenz-Niedbała, M. Krznarić Škrivanko, R. Kurti, P. Kuzman, A.M. Lawson, C. Lazar, K. Leshtakov, T.E. Levy, I. Liritzis, K.O. Lorentz, S. Łukasik, M. Mah, S. Mallick, K. Mandl, K. Martirosyan-Olshansky, R. Matthews, W. Matthews, K. McSweeney, V. Melikyan, A. Micco, M. Michel, L. Milasinovic, A. Mittnik, J.M. Monge, G. Nekhrizov, R. Nicholls, A.G. Nikitin, V. Nikolov, M. Novak, I. Olalde, J. Oppenheimer, A. Osterholtz, C. Özdemir, K. Toykan Özdoğan, N. Öztürk, N. Papadimitriou, N. Papakonstantinou, A. Papathanasiou, L. Paraman, E.G. Paskary, N. Patterson, I. Petrakiev, L. Petrosyan, V. Petrova, A. Philippa-Touchais, A. Piliposyan, N. Pocuca Kuzman, H. Potrebica, B. Preda-Bălănică, Z. Premužić, T.D. Price, L. Qiu, S. Radović, K. Raeuf Aziz, P. Rajić Šikanjić, K. Rasheed Raheem, S. Razumov, A. Richardson, J. Roodenberg, R. Ruka, V. Russeva, M. Şahin, A. Şarbak, E. Savaş, C. Schattke, L. Schepartz, T. Selçuk, A. Sevim-Erol, M. Shamoon-Pour, H.M. Shephard, A. Sideris, A. Simalcsik, H. Simonyan, V. Sinika, K. Sirak, G. Sirbu, M. Šlaus, A. Soficaru, B. Söğüt, A. Sołtysiak, Ç. Sönmez-Sözer, M. Stathi, M. Steskal, K. Stewardson, S. Stocker, F. Suata-Alpaslan, A. Suvorov, A. Szécsényi- Nagy, T. Szeniczey, N. Telnov, S. Temov, N. Todorova, U. Tota, G. Touchais, S. Triantaphyllou, A. Türker, M. Ugarković, T. Valchev, F. Veljanovska, Z. Videvski, C. Virag, A. Wagner, S. Walsh, P. Włodarczak, J.N. Workman, A. Yardumian, E. Yarovoy, A. Yener Yavuz, H. Yılmaz, F. Zalzala, A. Zettl, Z. Zhang, R. Çavuşoğlu, N. Rohland, R. Pinhasi, D. Reich.

By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra–West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.

“Ancient DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia.” Science 377: 6609, 982-987 (2022).

We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia.

“A genetic probe into the ancient and medieval history of Southern Europe and West Asia.” Science 377: 6609, 940-951 (2022).

Literary and archaeological sources have preserved a rich history of Southern Europe and West Asia since the Bronze Age that can be complemented by genetics. Mycenaean period elites in Greece did not differ from the general population and included both people with some steppe ancestry and others, like the Griffin Warrior, without it. Similarly, people in the central area of the Urartian Kingdom around Lake Van lacked the steppe ancestry characteristic of the kingdom’s northern provinces. Anatolia exhibited extraordinary continuity down to the Roman and Byzantine periods, with its people serving as the demographic core of much of the Roman Empire, including the city of Rome itself. During medieval times, migrations associated with Slavic and Turkic speakers profoundly affected the region.

“Ancient Yersinia pestis and Salmonella enterica genomes from Bronze Age Crete.” Current Biology 32, 1-9 (2022).

G.U. Neumann, E. Skourtanioti, M. Burri, E.A. Nelson, M. Michel, A.N. Hiss, P.J.P. McGeorge, P.P. Betancourt, M.A. Spyrou, J. Krause, P.W. Stockhammer.

During the late 3rd millennium BCE, the Eastern Mediterranean and Near East witnessed societal changes in many regions, which are usually explained with a combination of social and climatic factors. However, recent archaeogenetic research forces us to rethink models regarding the role of infectious diseases in past societal trajectories. The plague bacterium Yersinia pestis, which was involved in some of the most destructive historical pandemics, circulated across Eurasia at least from the onset of the 3rd millennium BCE, but the challenging preservation of ancient DNA in warmer climates has restricted the identification of Y. pestis from this period to temperate climatic regions. As such, evidence from culturally prominent regions such as the Eastern Mediterranean is currently lacking. Here, we present genetic evidence for the presence of Y. pestis and Salmonella enterica, the causative agent of typhoid/enteric fever, from this period of transformation in Crete, detected at the cave site Hagios Charalambos. We reconstructed one Y. pestis genome that forms part of a now-extinct lineage of Y. pestis strains from the Late Neolithic and Bronze Age that were likely not yet adapted for transmission via fleas. Furthermore, we reconstructed two ancient S. enterica genomes from the Para C lineage, which cluster with contemporary strains that were likely not yet fully host adapted to humans. The occurrence of these two virulent pathogens at the end of the Early Minoan period in Crete emphasizes the necessity to re-introduce infectious diseases as an additional factor possibly contributing to the transformation of early complex societies in the Aegean and beyond.

“The source of the Black Death in fourteenth-century central Eurasia.” Nature 606, 718–724 (2022).

M.A. Spyrou, L. Musralina, G.A. Gnecchi Ruscone, A. Kocher, P. Borbone, V.I. Khartanovich, A. Buzhilova, L. Djansugurova, K.I. Bos, D. Kühnert, W. Haak, P. Slavin, J. Krause.

The origin of the medieval Black Death pandemic (AD 1346–1353) has been a topic of continuous investigation because of the pandemic’s extensive demographic impact and long-lasting consequences. Until now, the most debated archaeological evidence potentially associated with the pandemic’s initiation derives from cemeteries located near Lake Issyk-Kul of modern-day Kyrgyzstan. These sites are thought to have housed victims of a fourteenth-century epidemic as tombstone inscriptions directly dated to 1338–1339 state ‘pestilence’ as the cause of death for the buried individuals. Here we report ancient DNA data from seven individuals exhumed from two of these cemeteries, Kara-Djigach and Burana. Our synthesis of archaeological, historical and ancient genomic data shows a clear involvement of the plague bacterium Yersinia pestis in this epidemic event. Two reconstructed ancient Y. pestis genomes represent a single strain and are identified as the most recent common ancestor of a major diversification commonly associated with the pandemic’s emergence, here dated to the first half of the fourteenth century. Comparisons with present-day diversity from Y. pestis reservoirs in the extended Tian Shan region support a local emergence of the recovered ancient strain. Through multiple lines of evidence, our data support an early fourteenth-century source of the second plague pandemic in central Eurasia.

“Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history.” Nature Communications 13:2399 (2022).

H. Yu, A. Jamieson, A. Hulme-Beaman, C.J. Conroy, B. Knight, C. Speller, H. Al-Jarah, H. Eager, A. Trinks, G. Adikari, H. Baron, B. Böhlendorf-Arslan, W. Bohingamuwa, A. Crowther, T. Cucchi, K. Esser, J. Fleisher, L. Gidney, E. Gladilina, P. Gol’din, S.M. Goodman, S. Hamilton-Dyer, R. Helm, J.C. Hillman, N. Kallala, H. Kivikero, Z.E. Kovács, G. Karl Kunst, R. Kyselý, A. Linderholm, B. Maraoui-Telmini, N. Marković, A. Morales-Muñiz, M. Nabais, T. O’Connor, T. Oueslati, E.M. Quintana Morales, K. Pasda, J. Perera, N. Perera, S. Radbauer, J. Ramon, E. Rannamäe, J. Sanmartí Grego, E. Treasure, S. Valenzuela-Lamas, I. van der Jagt, W. Van Neer, J.-D. Vigne, T. Walker, S. Wynne-Jones, J. Zeiler, K. Dobney, N. Boivin, J.B. Searle, B. Krause-Kyora, J. Krause, G. Larson, D. Orton.

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we first generate a de novo genome assembly of the black rat. We then sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of our newly reported sequences, together with published mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.

“Ancient genomes from the Himalayas illuminate the genetic history of Tibetans and their Tibeto-Burman speaking neighbors.” Nature Communications 13:1203 (2022).

C. Liu, D. Witonsky, H. Ringbauer, R. Hagan, C. Hofman, N. Patel, R. Stahl, J. Novembre, M. Aldenderfer, C. Warinner, A. Di Rienzo, C. Jeong.

Present-day Tibetans have adapted both genetically and culturally to the high altitude environment of the Tibetan Plateau, but fundamental questions about their origins remain unanswered. Recent archaeological and genetic research suggests the presence of an early population on the Plateau within the past 40 thousand years, followed by the arrival of subsequent groups within the past 10 thousand years. Here, we obtain new genome-wide data for 33 ancient individuals from high elevation sites on the southern fringe of the Tibetan Plateau in Nepal, who we show are most closely related to present-day Tibetans. They derive most of their ancestry from groups related to Late Neolithic populations at the northeastern edge of the Tibetan Plateau but also harbor a minor genetic component from a distinct and deep Paleolithic Eurasian ancestry. In contrast to their Tibetan neighbors, present-day non-Tibetan Tibeto-Burman speakers living at mid-elevations along the southern and eastern margins of the Plateau form a genetic cline that reflects a distinct genetic history. Finally, a comparison between ancient and present-day highlanders confirms ongoing positive selection of high altitude adaptive alleles.

“Ancient DNA and deep population structure in sub-Saharan African foragers.” Nature 603: 290–296 (2022).

M. Lipson, E.A. Sawchuk, J.C. Thompson, J. Oppenheimer, C.A. Tryon, K.L. Ranhorn, K.M. de Luna, K.A. Sirak, I. Olalde, S.H. Ambrose, J.W. Arthur, K.J.W. Arthur, G. Ayodo, A. Bertacchi, J.I. Cerezo-Roman, B.J. Culleton, M.C. Curtis, J. Davis, A.O. Gidna, A. Hanson, P. Kaliba, M. Katongo, A. Kwekason, M.F. Laird, J. Lewis, A.Z.P. Mabulla, F. Mapemba, A. Morris, G. Mudenda, R. Mwafulirwa, D. Mwangomba, E. Ndiema, C. Ogola, F. Schilt, P.R. Willoughby, D.K. Wright, A. Zipkin, R. Pinhasi, D.J. Kennett, F.K. Manthi, N. Rohland, N. Patterson, D. Reich, M. Prendergast.

Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations. Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80–20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.

“Paleoproteomics.” Chemical Reviews (2022).

C. Warinner, K. Richter, M. Collins.

Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human–animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored “dark” proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.

“Lowest Common Ancestor for SAM/BAM/CRAM alignment files.” Journal of Open Source Science 7(74), 4360 (2022).

M. Borry, A. Hübner, C. Warinner C.

sam2lca is a program performing reference sequence disambiguation for reads mapping to multiple reference sequences in a shotgun metagenomics sequencing dataset. To do so, it takes as input the common SAM sequence alignment format and applies the lowest common ancestor algorithm.

“A primer for ZooMS applications in archaeology.” PNAS 119(20) e2109323119 (2022).

K. Richter, M. Seabrook, M. Codlin M, C. Warinner.

Collagen peptide mass fingerprinting by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, also known as zooarchaeology by mass spectrometry (ZooMS), is a rapidly growing analytical technique in the fields of archaeology, ecology, and cultural heritage. Minimally destructive and cost effective, ZooMS enables rapid taxonomic identification of large bone assemblages, cultural heritage objects, and other organic materials of animal origin. As its importance grows as both a research and a conservation tool, it is critical to ensure that its expanding body of users understands its fundamental principles, strengths, and limitations. Here, we outline the basic functionality of ZooMS and provide guidance on interpreting collagen spectra from archaeological bones. We further examine the growing potential of applying ZooMS to nonmammalian assemblages, discuss available options for minimally and nondestructive analyses, and explore the potential for peptide mass fingerprinting to be expanded to noncollagenous proteins. We describe the current limitations of the method regarding accessibility, and we propose solutions for the future. Finally, we review the explosive growth of ZooMS over the past decade and highlight the remarkably diverse applications for which the technique is suited. Zooarchaeology by mass spectrometry (ZooMS) is a powerful application of collagen peptide mass fingerprinting (PMF) first developed just over a decade ago. Based on the measurement of tryptic collagen peptides using a matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometer, it leverages the high abundance and long-term preservation of collagen in bone and other animal tissues with the analytical power of mass spectrometry (MS) in order to provide robust taxonomic identifications using minimally destructive methods. Since 2009, ZooMS has been used for diverse applications in archaeology and paleontology, ecology and conservation, and cultural heritage. The key features of ZooMS that have led to its rapid expansion are its low sample input requirements and its relatively low analytical cost per sample compared with other biomolecular identification methods. This allows for large-scale taxonomic investigations that can augment morphological analyses of faunal assemblages as well as provide taxonomic clarity for animal remains or products lacking diagnostic features, as is common for worked bone artifacts and cultural heritage objects.

“Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague.” PNAS 119(17): e2116722119 (2022).

A. Andrades Valtueña, G.U. Neumann, M.A. Spyrou, L. Musralina, F. Aron, A. Beisenov, A.B. Belinskiy, K.I. Bos, A. Buzhilova, M. Conrad, L.B. Djansugurova, M. Dobes, M. Ernée, J. Fernández-eraso, B. Frohlich, M. Furmanek, A. Haluszko, S. Hansen, É. Harney, A.N. Hiss, A. Hübner, F.M. Key, E. Khussainova, Y. Kitov, A.O. Kitova, C. Knipper, D. Kühnert, C. Lalueza-Fox, J. Littleton, K. Massey, A. Mittnik, J.A. Mujika-Alustiza, I. Olalde, L. Papac, S. Penske, J. Peska, R. Pinhasi, D. Reich, S. Reinhold, R. Stahl, H. Stäuble, R.I. Tukhbatova, S. Vasilyev, E. Veselovskaya, C. Warinner, P.W. Stockhammer, W. Haak, J. Krause, A. Herbig.

The bacterium Yersinia pestis has caused numerous historically documented outbreaks of plague and research using ancient DNA could demonstrate that it already affected human populations during the Neolithic. However, the pathogen’s genetic diversity, geographic spread, and transmission dynamics during this early period of Y. pestis evolution are largely unexplored. Here, we describe a set of ancient plague genomes up to 5,000 y old from across Eurasia. Our data demonstrate that two genetically distinct forms of Y. pestis evolved in parallel and were both distributed across vast geographic distances, potentially occupying different ecological niches. Interpreted within the archeological context, our results suggest that the spread of plague during this period was linked to increased human mobility and intensification of animal husbandry.

“Emergence and intensification of dairying in the Caucasus and Eurasian steppes.” Nature Ecology and Evolution 6, 813–822 (2022).

A. Scott, S. Reinhold, T. Hermes, A.A. Kalmykov, A. Belinskiy, A. Buzhilova, N. Berezina, A.R. Kantorovich, V.E. Maslov, F. Guliyev, B. Lyonnet, P. Gasimov, B. Jalilov, J. Eminli, E. Iskandarov, E. Hammer, S. Nugent, R. Hagan, K. Majander, P. Onkamo, K. Nordqvist, N. Shishlina, E. Kaverzneva, A. Korolev, A.A. Khokhlov, R.V. Smolyaninov, S.V. Sharapova, R. Krause, M. Karapetian, E. Stolarczyk, J. Krause, S. Hansen, W. Haak, C. Warinner. 2022)

Archaeological and archaeogenetic evidence points to the Pontic–Caspian steppe zone between the Caucasus and the Black Sea as the crucible from which the earliest steppe pastoralist societies arose and spread, ultimately influencing populations from Europe to Inner Asia. However, little is known about their economic foundations and the factors that may have contributed to their extensive mobility. Here, we investigate dietary proteins within the dental calculus proteomes of 45 individuals spanning the Neolithic to Greco-Roman periods in the Pontic–Caspian Steppe and neighbouring South Caucasus, Oka–Volga–Don and East Urals regions. We find that sheep dairying accompanies the earliest forms of Eneolithic pastoralism in the North Caucasus. During the fourth millennium BC, Maykop and early Yamnaya populations also focused dairying exclusively on sheep while reserving cattle for traction and other purposes. We observe a breakdown in livestock specialization and an economic diversification of dairy herds coinciding with aridification during the subsequent late Yamnaya and North Caucasus Culture phases, followed by severe climate deterioration during the Catacomb and Lola periods. The need for additional pastures to support these herds may have driven the heightened mobility of the Middle and Late Bronze Age periods. Following a hiatus of more than 500 years, the North Caucasian steppe was repopulated by Early Iron Age societies with a broad mobile dairy economy, including a new focus on horse milking.

“Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation.” FEMS Microbes 3: xtac006 (2022).

Z. Fagernäs, D.C. Salazar-Garcia, A. Avilés Ferández, M. Haber Uriarte, A. Henry, J. Lomba Maurandi, A. Ozga, I.M. Velsko, C. Warinner.

The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500–5000 BP). Interindividual differences in microbial composition are found to be much larger than intraindividual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples is likely of postmortem origin, demonstrating the importance of including environmental controls or additional lines of biomolecular evidence in dietary interpretations.

“The spatiotemporal patterns of major human admixture events during the European Holocene.” eLife 77625 (2022).

M. Chintalapati, N. Patterson, P. Moorjani.

Recent studies have shown that admixture has been pervasive throughout human history. While several methods exist for dating admixture in contemporary populations, they are not suitable for sparse, low coverage ancient genomic data. Thus, we developed DATES (Distribution of Ancestry Tracts of Evolutionary Signals) that leverages ancestry covariance patterns across the genome of a single individual to infer the timing of admixture. DATES provides reliable estimates under various demographic scenarios and outperforms available methods for ancient DNA applications. Using DATES on~1100 ancient genomes from sixteen regions in Europe and west Asia, we reconstruct the chronology of the formation of the ancestral populations and the fine-scale details of the spread of Neolithic farming and Steppe pastoralist-related ancestry across Europe. By studying the genetic formation of Anatolian farmers, we infer that gene flow related to Iranian Neolithic farmers occurred before 9600 BCE, predating the advent of agriculture in Anatolia. Contrary to the archaeological evidence, we estimate that early Steppe pastoralist groups (Yamnaya and Afanasievo) were genetically formed more than a millennium before the start of Steppe pastoralism. Our analyses provide new insights on the origins and spread of farming and Indo-European languages, highlighting the power of genomic dating methods to elucidate the legacy of human migrations.

“Ancient Human DNA and African Population History.” Oxford Research Encyclopedia of Anthropology (2022).

K.A. Sirak, E.A. Sawchuk, M.E. Prendergast.

Ancient DNA has emerged as a powerful tool for investigating the human past and reconstructing the movements, mixtures, and adaptations that have structured genetic variation throughout human history. While the study of genome-wide ancient human DNA was initially restricted to regions with temperate climates, methodological breakthroughs have now extended the reach of ancient DNA analysis to parts of the world with hot and humid climates that are less conducive to biomolecular preservation. This includes Africa, where people harbor more genetic diversity than can be found anywhere else on the planet, reflecting deep and complex population histories. Since the first ancient African genome was published in 2015, the number of individuals with genome-wide data has increased to nearly 200, with greater coverage of diverse geographical, temporal, and cultural contexts. Ancient DNA sequences have revealed genetic variation in ancient African foragers that no longer exists in unadmixed form; illuminated how local-, regional-, and continental-scale demographic processes associated with the spread of food production and new technologies changed genetic landscapes; and discerned notable variation in interactions among people with distinct genetic ancestries, cultural practices, and, likely, languages. Despite an increasing number of studies focused on African ancient DNA, multiple regions and time periods have yet to be explored. Research to date has primarily focused on the past several thousand years in eastern and southern Africa, setting up northern, western, and central Africa, as well as deeper time periods, as key areas for future investigation. As ancient DNA research becomes increasingly integrated with anthropology and archaeology, it is advantageous to understand the basic methodological and analytical techniques, the types of questions that can be investigated, and the ways in which the discipline may continue to grow and evolve. Critically, the growth and evolution of ancient DNA research must include attention to the ethics of this work, both in African contexts and globally. In particular, it is essential that research is conducted in a way that minimizes the potential of harm to both the living and the dead. Scientists conducting ancient DNA research in Africa especially must also contend with structural challenges, including a lack of ancient DNA facilities on the continent, the extensive fragmentation of African heritage (including ancient human remains) among curating institutions worldwide, and the complexities of identifying descendant groups and other stakeholders in the wake of colonial and postcolonial disruptions and displacements. Ancient DNA research projects should be designed in a way that contributes to capacity building and the reduction of inequities between the Global North and South to ensure that the research benefits the people and communities with connections to the ancient individuals studied. While ensuring that future studies are rooted in ethical and equitable practices will require considerable collective action, ancient DNA research has already become an integral part of our understanding of African population history and will continue to shape our understanding of the African past.

“An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers.” PNAS 119, e2106743119 (2022).

S. Marciniak, C.M. Bergey, A.M. Silva, A. Hałuszkof, M. Furmanek, B. Veselka, P. Veleminsky, G. Vercellotti, J. Wahl, G. Zarina, C. Longhi, J. Kolar, R. Garrido-pena, R. Flores-Fernandez, A.M. Herrero-Corral, A. Simalcsik, W. Muller, A. Sheridan, Z. Miliauskiene, R. Jankauskas, V. Moiseyev, K. Kohler, A. Kiraly, B. Gamarra, O. Cheronet, V. Szeverenyi, V. Kiss, T. Szeniczey, K. Kiss, Z.K. Zoffmann, J. Koos, M. Hellebrandt, R.M. Maier, L. Domboroczki, C. Virag, M. Novak, D. Reich, T. Hajdu, N. von Cramon-Taubadel, R. Pinhasi, G.H. Perry.

Human culture, biology, and health were shaped dramatically by the onset of agriculture ∼12,000 y B.P. This shift is hypothesized to have resulted in increased individual fitness and population growth as evidenced by archaeological and population genomic data alongside a decline in physiological health as inferred from skeletal remains. Here, we consider osteological and ancient DNA data from the same prehistoric individuals to study human stature variation as a proxy for health across a transition to agriculture. Specifically, we compared “predicted” genetic contributions to height from paleogenomic data and “achieved” adult osteological height estimated from long bone measurements for 167 individuals across Europe spanning the Upper Paleolithic to Iron Age (∼38,000 to 2,400 B.P.). We found that individuals from the Neolithic were shorter than expected (given their individual polygenic height scores) by an average of −3.82 cm relative to individuals from the Upper Paleolithic and Mesolithic (P = 0.040) and −2.21 cm shorter relative to post-Neolithic individuals (P = 0.068), with osteological vs. expected stature steadily increasing across the Copper (+1.95 cm relative to the Neolithic), Bronze (+2.70 cm), and Iron (+3.27 cm) Ages. These results were attenuated when we additionally accounted for genome-wide genetic ancestry variation: for example, with Neolithic individuals −2.82 cm shorter than expected on average relative to pre-Neolithic individuals (P = 0.120). We also incorporated observations of paleopathological indicators of nonspecific stress that can persist from childhood to adulthood in skeletal remains into our model. Overall, our work highlights the potential of integrating disparate datasets to explore proxies of health in prehistory.

“The Eneolithic cemetery at Khvalynsk on the Volga River.” Praehistorische Zeitschrift 97 (1) 22-67 (2022).

D.W. Anthony, A.A. Khokhlov, S.A. Agapov, D.S. Agapov, R. Schulting, I. Olalde, D. Reich.

The genetically attested migrations of the third millennium BC have made the origins and nature of the Yamnaya culture a question of broad relevance across northern Eurasia. But none of the key archaeological sites most important for understanding the evolution of Yamnaya culture is published in western languages. These key sites include the fifth-millennium BC Khvalynsk cemetery in the middle Volga steppes. When the first part of the Eneolithic cemetery (Khvalynsk I) was discovered in 1977–1979, the graves displayed many material and ritual traits that were quickly recognized as similar and probably ancestral to Yamnaya customs, but without the Yamnaya kurgans. With the discovery of a second burial plot (Khvalynsk II) 120 m to the south in 1987–1988, Khvalynsk became the largest excavated Eneolithic cemetery in the Don-Volga-Ural steppes (201 recorded graves), dated about 4500–4300 BCE. It has the largest copper assemblage of the fifth millennium BC in the steppes (373 objects) and the largest assemblage of sacrificed domesticated animals (at least 106 sheep-goat, 29 cattle, and 16 horses); and it produced four polished stone maces from well-documented grave contexts. The human skeletons have been sampled extensively for ancient DNA, the basis for an analysis of family relationships. This report compiles information from the relevant Russian-language publications and from the archaeologists who excavated the site, two of whom are co-authors, about the history of excavations, radiocarbon dates, copper finds, domesticated animal sacrifices, polished stone maces, genetic and skeletal studies, and relationships with other steppe cultures as well as agricultural cultures of the North Caucasus (Svobodnoe-Meshoko) and southeastern Europe (Varna and Cucuteni-Tripol’ye B1). Khvalynsk is described as a coalescent culture, integrating and combining northern and southern elements, a hybrid that can be recognized genetically, in cranio-facial types, in exchanged artifacts, and in social segments within the cemetery. Stone maces symbolized the unification and integration of socially defined segments at Khvalynsk.

“Ancient genomes reveal origin and rapid trans-Eurasian migration of 7^th century Avar elites.” Cell 185, 1402-13 (2022).

G.A. Gnecchi-Ruscone, A. Szecsenyi-Nagy, I. Koncz, G. Csiky, Z. Racz, A.B. Rohrlach, G. Brandt, N. Rohland, V. Csaky, O. Cheronet, B. Szeifert, T.A. Racz, A. Benedek, Z. Bernert, N. Berta, S. Czifra, J. Dani, Z. Farkas, T. Haga, T. Hajdu, M. Jaszberenyi, V. Kisjuhasz, B. Kolozsi, P. Major, A. Marcsik, B.N. Kovacsoczy, C. Balogh, G.M. Lezsak, J.G. Odor, M. Szelekovszky, T. Szeniczey, J. Tarnoki, Z. Toth, E.K. Tutkovics, B.G. Mende, P. Geary, W. Pohl, T. Vida, R. Pinhasi, D. Reich, Z. Hofmanova, C. Jeong, J. Krause.

The Avars settled the Carpathian Basin in 567/68 CE, establishing an empire lasting over 200 years. Who they were and where they came from is highly debated. Contemporaries have disagreed about whether they were, as they claimed, the direct successors of the Mongolian Steppe Rouran empire that was destroyed by the Turks in ∼550 CE. Here, we analyze new genome-wide data from 66 pre-Avar and Avar-period Carpathian Basin individuals, including the 8 richest Avar-period burials and further elite sites from Avar’s empire core region. Our results provide support for a rapid long-distance trans-Eurasian migration of Avar-period elites. These individuals carried Northeast Asian ancestry matching the profile of preceding Mongolian Steppe populations, particularly a genome available from the Rouran period. Some of the later elite individuals carried an additional non-local ancestry component broadly matching the steppe, which could point to a later migration or reflect greater genetic diversity within the initial migrant population.

“South-to-north migration preceded the advent of intensive farming in the Maya region.” Nature Communications 13, 1530 (2022).

D.J. Kennett, M. Lipson, K.M. Prufer, D. Mora-Marin, R.J. George, N. Rohland, M. Robinson, W.R. Trask, H.H.J. Edgar, E.C. Hill, E.E. Ray, P. Lynch, E. Moes, L. O'Donnell, T.K. Harper, E.J. Kate, J. Ramos, J. Morris, S.M. Gutierrez, T.M. Ryan, B.J. Culleton, J.J. Awe, D. Reich.

The genetic prehistory of human populations in Central America is largely unexplored leaving an important gap in our knowledge of the global expansion of humans. We report genome-wide ancient DNA data for a transect of twenty individuals from two Belize rock-shelters dating between 9,600-3,700 calibrated radiocarbon years before present (cal. BP). The oldest individuals (9,600-7,300 cal. BP) descend from an Early Holocene Native American lineage with only distant relatedness to present-day Mesoamericans, including Mayan-speaking populations. After ~5,600 cal. BP a previously unknown human dispersal from the south made a major demographic impact on the region, contributing more than 50% of the ancestry of all later individuals. This new ancestry derived from a source related to present-day Chibchan speakers living from Costa Rica to Colombia. Its arrival corresponds to the first clear evidence for forest clearing and maize horticulture in what later became the Maya region.

“A unified genealogy of modern and ancient genomes.” Science 375, eabi8264 (2022).

A.W. Wohns, Y. Wong, B. Jeffrey, A. Akbari, S. Mallick, R. Pinhasi, N. Patterson, D. Reich, J. Kelleher, G. McVean.

The sequencing of modern and ancient genomes from around the world has revolutionized our understanding of human history and evolution. However, the problem of how best to characterize ancestral relationships from the totality of human genomic variation remains unsolved. Here, we address this challenge with nonparametric methods that enable us to infer a unified genealogy of modern and ancient humans. This compact representation of multiple datasets explores the challenges of missing and erroneous data and uses ancient samples to constrain and date relationships. We demonstrate the power of the method to recover relationships between individuals and populations as well as to identify descendants of ancient samples. Finally, we introduce a simple nonparametric estimator of the geographical location of ancestors that recapitulates key events in human history.

“Indian genetic heritage in Southeast Asian populations.” PLoS Genetics 18(2): e1010036 (2022).

P. Changmai, K. Jaisamut, J. Kampuansai, W. Kutanan, N.E. Altınışık, O. Flegontova, A. Inta, E. Yuncu, W. Boonthai, H. Pamjav, D. Reich, P. Flegontov.

The great ethnolinguistic diversity found today in mainland Southeast Asia (MSEA) reflects multiple migration waves of people in the past. Maritime trading between MSEA and India was established at the latest 300 BCE, and the formation of early states in Southeast Asia during the first millennium CE was strongly influenced by Indian culture, a cultural influence that is still prominent today. Several ancient Indian-influenced states were located in present-day Thailand, and various populations in the country are likely to be descendants of people from those states. To systematically explore Indian genetic heritage in MSEA populations, we generated genome-wide SNP data (using the Affymetrix Human Origins array) for 119 present-day individuals belonging to 10 ethnic groups from Thailand and co-analyzed them with published data using PCA, ADMIXTURE, and methods relying on f-statistics and on autosomal haplotypes. We found low levels of South Asian admixture in various MSEA populations for whom there is evidence of historical connections with the ancient Indian-influenced states but failed to find this genetic component in present-day hunter-gatherer groups and relatively isolated groups from the highlands of Northern Thailand. The results suggest that migration of Indian populations to MSEA may have been responsible for the spread of Indian culture in the region. Our results also support close genetic affinity between Kra-Dai-speaking (also known as Tai-Kadai) and Austronesian-speaking populations, which fits a linguistic hypothesis suggesting cladality of the two language families.

“Ancient DNA reveals five streams of migration into Micronesia and matrilocality in early Pacific seafarers.” Science 377: 6601, 72-9 (2022).

Y.C. Liu, R. Hunter-Anderson, O. Cheronet, J. Eakin, F. Camacho, M. Pietrusewsky, N. Rohland, A. Ioannidis, J.S. Athens, M.T. Douglas, M.I. Ikehara-Quebral, R. Bernardos, B.J. Culleton, M. Mah, N. Adamski, N. Broomandkhoshbacht, K. Callan, A.M. Lawson, K. Mandl, M. Michel, J. Oppenheimer, K. Stewardson, F. Zalzala, K. Kidd, J. Kidd, T.G. Schurr, K. Auckland, A.V.S. Hill, A.J. Mentzer, C.D. Quinto-Cortés, K. Robson, D.J. Kennett, N. Patterson, C.D. Bustamante, A. Moreno-Estrada, M. Spriggs, M. Vilar, M. Lipson, R. Pinhasi, D. Reich.

Micronesia began to be peopled earlier than other parts of Remote Oceania, but the origins of its inhabitants remain unclear. We generated genome-wide data from 164 ancient and 112 modern individuals. Analysis reveals five migratory streams into Micronesia. Three are East Asian related, one is Polynesian, and a fifth is a Papuan source related to mainland New Guineans that is different from the New Britain–related Papuan source for southwest Pacific populations but is similarly derived from male migrants ~2500 to 2000 years ago. People of the Mariana Archipelago may derive all of their precolonial ancestry from East Asian sources, making them the only Remote Oceanians without Papuan ancestry. Female-inherited mitochondrial DNA was highly differentiated across early Remote Oceanian communities but homogeneous within, implying matrilocal practices whereby women almost never raised their children in communities different from the ones in which they grew up.

2021

“Ancient DNA analysis.” Nature Reviews Methods Primers 1:14 (2021).

L. Orlando, R. Allaby, P. Skoglund, C. Sarkissian, P.W. Stockhammer, M. Avila, Q. Fu, J. Krause, E. Willerslev, A. Stone, C. Warinner.

Although the first ancient DNA molecules were extracted more than three decades ago, the first ancient nuclear genomes could only be characterized after high-throughput sequencing was invented. Genome-scale data have now been gathered from thousands of ancient archaeological specimens, and the number of ancient biological tissues amenable to genome sequencing is growing steadily. Ancient DNA fragments are typically ultrashort molecules and carry extensive amounts of chemical damage accumulated after death. Their extraction, manipulation and authentication require specific experimental wet-laboratory and dry-laboratory procedures before patterns of genetic variation from past individuals, populations and species can be interpreted. Ancient DNA data help to address an entire array of questions in anthropology, evolutionary biology and the environmental and archaeological sciences. The data have revealed a considerably more dynamic past than previously appreciated and have revolutionized our understanding of many major prehistoric and historic events. This Primer provides an overview of concepts and state-of-the-art methods underlying ancient DNA analysis and illustrates the diversity of resulting applications. The article also addresses some of the ethical challenges associated with the destructive analysis of irreplaceable material, emphasizes the need to fully involve archaeologists and stakeholders as part of the research design and analytical process, and discusses future perspectives.

“Gregory of Tours on Sixth-Century Plague and Other Epidemics.” Speculum 96:1 (2021).

M. McCormick.

Analyzes philologically and historically all testimony in the works of Gregory of Tours about various epidemics that struck Gaul, Iberia, and Italy in the sixth century; in particular, those of the most serious disease, “inguinal epidemic,” that is, bubonic plague (Yersinia pestis), as well as an illness that may have been smallpox (Variola major). Establishes that Gregory’s testimony, inspired by his personal and pastoral-theological concerns, is reliable and informative; delineates the motivations and sources for reporting the recurring epidemics of plague as they emerge from his writings; shows that Gregory’s information is robust but geographically constrained: of the twenty-two places and regions where he knows unambiguously about plague, only four are further than 400 km from his familial Clermont. Gregory’s twenty-two mentions of plague also refer to six epidemics between c. 543–47 and c. 591–94, of which he treats four in greater detail; his silences are confirmed to be significant only rarely. Two epidemics are newly dated to springtime, and the initial outbreak is shown as likely to have reached Gaul from a western port. Contagion mirrors communications infrastructures and affected the countryside as well as towns, which populations tended to flee. Symptoms, epidemiology, and heavy mortality align with the ancient DNA proof that the pathogen was Yersinia pestis; pneumonic plague is suggested in two cases. Gregory’s historical testimony is confirmed by and integrated into the new biomolecular archaeological discoveries of early medieval plague victims in western Europe.

“Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt.” Communications Biology 4:169 (2021).

S. Rampelli, S. Turroni, C. Mallol, C. Hernandez, B. Galván, A. Sistiaga, E. Biagi, A. Astolfi, P. Brigidi, S. Benazzi, C.M. Lewis, C. Warinner, C.A. Hofman, S.L. Schnorr, M. Candela.

A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.

“An Egyptian Boy from South America.” Announcements of the Berlin Society for Anthropology, Ethnology and Prehistory 41, 2020 (2021): 107-118.

B. Teẞmann, A. Stoessel, R.A. Bianco.

In the Rudolf Virchow skull collection, a child's skull is inventoried under the inventory number RV 544, which is said to have come from Egypt. Information about the exact circumstances of the find, the location or the collector is not known. Due to its supposed origin from Egypt, the skull was selected for a genetic examination for a cooperation project with the Max Planck Institute for Human History in Jena (MPI Jena-SHH). The anthropological investigation showed that the skull comes from a boy of about six years old. The skull was artificially deformed with the special feature that the external protuberance was carefully pressed in immediately after birth. This finding is clearly visible in the CT image. This type of deformation is not known from Egypt, but it is typical of Meso and South America.

“Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir.” Nature Scientific Data 8:31 (2021).

J. Fellows Yates, A. Andrades Valtueña, A.J. Vägene, B. Cribdon, I.M. Velsko, M. Borry, M.J. Bravo-López, A. Fernandez-Guerra, E.J. Green, S.L. Ramachandran, P.D. Heintzman, M.A. Spyrou, A. Hübner, A.S. Gancz, J. Hider, A.F. Allshouse, C. Warinner.

Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual taxa and communities of both microbes and eukaryotes. AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833) is a collection of annotated metagenomic sample lists derived from published studies that provide basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These tables are community-curated and span multiple sub-disciplines to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks facilitate compatibility with established sequence-read archives and term-ontologies, and ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies.

“Genome-wide analysis of nearly all the victims of a 6200 year old massacre.” PLoS ONE 16:3 (2021).

M. Novak, I. Olalde, H. Ringbauer, N. Rohland, J. Ahern, J. Balen, I. Jankovic, H. Potrebica, R. Pinhasi, D. Reich.

Paleogenomic and bioanthropological studies of ancient massacres have highlighted sites where the victims were male and plausibly died all in battle, or were executed members of the same family as might be expected from a killing intentionally directed at subsets of a community, or where the massacred individuals were plausibly members of a migrant community in conflict with previously established groups, or where there was evidence that the killing was part of a religious ritual. Here we provide evidence of killing on a massive scale in prehistory that was not directed to a specific family, based on genome-wide ancient DNA for 38 of the 41 documented victims of a 6,200 year old massacre in Potočani, Croatia and combining our results with bioanthropological data. We highlight three results: (i) the majority of individuals were unrelated and instead were a sample of what was clearly a large farming population, (ii) the ancestry of the individuals was homogenous which makes it unlikely that the massacre was linked to the arrival of new genetic ancestry, and (iii) there were approximately equal numbers of males and females. Combined with the bioanthropological evidence that the victims were of a wide range of ages, these results show that large-scale indiscriminate killing is a horror that is not just a feature of the modern and historic periods, but was also a significant process in pre-state societies.

“Evidence for early dispersal of domestic sheep into Central Asia.” Nature Human Behavior (2021).

W.T.T. Taylor, M. Pruvost , C. Posth , W. Rendu, M.T. Krajcarz, A. Abdykanova, G. Brancaleoni , R. Spengler , T. Hermes, S. Schiavinato, G. Hodgins, R. Stahl, J. Min, S. Alisher kyzy , S. Fedorowicz, L. Orlando, K. Douka , A. Krivoshapkin, C. Jeong, C. Warinner, S. Shnaider.

The development and dispersal of agropastoralism transformed the cultural and ecological landscapes of the Old World, but little is known about when or how this process first impacted Central Asia. Here, we present archaeological and biomolecular evidence from Obishir V in southern Kyrgyzstan, establishing the presence of domesticated sheep by ca. 6,000 BCE. Zooarchaeological and collagen peptide mass fingerprinting show exploitation of Ovis and Capra, while cementum analysis of intact teeth implicates possible pastoral slaughter during the fall season. Most significantly, ancient DNA reveals these directly dated specimens as the domestic O. aries, within the genetic diversity of domesticated sheep lineages. Together, these results provide the earliest evidence for the use of livestock in the mountains of the Ferghana Valley, predating previous evidence by 3,000 years and suggesting that domestic animal economies reached the mountains of interior Central Asia far earlier than previously recognized.

“La pandémie de Justinien d’après les derniers travaux du MHAAM.” Académie des Inscriptions et Belles-Lettres. Comptes rendus des séances 2019 [2021].

M. McCormick

“Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians.” Science Advances 7:13 (2021).

G.A. Gnecchi-Ruscone, E. Khussainova, N. Kahbatkyzy, L. Musralina, M.A. Spyrou, R.A. Bianco, R. Radzeviciute, N.F. Gomes Martins, C. Freund, O. Iksan, A. Garshin, Z. Zhaniyazov, B. Bekmanov, E. Kitov, Z. Samashev, A. Beisenov, N. Berezina, Y. Berezin, A. Zsolt Bíró, S. Évinger, A. Bissembaev, G. Akhatov, A. Mamedov, A. Onggaruly, D. Voyakin, A. Chotbayev, Y. Kariyev, A. Buzhilova, L. Djansugurova, C. Jeong, J. Krause.

The Scythians were a multitude of horse-warrior nomad cultures dwelling in the Eurasian steppe during the first millennium BCE. Because of the lack of first-hand written records, little is known about the origins and relations among the different cultures. To address these questions, we produced genome-wide data for 111 ancient individuals retrieved from 39 archaeological sites from the first millennia BCE and CE across the Central Asian Steppe. We uncovered major admixture events in the Late Bronze Age forming the genetic substratum for two main Iron Age gene-pools emerging around the Altai and the Urals respectively. Their demise was mirrored by new genetic turnovers, linked to the spread of the eastern nomad empires in the first centuries CE. Compared to the high genetic heterogeneity of the past, the homogenization of the present-day Kazakhs gene pool is notable, likely a result of 400 years of strict exogamous social rules.

“A short history of humanity.” Translated by Caroline Waight. New York, Random House, 2021.

J. Krause, T. Trappe.

“Parental relatedness through time revealed by runs of homozygosity in ancient DNA.” Nature Communications 12: 5425 (2021).

H. Ringbauer, J. Novembre, M. Steinrücken.

Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past. Here we analyze ancient DNA, leveraging that parental relatedness leaves genomic traces in the form of runs of homozygosity. We present an approach to identify such runs in low-coverage ancient DNA data aided by haplotype information from a modern phased reference panel. Simulation and experiments show that this method robustly detects runs of homozygosity longer than 4 centimorgan for ancient individuals with at least 0.3 × coverage. Analyzing genomic data from 1,785 ancient humans who lived in the last 45,000 years, we detect low rates of first cousin or closer unions across most ancient populations. Moreover, we find a marked decay in background parental relatedness co-occurring with or shortly after the advent of sedentary agriculture. We observe this signal, likely linked to increasing local population sizes, across several geographic transects worldwide.

“Human mobility at Tell Atchana (Alalakh), Hatay, Turkey, during the 2nd millennium BC: Integration of isotopic and genomic evidence.” PlosOne (2021).

T. Ingman, S. Eisenmann, E. Skourtanioti, M. Akar, J. Ilgner, G.A. Gnecchi Ruscone, P. le Roux, R. Shafiq, G.U. Neumann, M. Keller, C. Freund, S. Marzo, M. Lucas, J. Krause, P. Roberts, K.A. Yener, P.W. Stockhammer.

The Middle and Late Bronze Age, a period roughly spanning the 2nd millennium BC (ca. 2000–1200 BC) in the Near East, is frequently referred to as the first ‘international age’, characterized by intense and far-reaching contacts between different entities from the eastern Mediterranean to the Near East and beyond. In a large-scale tandem study of stable isotopes and ancient DNA of individuals excavated at Tell Atchana (Alalakh, located in Hatay, Turkey), we explored the role of mobility at the capital of a regional kingdom, named Mukish during the Late Bronze Age, which spanned the Amuq Valley and some areas beyond. We generated strontium and oxygen isotope data from dental enamel for 53 individuals and 77 individuals, respectively, and added ancient DNA data of 10 newly sequenced individuals to a dataset of 27 individuals published in 2020. Additionally, we improved the DNA coverage of one individual from this 2020 dataset. The DNA data revealed a very homogeneous gene pool. This picture of an overwhelmingly local ancestry was consistent with the evidence of local upbringing in most of the individuals indicated by the isotopic data, where only five were found to be non-local. High levels of contact, trade, and exchange of ideas and goods in the Middle and Late Bronze Ages, therefore, seem not to have translated into high levels of individual mobility detectable at Tell Atchana.

“The origin and legacy of the Etruscans through a 2000-year archeogenomic time transect.” Science Advances 7:39 (2021).

C. Posth, V. Zaro, M.A. Spyrou, S. Vai, G.A. Gnecchi-Ruscone, A. Modi, A. Peltzer, A. Mötsch, K. Nägele, Å.J. Vågene, E.A. Nelson, R. Radzevičiūtė, C. Freund, L.M. Bondioli, L. Cappuccini, H. Frenzel, E. Pacciani, F. Boschin, G. Capecchi, I. Martini, A. Moroni, S. Ricci, A. Sperduti, M.A. Turchetti, A. Riga, M. Zavattaro, A. Zifferero, H.O. Heyne, E. Fernández-Domínguez, G.J. Kroonen, M. McCormick, W. Haak, M. Lari, G. Barbujani, L. Bondioli, K.I. Box, D. Caramelli, J. Krause.

The origin, development, and legacy of the enigmatic Etruscan civilization from the central region of the Italian peninsula known as Etruria have been debated for centuries. Here we report a genomic time transect of 82 individuals spanning almost two millennia (800 BCE to 1000 CE) across Etruria and southern Italy. During the Iron Age, we detect a component of Indo-European–associated steppe ancestry and the lack of recent Anatolian-related admixture among the putative non–Indo-European–speaking Etruscans. Despite comprising diverse individuals of central European, northern African, and Near Eastern ancestry, the local gene pool is largely maintained across the first millennium BCE. This drastically changes during the Roman Imperial period where we report an abrupt population-wide shift to ~50% admixture with eastern Mediterranean ancestry. Last, we identify northern European components appearing in central Italy during the Early Middle Ages, which thus formed the genetic landscape of present-day Italian populations.

“The evolution and changing ecology of the African hominid oral microbiome.” PNAS 118 (20) e2021655118 (2021).

J. Fellows Yates, I. Velsko, F. Aron, C. Hofman, R. Austin, J. Arthur, I. Crevecoeur, L. Dalén, M. Gonzalez Morales, K. Guschanski, A.G. Henry, L.T. Humphrey, A.E. Mann, K. Nägele, C.E. Parker, C. Posth, H. Rougier, P. Semal, J. Stock, L. Guy Strauss, K. Weedman Arthur, R. Wrangham, M. Curtis, J.C. Diez, V. Gibbon, M. Menedez, M. Peresani, M. Roksandic, M.J. Walker, R.C. Power, C.M. Lewis, K. Sankaranarayan, D.C. Salazar-Garcia, J. Krause, A. Herbig, C. Warinner.

The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine–platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.

“Pydamage: automated ancient damage identification and estimation for contigs in ancient DNA de Novo assembly.” PeerJ 9:e11845 (2021).

M. Borry, A. Hübner, A.B. Rohrlach, W. Haak, C. Warinner.

DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences, but existing tools for inspecting and filtering aDNA damage either compute it at the read level, which leads to high data loss and lower quality when used in combination with de novo assembly, or require manual inspection, which is impractical for ancient assemblies that typically contain tens to hundreds of thousands of contigs. To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA. PyDamage uses a likelihood ratio based approach to discriminate between truly ancient contigs and contigs originating from modern contamination. We test PyDamage on both on simulated aDNA data and archaeological paleofeces, and we demonstrate its ability to reliably and automatically identify contigs bearing DNA damage characteristic of aDNA. Coupled with aDNA de novo assembly, Pydamage opens up new doors to explore functional diversity in ancient metagenomic datasets.

“Reconstruction of ancient microbial genomes from the human gut.” Nature 594 (2021).

M.C. Wibowo, Z. Yang, B.T. Tierney, M. Borry, A. Huebner, F. Barajas-Olmos, C. Contreras-Cubas, H. García-Ortiz, A. Martínez-Hernández, J.M. Luber, P. Kirstahler, T. Blohm, S. Zimmerman, F.E. Smiley, S.A. Ballal, S.J. Pamp, K. Reinhard, J. Russ, L. Orozco, C. Warinner, M. Snow, S. LeBlanc, A.D. Kostic.

Loss of gut microbial diversity in industrial populations is associated with chronic diseases, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces.

“Ten millennia of hepatitis B virus evolution.” Science 374:6565 (2021).

A. Kocher, L. Papac, R. Barquera, F. Key, M.A. Spyrou, R. Hübler, K. Prüfer, A.J. Rohrlach, F. Aron, R. Stahl, A. Wissgott, A. Mittnik, M. Feldman, G. Neumann, V. Villalba, K. Majander, A. Ghalichi, M. Rivollat, S. Penske, R.I. Tukhbatova, M. Keller, L. Musralin, E. Nelson, M. van de Loosdrecht, K. Nägele, M. Michel, T. Ferraz da Silva, S. Sabin, J. Gretzinger, E. Skourtanioti, C. Parker, G.A. Gnecchi Ruscone, K. Giffin, S. Friederlich, H. Meller, M. Ernee, M. Dobes, K. Massy, R. Skeates, Y.S. Erdal, D. Sayer, M. Küßner, M.F. Deguilloux, K. Mannerma, V. Moiseyev, H. Steiner, D.C. Salazar-Garcia, E. Guevara, T.A. Tung, M. Mannino, V. Schimmernti, F. Hallgren, E.P. Kitov, D.I. Hernández-Zaragoza, L. Máquez-Morfín, K. Rademaker, E. Carmona Ballestero, M. Harbeck, N. Shishlina, E. Kaverzneva, P. Utrilla, S. Lösch, S. Shnayder, V. Mazzarello, M. Schultz, A. Sperduit, P. Semal, S. Rottier, P. Ramsl, K. Van de Vijver, C. Sagona, C. Read, Z. Samashev, A.Z. Beisenov, L.B. Djansugurova, E. Khussainova, M. Rojo-Guerra, C. Tejedor-Rodriguez, I. Garcia-Martinez de Lagran, H. Aarcusa-Magallon, R. Garrido-Pena, J.I. Royo-Guillen, M. Roksandic, Y. Chinique de Armas, S.T. Hernandez Godoy, M. Kostka, S. Kacki, S. Saintot, D. Baird, E. Fernandez-Dominguez, P. Veleminsky, P. Limbursky, P. Lefranc, D. Binder, L. Amkreutz, E. Altena, B. Llamas, M. Alvarez Calmet, R. Krauß, V. Slavchev, E. Rosenstock, M. Francken, M.K. Karapetian, M.S. Chaplygin, V.V. Kufterin, A.A. Khohlov, A.A. Chizhevsky, D.A. Stashenkov, A.F. Kochkina, M. Longova, A. Danielisova, C. Warinner, S. Schiffels, P.W. Stockhammer, K. Bos, C. Posth, A. Herbig, W. Haak, J. Krause, D. Kühnert.

Hepatitis B virus (HBV) has been infecting humans for millennia and remains a global health problem, but its past diversity and dispersal routes are largely unknown. We generated HBV genomic data from 137 Eurasians and Native Americans dated between ~10,500 and ~400 years ago. We date the most recent common ancestor of all HBV lineages to between ~20,000 and 12,000 years ago, with the virus present in European and South American hunter-gatherers during the early Holocene. After the European Neolithic transition, Mesolithic HBV strains were replaced by a lineage likely disseminated by early farmers that prevailed throughout western Eurasia for ~4000 years, declining around the end of the 2nd millennium BCE. The only remnant of this prehistoric HBV diversity is the rare genotype G, which appears to have reemerged during the HIV pandemic.

“The genomic origins of the Bronze Age Tarim mummies.” Nature (2021).

F. Zhang, N. Chao, A. Scott, Q. Fu, R. Bjorn, W. Li, D. Wei, W. Wang, L. Fan, I. Abuduresule, X. Hu, Q. Ruan, A. Niyazi, G. Dong, P. Cao, F. Liu, Q. Dai, X. Feng, R. Yang, Z. Tang, P. Ma, C. Li, S. Gao, Y. Xu, S. Wu, S. Wen, H. Zhu, H. Zhou, M. Roberts, V. Kumar, J. Krause, C. Warinner, C. Jeong, Y. Cui.

The identity of the earliest inhabitants of Xinjiang, in the heart of Inner Asia, and the languages that they spoke have long been debated and remain contentious. Here we present genomic data from 5 individuals dating to around 3000–2800 BC from the Dzungarian Basin and 13 individuals dating to around 2100–1700 BC from the Tarim Basin, representing the earliest yet discovered human remains from North and South Xinjiang, respectively. We find that the Early Bronze Age Dzungarian individuals exhibit a predominantly Afanasievo ancestry with an additional local contribution, and the Early–Middle Bronze Age Tarim individuals contain only a local ancestry. The Tarim individuals from the site of Xiaohe further exhibit strong evidence of milk proteins in their dental calculus, indicating a reliance on dairy pastoralism at the site since its founding. Our results do not support previous hypotheses for the origin of the Tarim mummies, who were argued to be Proto-Tocharian-speaking pastoralists descended from the Afanasievo or to have originated among the Bactria–Margiana Archaeological Complex or Inner Asian Mountain Corridor cultures. Instead, although Tocharian may have been plausibly introduced to the Dzungarian Basin by Afanasievo migrants during the Early Bronze Age, we find that the earliest Tarim Basin cultures appear to have arisen from a genetically isolated local population that adopted neighbouring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert.

“Ethics of DNA research on human remains: five globally applicable guidelines.” Nature (2021).

S. Alpaslan-Roodenberg, D. Anthony, H. Babiker, E. Bánffy, T. Booth, P. Capone, A. Deshpande-Mukherjee, S. Eisenmann, L. Fehren-Schmitz, M. Frachetti, R. Fujita, C.J. Frieman, Q. Fu, V. Gibbon, W. Haak, M. Hajdinjak, K.P. Hofmann, B. Holguin, T. Inomata, H. Kanzawa-Kiriyama, W. Keegan, J. Kelso, J. Krause, G. Kumaresan, C. Kusimba, S. Kusimba, C. Lalueza-Fox, B. Llamas, S. MacEachern, S. Mallick, H. Matsumura, A.Y. Morales-Arce, G. Motuzaite Matuzeviciute, V. Mushrif-Tripathy, N. Nakatsuka, R. Nores, C. Ogola, M. Okumura, N. Patterson, R. Pinhasi, S.P.R. Prasad, M.E. Prendergast, J.L. Punzo, D. Reich, R. Sawafuji, E. Sawchuk, S. Schiffels, J. Sedig, S. Shnaider, K. Sirak, P. Skoglund, V. Slon, M. Snow, M. Soressi, M. Spriggs, P.W. Stockhammer, A. Szécsényi-Nagy, K. Thangaraj, V. Tiesler, R. Tobler, C.C. Wang, C. Warinner, S. Yasawardene, M. Zahir.

We are a group of archaeologists, anthropologists, curators and geneticists representing diverse global communities and 31 countries. All of us met in a virtual workshop dedicated to ethics in ancient DNA research held in November 2020. There was widespread agreement that globally applicable ethical guidelines are needed, but that recent recommendations grounded in discussion about research on human remains from North America are not always generalizable worldwide. Here we propose the following globally applicable guidelines, taking into consideration diverse contexts. These hold that: (1) researchers must ensure that all regulations were followed in the places where they work and from which the human remains derived; (2) researchers must prepare a detailed plan prior to beginning any study; (3) researchers must minimize damage to human remains; (4) researchers must ensure that data are made available following publication to allow critical re-examination of scientific findings; and (5) researchers must engage with other stakeholders from the beginning of a study and ensure respect and sensitivity to stakeholder perspectives. We commit to adhering to these guidelines and expect they will promote a high ethical standard in DNA research on human remains going forward.

“Doğu Marmara’nın İlk Çiftçi Köylerinde Neler Oldu: Şiddet, İnsan Yaşamının Bir Parçası mıydı?” (“What happened in the first farming villages of the eastern Marmara: was violence a part of human life?”) Arkeoloji ve Sanat 167, 21-36 (2021).

M.S. Alpaslan-Roodenberg, J. Roodenberg.

Violence and brute force inevitably occur in every period and environment in which people live together. Therefore, osteological studies show that prehistoric farmers not only lived their existence in tranquility and peace, but also experienced moments of physical threat that sometimes led to death. The lowlands east and southeast of the Sea of Marmara comprise a large number of prehistoric mound sites (hüyükler), many of which were occupied from the Early Bronze Age on. A lesser amount also included deposits from earlier occupation i.e. from the Neolithic. Since the late 80ties four of the latter period, namely Ilıpınar, Menteşe, Barcın and Aktopraklık, have been subjected to systematic and intensive archaeological investigations, much of which has already been published. Lesser known aspects of these early villages, namely general health of the inhabitants, burial customs and occurring traces of violence on their skeletons are brought together and re-examined from a bio-archaeological perspective. This study is based on data obtained by the standard methods of this discipline and the results are collected below under different headings. Besides these methods, research on ancient human genes has recently proven to contribute significantly to determining the relationships between past human populations. Analysis of human material from the villages has already yielded interesting issues.

“Where Asia meets Europe – recent insights from ancient human genomics.” Annals of Human Biology 48:3 (2021).

M. Feldman, G. A. Gnecchi-Ruscone, T. C. Lamnidis, C. Posth.

The peopling of Europe by modern humans is a widely debated topic in the field of modern and ancient genomics. While several recent syntheses have focussed on this topic, little has been discussed about the genetic history of populations in the continent’s surrounding regions. We explore genetic transformations in three key areas that played an essential role in the formation of the European genetic landscape through time, focussing on the periods spanning from the Epipalaeolithic/Mesolithic and up until the Iron Age. We review published ancient genomic studies and integrate the associated data to provide a quantification and visualisation of major trends in the population histories of the Near East, the western Eurasian Steppe and North East Europe. We describe cross-regional as well as localised prehistoric demographic shifts and discuss potential research directions while highlighting geo-temporal gaps in the data. In recent years, archaeogenetic studies have contributed to the understanding of human genetic diversity through time in regions located at the doorstep of Europe. Further studies focussing on these areas will allow for a better characterisation of genetic shifts and regionally-specific patterns of admixture across western Eurasia.

“Genomic transformation and social organization during the Copper Age–Bronze Age transition in southern Iberia.” Science Advances 7: 47 (2021).

V. Villalba-Mouco, C. Rihuete-Herrada, A. Childebayeva, A. B. Rohrlach, M. I. Fregeiro, E. Celdrán Beltrán, C. Velasco-Felipe, F. Aron, M. Himmel, C. Freund, K. W. Alt, D. C. Salazar-García, G. García Atiénzar, M. Paz de Miguel Ibáñez, M. S. Hernández Pérez, V. Barciela, A. Romero, J. Ponce, A. Martínez, J. Lomba, J. Soler, A. Pujante Martínez, A. Avilés Fernández, M. Haber-Uriarte, C. Roca de Togores Muñoz, I. Olalde, C. Lalueza-Fox, D. Reich, J. Krause, L. G. Sanjuán, V. Lull, R. Micó, R., W. Haak.

The emerging Bronze Age (BA) of southeastern Iberia saw marked social changes. Late Copper Age (CA) settlements were abandoned in favor of hilltop sites, and collective graves were largely replaced by single or double burials with often distinctive grave goods indirectly reflecting a hierarchical social organization, as exemplified by the BA El Argar group. We explored this transition from a genomic viewpoint by tripling the amount of data available for this period. Concomitant with the rise of El Argar starting ~2200 cal BCE, we observe a complete turnover of Y-chromosome lineages along with the arrival of steppe-related ancestry. This pattern is consistent with a founder effect in male lineages, supported by our finding that males shared more relatives at sites than females. However, simple two-source models do not find support in some El Argar groups, suggesting additional genetic contributions from the Mediterranean that could predate the BA.

“Reconstructing genetic histories and social organisation in Neolithic and Bronze Age Croatia.” Nature Scientific Reports 11: 16729 (2021).

S. Freilich, H. Ringbauer, D. Los, M. Novak, D. Tresić Pavičić, S. Schiffels, R. Pinhasi.

Ancient DNA studies have revealed how human migrations from the Neolithic to the Bronze Age transformed the social and genetic structure of European societies. Present-day Croatia lies at the heart of ancient migration routes through Europe, yet our knowledge about social and genetic processes here remains sparse. To shed light on these questions, we report new whole-genome data for 28 individuals dated to between ~ 4700 BCE–400 CE from two sites in present-day eastern Croatia. In the Middle Neolithic we evidence first cousin mating practices and strong genetic continuity from the Early Neolithic. In the Middle Bronze Age community that we studied, we find multiple closely related males suggesting a patrilocal social organisation. We also find in that community an unexpected genetic ancestry profile distinct from individuals found at contemporaneous sites in the region, due to the addition of hunter-gatherer-related ancestry. These findings support archaeological evidence for contacts with communities further north in the Carpathian Basin. Finally, an individual dated to Roman times exhibits an ancestry profile that is broadly present in the region today, adding an important data point to the substantial shift in ancestry that occurred in the region between the Bronze Age and today.

Hybris. Die Reise der Menschheit: Zwischen Aufbruch und Scheitern. (Hubris: Humanity’s Trajectory between Take-Off and Failure) Berlin: Propyläen Verlag (2021).

J. Krause, T. Trappe.

Humans have subjected the planet to their needs at a breathtaking pace. In the 21st century they are faced with the broken pieces of what they are doing: natural resources have been exhausted, global warming is a deadly threat, and global pandemics are an acute danger. Will we overcome this crisis too? The bestselling authors Johannes Krause and Thomas Trappe show what we can learn from the past for our survival - and what dangers lie in the unbridled strength of humans.

“Archaeometric evidence for the earliest exploitation of lignite from the bronze age Eastern Mediterranean.” Nature Scientific Reports 11: 24185 (2021).

S. Buckley, R.C. Power, M. Andreadaki‑Vlazaki, M. Akar, J. Becher, M. Belser, S. Cafsso, S. Eisenmann, J. Fletcher, M. Francken, B. Hallager, K. Harvati, T. Ingman, E. Kataki, J. Maran, M.A.S. Martin, P.J.P. McGeorge, I. Milevski, A. Papadimitriou, E. Protopapadaki, D.C. Salazar‑García, T. Schmidt‑Schultz, V.J. Schuenemann, R. Shafq, I. Stuijts, D. Yegorov, K. Aslιhan Yener, M. Schultz, C. Spiteri, P.W. Stockhammer.

This paper presents the earliest evidence for the exploitation of lignite (brown coal) in Europe and sheds new light on the use of combustion fuel sources in the 2nd millennium BCE Eastern Mediterranean. We applied Thermal Desorption/Pyrolysis–Gas Chromatography-Mass Spectrometry and Polarizing Microscopy to the dental calculus of 67 individuals and we identifed clear evidence for combustion markers embedded within this calculus. In contrast to the scant evidence for combustion markers within the calculus samples from Egypt, all other individuals show the inhalation of smoke from fires burning wood identifed as Pinaceae, in addition to hardwood, such as oak and olive, and/ or dung. Importantly, individuals from the Palatial Period at the Mycenaean citadel of Tiryns and the Cretan harbour site of Chania also show the inhalation of fire-smoke from lignite, consistent with the chemical signature of sources in the northwestern Peloponnese and Western Crete respectively. This frst evidence for lignite exploitation was likely connected to and at the same time enabled Late Bronze Age Aegean metal and pottery production, signifcantly by both male and female individuals.

“Enduring Cycles: Documenting dairying in Mongolia and the Alps.” Current Anthropology 62, supplement 24 (2021).

B. Reichhardt, Z. Enkh-Amgalan, C. Warinner, M. Rest.

In this photo essay we elaborate on artisanal dairying practices in the European Alps and Mongolia. By comparing these geographically distant dairying practices, we view milk fermentation as a multispecies, multidomain food ecology that links bacteria, fungi, plants, animals, and humans in unbroken cycles of production and reproduction that have endured for millennia. We focus on how peasant dairy producers actively engage with microbial communities in form of their starter cultures, which carry locally specific values with them and form biosocial assemblages of heritage. Finally, we introduce the Dairy Cultures Ethnographic Database as an open access resource that documents local and comparative analyses of dairy practices, techniques, and embedded cultural frameworks.

“Cultures of Fermentation: Living with Microbes.” Current Anthropology 62, supplement 24 (2021).

J. Hendy, M. Rest, B. Reichhardt, M. Aldenderfer, C. Warinner.

Recent discoveries on the importance of microbes for human biology, health, and culture, the rise of antimicrobial resistance, and developing technological advancements necessitate new dialogues about human relationships with microbes. Long perceptible only through their transformations—from epidemic disease to alcoholic beverages—it is now possible to more fully perceive the diversity of ways in which we influence and are influenced by microbes and to understand that human and microbial cultures are fundamentally intertwined. In the introduction to this supplement, we outline the current state of the art of an “anthropology of microbes” in three subfields of anthropology: biological anthropology, cultural anthropology, and archaeology. Moreover, as a result of dialogues borne out of the symposium associated with this issue, and now reflected in the articles themselves, we discuss the interactions between and within the subfields of anthropology. This supplement is committed to the development of a common language for an emerging anthropology of microbes, and in order to shape genuine transdisciplinarity we argue for the continued necessity of “trading zone” points of intersection—such as the Wenner-Gren Foundation’s symposium “Cultures of Fermentation.”

“Large-scale migration into Britain during the Middle to Late Bronze Age.” Nature (2021).

N. Patterson, M. Isakov, T. Booth, L. Büster, C.-E. Fischer, I. Olalde, H. Ringbauer, A. Akbari, O. Cheronet, M. Bleasdale, N. Adamski, E. Altena, R. Bernardos, S. Brace, N. Broomandkhoshbacht, K. Callan, F. Candilio, B. Culleton, E. Curtis, L. Demetz, K.S. Duffett Carlson, D.M. Fernandes, M.G.B. Foody, S. Freilich, H. Goodchild, A. Kearns, A.M. Lawson, I. Lazaridis, M. Mah, S. Mallick, K. Mandl, A. Micco, M. Michel, G. Bravo Morante, J. Oppenheimer, K. Toykan Özdoğan, L. Qiu, C. Schattke, K. Stewardson, J. N. Workman, F. Zalzala, Z. Zhang, B. Agustí, T. Allen, K. Almássy, L. Amkreutz, A. Ash, C. Baillif-Ducros, A. Barclay, L. Bartosiewicz, K. Baxter, Z. Bernert, J. Blažek, M. Bodružić, P. Boissinot, C. Bonsall, P. Bradley, M. Brittain, A. Brookes, F. Brown, L. Brown, R. Brunning, C. Budd, J. Burmaz, S. Canet, S. Carnicero-Cáceres, M. Čaušević-Bully, A. Chamberlain, S. Chauvin, S. Clough, N. Čondić, A. Coppa, O. Craig, M. Črešnar, V. Cummings, S. Czifra, A. Danielisová, R. Daniels, A. Davies, P. Jersey, J. Deacon, C. Deminger, P.W. Ditchfield, M. Dizdar, M. Dobeš, M. Dobisíková, L. Domboróczki, G. Drinkall, A. Đukić, C.J. Edwards, M. Ernée, C. Evans, J. Evans, M. Fernández-Götz, S. Filipović, A. Fitzpatrick, H. Fokkens, C. Fowler, A. Fox, Z. Gallina, M. Gamble, M.R.González Morales, B. González-Rabanal, A. Green, K. Gyenesei, D. Habermehl, T. Hajdu, D. Hamilton, J. Harris, C. Hayden, J. Hendriks, B. Hernu, G. Hey, M. Horňák, G. Ilon, E. Istvánovits, A.M. Jones, M. Blečić Kavur, K. Kazek, R.A. Kenyon, A. Khreisheh, V. Kiss, J. Kleijne, M. Knight, L.M. Kootker, P.F. Kovács, A. Kozubová, G. Kulcsár, V. Kulcsár, C. LePennec, M. Legge, M. Leivers, L. Loe, O. López-Costas, T. Lord, D. Los, J. Lyall, A.B. Marín-Arroyo, P. Mason, D. Matošević, A. Maxted, L. McIntyre, J. McKinley, K. McSweeney, B. Meijlink, B.G. Mende, M. Menđušić, M. Metlička, S. Meyer, K. Mihovilić, L. Milasinovic, S. Minnitt, J. Moore, G. Morley, G. Mullan, M. Musilová, B. Neil, R. Nicholls, M. Novak, M. Pala, M. Papworth, C. Paresys, R. Patten, D. Perkić, K. Pesti, A. Petit, K. Petriščáková, C. Pichon, C. Pickard, Z. Pilling, T.D. Price, S. Radović, R. Redfern, B. Resutík, D.T. Rhodes, M.B. Richards, A. Roberts, J. Roefstra, P. Sankot, A. Šefčáková, A. Sheridan, S. Skae, M. Šmolíková, K. Somogyi, Á. Somogyvári, M. Stephens, G. Szabó, A. Szécsényi-Nagy, T. Szeniczey, J. Tabor, K. Tankó, C. Tavarez Maria, R. Terry, B. Teržan, M. Teschler-Nicola, J.F. Torres-Martínez, J. Trapp, R. Turle, F. Ujvári, M. Heiden, P. Veleminsky, B. Veselka, Z. Vytlačil, C. Waddington, P. Ware, P. Wilkinson, L. Wilson, R. Wiseman, E. Young, J. Zaninović, A. Žitňan, C. Lalueza-Fox, P. Knijff, I. Barnes, P. Halkon, M.G. Thomas, D.J. Kennett, B. Cunliffe, M. Lillie, N. Rohland, R. Pinhasi, I. Armit, D. Reich.

Present-day people from England and Wales harbour more ancestry derived from Early European Farmers (EEF) than people of the Early Bronze Age. To understand this, we generated genome-wide data from 793 individuals, increasing data from the Middle to Late Bronze and Iron Age in Britain by 12-fold, and Western and Central Europe by 3.5-fold. Between 1000 and 875 bc, EEF ancestry increased in southern Britain (England and Wales) but not northern Britain (Scotland) due to incorporation of migrants who arrived at this time and over previous centuries, and who were genetically most similar to ancient individuals from France. These migrants contributed about half the ancestry of Iron Age people of England and Wales, thereby creating a plausible vector for the spread of early Celtic languages into Britain. These patterns are part of a broader trend of EEF ancestry becoming more similar across central and western Europe in the Middle to Late Bronze Age, coincident with archaeological evidence of intensifed cultural exchange. There was comparatively less gene flow from continental Europe during the Iron Age, and Britain’s independent genetic trajectory is also reflected in the rise of the allele conferring lactase persistence to ~50% by this time compared to ~7% in central Europe where it rose rapidly in frequency only a millennium later. This suggests that dairy products were used in qualitatively different ways in Britain and in central Europe over this period.

“A high-resolution picture of kinship practices in an Early Neolithic tomb.” Nature (2021).

C. Fowler, I. Olalde, V. Cummings, I. Armit, L. Büster, S. Cuthbert, N. Rohland, O. Cheronet, R. Pinhasi, D. Reich.

To explore kinship practices at chambered tombs in Early Neolithic Britain, here we combined archaeological and genetic analyses of 35 individuals who lived about 5,700 years ago and were entombed at Hazleton North long cairn. Twenty-seven individuals are part of the first extended pedigree reconstructed from ancient DNA, a five-generation family whose many interrelationships provide statistical power to document kinship practices that were invisible without direct genetic data. Patrilineal descent was key in determining who was buried in the tomb, as all 15 intergenerational transmissions were through men. The presence of women who had reproduced with lineage men and the absence of adult lineage daughters suggest virilocal burial and female exogamy. We demonstrate that one male progenitor reproduced with four women: the descendants of two of those women were buried in the same half of the tomb over all generations. This suggests that maternal sub-lineages were grouped into branches whose distinctiveness was recognized during the construction of the tomb. Four men descended from non-lineage fathers and mothers who also reproduced with lineage male individuals, suggesting that some men adopted the children of their reproductive partners by other men into their patriline. Eight individuals were not close biological relatives of the main lineage, raising the possibility that kinship also encompassed social bonds independent of biological relatedness.

“Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia.” Nature Communications 12: 7283 (2021).

K. Sirak, D.M. Fernandes, M. Lipson, S. Mallick, M. Mah, I. Olalde, H. Ringbauer, N. Rohland, C.S. Hadden, É. Harney, N. Adamski, R. Bernardos, N. Broomandkhoshbacht, K. Callan, M. Ferry, A.M. Lawson, M. Michel, J. Oppenheimer, K. Stewardson, F. Zalzala, N. Patterson, R. Pinhasi, J.C. Thompson, D. Van Gerven, D. Reich.

Relatively little is known about Nubia’s genetic landscape prior to the influence of the Islamic migrations that began in the late 1st millennium CE. Here, we increase the number of ancient individuals with genome-level data from the Nile Valley from three to 69, reporting data for 66 individuals from two cemeteries at the Christian Period (~650–1000 CE) site of Kulubnarti, where multiple lines of evidence suggest social stratification. The Kulubnarti Nubians had ~43% Nilotic-related ancestry (individual variation between ~36–54%) with the remaining ancestry consistent with being introduced through Egypt and ultimately deriving from an ancestry pool like that found in the Bronze and Iron Age Levant. The Kulubnarti gene pool – shaped over a millennium – harbors disproportionately female-associated West Eurasian-related ancestry. Genetic similarity among individuals from the two cemeteries supports a hypothesis of social division without genetic distinction. Seven pairs of inter-cemetery relatives suggest fluidity between cemetery groups. Present-day Nubians are not directly descended from the Kulubnarti Nubians, attesting to additional genetic input since the Christian Period.

2020

“Emergence of human-adapted Salmonella enterica is linked to the Neolithization process.” Nature Ecology & Evolution 4 (2020): 324–33.

F.M. Key, C. Posth , L.R. Esquivel-Gomez, R. Hübler, M.A. Spyrou , G.U. Neumann, A. Furtwängler, S. Sabin , M. Burri, A. Wissgott, A.K. Lankapalli, Å.J. Vågene , M. Meyer, S. Nagel, R. Tukhbatova, A. Khokhlov, A. Chizhevsky, S. Hansen, A.B. Belinsky, A. Kalmykov, A.R. Kantorovich, V.E. Maslov, P.W. Stockhammer , S. Vai , M. Zavattaro, A. Riga , D. Caramelli , R. Skeates, J. Beckett, M.G. Gradoli, N. Steuri, A. Hafner , M. Ramstein, I. Siebke, S. Lösch , Y.S. Erdal, N. Alikhan, Z. Zhou, M. Achtman, K. Bos, S. Reinhold, W. Haak, D. Kühnert , A. Herbig, J. Krause.

It has been hypothesized that the Neolithic transition towards an agricultural and pastoralist economy facilitated the emergence of human-adapted pathogens. Here, we recovered eight Salmonella enterica subsp. enterica genomes from human skeletons of transitional foragers, pastoralists and agropastoralists in western Eurasia that were up to 6,500 yr old. Despite the high genetic diversity of S. enterica, all ancient bacterial genomes clustered in a single previously uncharacterized branch that contains S. enterica adapted to multiple mammalian species. All ancient bacterial genomes from prehistoric (agro-)pastoralists fall within a part of this branch that also includes the human-specific S. enterica Paratyphi C, illustrating the evolution of a human pathogen over a period of 5,000 yr. Bacterial genomic comparisons suggest that the earlier ancient strains were not host specific, differed in pathogenic potential and experienced convergent pseudogenization that accompanied their downstream host adaptation. These observations support the concept that the emergence of human-adapted S. enterica is linked to human cultural transformations.

“Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia.” Nature Communications 11, 939 (2020).

J.H. Marcus, C. Posth, H. Ringbauer, L. Lai, R. Skeates, C. Sidore, J. Beckett, A. Furtwängler, A. Olivieri, C.W.K. Chiang, H. Al-Asadi, K. Dey, T.A. Joseph, C. Liu, C. Der Sarkissian, R. Radzevičiūtė, M. Michel, M.G. Gradoli, P. Marongiu, S. Rubino, V. Mazzarello, D. Rovina, A. La Fragola, R.M. Serra, P. Bandiera, R. Bianucci, E. Pompianu, C. Murgia, M. Guirguis, R. Pla Orquin, N. Tuross, P. van Dommelen, W. Haak, D. Reich, D. Schlessinger, F. Cucca, J. Krause, J. Novembre.

The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia’s genetic history describes the island as harboring a founder population that was established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time.

“The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean.” Nature Ecology & Evolution 4 (2020): 334-45.

D.M. Fernandes, A. Mittnik, I. Olalde, I. Lazaridis, O. Cheronet, N. Rohland, S. Mallick, R. Bernardos, N. Broomandkhoshbacht, J. Carlsson, B.J. Culleton, M. Ferry, B. Gamarra, M. Lari, M. Mah, M. Michel, A. Modi, M. Novak, J. Oppenheimer, K.A. Sirak, K. Stewardson, K. Mandl, C. Schattke, K.T. Özdoğan, M. Lucci, G. Gasperetti, F. Candilio, G. Salis, S. Vai, E. Camarós, C. Calò, G. Catalano, M. Cueto, V. Forgia, M. Lozano, E. Marini, M. Micheletti, R.M. Miccichè, M.R. Palombo, D. Rams, V. Schimmenti, P. Sureda, L. Teira, M.Teschler-Nicola, D.J. Kennett, C. Lalueza-Fox, N. Patterson, L. Sineo, A. Coppa, D. Caramelli, R. Pinhasi, D. Reich.

Steppe-pastoralist-related ancestry reached Central Europe by at least 2500 BC, whereas Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BC. However, the spread of these ancestries into the western Mediterranean, where they have contributed to many populations that live today, remains poorly understood. Here, we generated genome-wide ancient-DNA data from the Balearic Islands, Sicily and Sardinia, increasing the number of individuals with reported data from 5 to 66. The oldest individual from the Balearic Islands (~2400 BC) carried ancestry from steppe pastoralists that probably derived from west-to-east migration from Iberia, although two later Balearic individuals had less ancestry from steppe pastoralists. In Sicily, steppe pastoralist ancestry arrived by ~2200 BC, in part from Iberia; Iranian-related ancestry arrived by the mid-second millennium BC, contemporary to its previously documented spread to the Aegean; and there was large-scale population replacement after the Bronze Age. In Sardinia, nearly all ancestry derived from the island’s early farmers until the first millennium BC, with the exception of an outlier from the third millennium BC, who had primarily North African ancestry and who—along with an approximately contemporary Iberian—documents widespread Africa-to-Europe gene flow in the Chalcolithic. Major immigration into Sardinia began in the first millennium BC and, at present, no more than 56–62% of Sardinian ancestry is from its first farmers. This value is lower than previous estimates, highlighting that Sardinia, similar to every other region in Europe, has been a stage for major movement and mixtures of people.

“Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus.” Cell 181, 5 (2020): 1158-75.

E. Skourtanioti, Y.S. Erdal, M. Frangipane, F.B. Restelli, K.A. Yener, F. Pinnock, P. Matthiae, R. Özbal, U. Schoop, F. Guliyev, T. Akhundov, B. Lyonnet, E.L. Hammer, S.E. Nugent, M. Burri, G.U. Neumann, S. Penske, T. Ingman, M. Akar, R. Shafiq, G. Palumbi, S. Eisenmann, M. D’Andrea, A.B. Rohrlach, C. Warinner, C. Jeong, P.W. Stockhammer, W. Haak, J. Krause.

Here, we report genome-wide data analyses from 110 ancient Near Eastern individuals spanning the Late Neolithic to Late Bronze Age, a period characterized by intense interregional interactions for the Near East. We find that 6^th millennium BCE populations of North/Central Anatolia and the Southern Caucasus shared mixed ancestry on a genetic cline that formed during the Neolithic between Western Anatolia and regions in today’s Southern Caucasus/Zagros. During the Late Chalcolithic and/or the Early Bronze Age, more than half of the Northern Levantine gene pool was replaced, while in the rest of Anatolia and the Southern Caucasus, we document genetic continuity with only transient gene flow. Additionally, we reveal a genetically distinct individual within the Late Bronze Age Northern Levant. Overall, our study uncovers multiple scales of population dynamics through time, from extensive admixture during the Neolithic period to long-distance mobility within the globalized societies of the Late Bronze Age.

“The Genomic History of the Bronze Age Southern Levant.” Cell 181, 5 (2020): 1146-57.

L. Agranat-Tamir, S. Waldman, M.A.S. Martin, D. Gokhman, N. Mishol, T. Eshel, O. Cheronet, N. Rohland, S. Mallick, N. Adamski, A.M. Lawson, M. Mah, M. Michel, J. Oppenheimer, K. Stewardson, F. Candilio, D. Keating, B. Gamarra, S. Tzur, M. Novak, R. Kalisher, S. Bechar, V. Eshed, D.J. Kennett, M. Faerman, N. Yahalom-Mack, J.M. Monge, Y. Govrin, Y. Erel, B. Yakir, R. Pinhasi, S. Carmi, I. Finkelstein, L. Carmel, D. Reich.

We report genome-wide DNA data for 73 individuals from five archaeological sites across the Bronze and Iron Ages Southern Levant. These individuals, who share the “Canaanite” material culture, can be modeled as descending from two sources: (1) earlier local Neolithic populations and (2) populations related to the Chalcolithic Zagros or the Bronze Age Caucasus. The non-local contribution increased over time, as evinced by three outliers who can be modeled as descendants of recent migrants. We show evidence that different “Canaanite” groups genetically resemble each other more than other populations. We find that Levant-related modern populations typically have substantial ancestry coming from populations related to the Chalcolithic Zagros and the Bronze Age Southern Levant. These groups also harbor ancestry from sources we cannot fully model with the available data, highlighting the critical role of post-Bronze-Age migrations into the region over the past 3,000 years.

“Growing up in Ancient Sardinia: Infant-toddler dietary changes revealed by the novel use of hydrogen isotopes (δ2H).” PLoS ONE 15, 7 (2020).

S.E. Ryan, L.M. Reynard, E. Pompianu, P. van Dommelen, C. Murgia, M.E. Subirà, N. Tuross.

Detailed information about the lives and deaths of children in antiquity is often in short supply. Childhood dietary histories are, however, recorded and maintained in the teeth of both juveniles and adults. Primary tooth dentinal collagen does not turn over, preserving a sequential record of dietary changes. The use of nitrogen (δ¹⁵N) and carbon (δ¹³C) isotope values of incrementally sampled dentin are used in the study of breastfeeding practices but evidence for the addition of weaning foods, both in terms of mode and, particularly, duration, has remained analytically inaccessible to date. Here, we demonstrate how the novel use hydrogen isotope (δ²H) values of sequentially micro-sampled dentin collagen, measured from individuals excavated from a Punic cemetery, in Sardinia, Italy, can serve as a proxy for weaning food type and duration in ancient childhood diet. The weaning rate and age, based on the decline in δ¹⁵N and δ¹³C values of permanent first molars and the concomitant increase in δ²H, appears to be broadly similar among six individuals. Hydrogen isotopes vary systematically from a low value soon after birth, rising through early childhood. The early post-birth values can be explained by the influence of ²H-depleted lipids from mother’s breastmilk and the later δ²H rise is consistent with, among other things, a substantial portion of boiled foodstuffs, such as the higher δ²H values observed in porridge. Overall δ²H in dentin shows great promise to elucidate infant and childhood feeding practices, and especially the introduction of supplementary foods during the weaning process.

“Mediterranean precipitation isoscape preserved in bone collagen δ²H.” Nature Scientific Reports 10, 8579 (2020).

L.M. Reynard, S.E. Ryan, M. Guirguis, M. Contreras-Martínez, E. Pompianu, D. Ramis, P. van Dommelen, N. Tuross.

The prehistory of the Mediterranean region has long been a subject of considerable interest, particularly the links between human groups and regions of origin. We utilize the spatial variation in the δ²H and δ¹⁸O values of precipitation (isoscapes) to develop proxies for geographic locations of fauna and humans. Bone collagen hydrogen isotope ratios (δ²H) in cattle (and to a lesser extent, ovicaprids) across the Mediterranean reflect the isotopic differences observed in rainfall (but δ¹⁸O values do not). We conclude that δ²H in herbivore bone collagen can be used as a geolocation tracer and for palaeoenvironmental studies such as tracing past isotopic variations in the global hydrological cycle. In contrast, human bone δ²H values are relatively tightly grouped and highly distinct from precipitation δ²H values, likely due to human-specific food practices and environmental modifications. Given the inter-species variability in δ²H, care should be taken in the species selected for study.

“Comparison of extraction methods for recovering ancient microbial DNA from paleofeces.” American Journal of Physical Anthropology 171, 2 (2020).

R.W. Hagan, C.A. Hofman, A. Hübner, K. Reinhard, S. Schnorr, C.M. Lewis, K. Sankaranarayanan, C. Warinner.

Paleofeces are valuable to archeologists and evolutionary biologists for their potential to yield health, dietary, and host information. As a rich source of preserved biomolecules from host‐associated microorganisms, they can also provide insights into the recent evolution and changing ecology of the gut microbiome. However, there is currently no standard method for DNA extraction from paleofeces, which combine the dual challenges of complex biological composition and degraded DNA. Due to the scarcity and relatively poor preservation of paleofeces when compared with other archeological remains, it is important to use efficient methods that maximize ancient DNA (aDNA) recovery while also minimizing downstream taxonomic biases. In this study, we use shotgun metagenomics to systematically compare the performance of five DNA extraction methods on a set of well‐preserved human and dog paleofeces from Mexico (~1,300 BP). Our results show that all tested DNA extraction methods yield a consistent microbial taxonomic profile, but that methods optimized for ancient samples recover significantly more DNA. These results show promise for future studies that seek to explore the evolution of the human gut microbiome by comparing aDNA data with those generated in modern studies.

“Biogeographic study of human gut associated crAssphage suggests impacts from industrialization and recent expansion.” PLoS ONE 15,1 (2020).

T. Honap, K. Sankaranarayananm, S.L. Schnorr, A.T. Ozga, C. Warinner, C. Lewis.

CrAssphage (cross-assembly phage) is a bacteriophage that was first discovered in human gut metagenomic data. CrAssphage belongs to a diverse family of crAss-like bacteriophages thought to infect gut commensal bacteria belonging to Bacteroides species. However, not much is known about the biogeography of crAssphage and whether certain strains are associated with specific human populations. In this study, we screened publicly available human gut metagenomic data from 3,341 samples for the presence of crAssphage sensu stricto (NC_024711.1). We found that crAssphage prevalence is low in traditional, hunter-gatherer populations, such as the Hadza from Tanzania and Matses from Peru, as compared to industrialized, urban populations. Statistical comparisons showed no association of crAssphage prevalence with variables such as age, sex, body mass index, and health status of individuals. Phylogenetic analyses show that crAssphage strains reconstructed from the same individual over multiple time-points, cluster together. CrAssphage strains from individuals from the same study population do not always cluster together. Some evidence of clustering is seen at the level of broadly defined geographic regions, however, the relative positions of these clusters within the crAssphage phylogeny are not well-supported. We hypothesize that this lack of strong biogeographic structuring is suggestive of an expansion event within crAssphage. Using a Bayesian dating approach, we estimate that this expansion has occurred fairly recently. Overall, we determine that crAssphage presence is associated with an industrialized lifestyle and the absence of strong biogeographic structuring within global crAssphage strains is likely due to a recent population expansion within this bacteriophage.

“Dairy pastoralism sustained Eastern Eurasian steppe populations for 5000 years.” Nature Ecology and Evolution 4 (2020): 346-55.

S. Wilkin, A. Ventresca Miller, W.T.T. Taylor, B.K. Miller, R.W. Hagan, M. Bleasdale, A. Scott, S. Gankhuyg, A. Ramsøe, C. Trachsel, P. Nanni, J. Grossmann, L. Orlando, M. Horton, P. Stockhammer, E. Myagmar, N. Boivin, C. Warinner, J. Hendy.

Dairy pastoralism is integral to contemporary and past lifeways on the eastern Eurasian steppe, facilitating survival in agriculturally challenging environments. While previous research has indicated that ruminant dairy pastoralism was practiced in the region by circa 1300 BC, the origin, extent and diversity of this custom remain poorly understood. Here, we analyse ancient proteins from human dental calculus recovered from geographically diverse locations across Mongolia and spanning 5,000 years. We present the earliest evidence for dairy consumption on the eastern Eurasian steppe by circa 3000 BC and the later emergence of horse milking at circa 1200 BC, concurrent with the first evidence for horse riding. We argue that ruminant dairying contributed to the demographic success of Bronze Age Mongolian populations and that the origins of traditional horse dairy products in eastern Eurasia are closely tied to the regional emergence of mounted herding societies during the late second millennium BC.

“A dynamic 6,000-year genetic history of Eurasia’s Eastern Steppe.” Cell 183, 1-15 (2020).

C. Jeong C, K. Wang, S. Wilkin, W.T.T. Taylor, B.K. Miller, J.H. Bemmann, R. Stahl, C. Chiovelli, F. Knolle, S. Ulziibayar, D. Khatanbaatar, D. Erdenebaatar, U. Erdenebat, A. Ochir, G. Ankhsanaa, C. Vanchigdash, B. Ochir, C. Munkhbayar, D. Tumen, A. Kovalev, N. Kradin, B.A. Bazarov, D.A. Miyagashev, P.B. Konovalov, E. Zhambaltarova, A. Ventresca Miller, W. Haak, S. Schiffels, J. Krause, N. Boivin, E. Myagmar, J. Hendy, C. Warinner.

The Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the region’s population history. Here, we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe.

“A unified protocol for simultaneous extraction of DNA and proteins from archaeological dental calculus.” Journal of Archaeological Science 118:105135 (2020).

Z. Fagernäs, M.I. Garcia Collado, J. Hendy, C. Hofman, C. Speller, I. Velsko, C. Warinner.

Archaeological materials are a finite resource, and efforts should be made to minimize destructive analyses. This can be achieved by using protocols combining extraction of several types of biomolecules or microparticles, which decreases the material needed for analyses while maximizing the information yield. Archaeological dental calculus is a source of several different types of biomolecules, as well as microfossils, and can tell us about the human host, microbiome, diet, and even occupational activities. Here, we present a unified protocol allowing for simultaneous extraction of DNA and proteins from a single sample of archaeological dental calculus. We evaluate the protocol on dental calculus from six individuals from a range of time periods and estimated preservation states, and compare it against previously published DNA-only and protein-only protocols. We find that most aspects of downstream analyses are unaltered by the unified protocol, although minor shifts in the recovered proteome can be detected, such as a slight loss of hydrophilic proteins. Total protein recovery depends on both the amount of starting material and choice of extraction protocol, whereas total DNA recovery is significantly reduced using the unified protocol (mean 43%). Nevertheless, total DNA recovery from dental calculus is generally very high, and we found no differences in DNA fragment characteristics or taxonomic profile between the protocols. In conclusion, the unified protocol allows for simultaneous extraction of two complementary lines of biomolecular evidence from archaeological dental calculus without compromising downstream results, thereby minimizing the need for destructive analysis of this finite resource.

“CoproID predicts the source of coprolites and paleofeces using microbiome composition and endogenous DNA content.” PeerJ 8:e9001 (2020).

M. Borry, B. Cordova, A. Perri, M.C. Wibowo, W.T.J. Ko, J. Yu, T.S. Kagone, N. Meda, H. Carabin, D. Jacobson, T. Honap, K. Reinhard, C.M. Lewis, A. Kostic, C. Jeong, A. Herbig, A. Hübner, C. Warinner.

Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts.

“Evidence for long-distance trade in exotic foods and spices from South Asia to the Near East in the 2^ndmillennium BCE.” Proceedings of the National Academy of Sciences 118:2 (2020).

A.S. Scott, R.C. Power, V. Altmann-Wendling, M. Artzy, M.A.S. Martin, S. Eisenmann, R. Hagan, D.C. Salazar-Garcia, Y. Salmon, D. Yegorov, I. Milevski, I. Finkelstein, P.W. Stockhammer, C. Warinner.

Here we report the identification of staple and exotic food remains in Bronze and Early Iron Age dental calculus from the Southern Levant. The analysis of dietary plant microremains and proteins sheds new light on consumed exotic foods from South and East Asia during the second millennium BCE. We provide the earliest direct evidence in the Mediterranean to date for the consumption of sesame, soybean, probable banana, and turmeric. The recovery and identification of diverse foodstuffs using molecular and microscopic techniques enables a new understanding of the complexity of early trade routes and nascent globalization in the ancient Near East and raises questions about the long-term maintenance and continuity of this trade system into later periods.

2019

“Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia.” Nature Communications 10 (2019): 1218. doi: 10.1038/s41467-019-09209-7.

M. Feldman, E. Fernández-Domínguez, L. Reynolds, D. Baird, J. Pearson, I. Hershkovitz, H. May, N. Goring-Morris, M. Benz, J. Gresky, R. A. Bianco, A. Fairbairn, G. Mustafaoğlu, P.W. Stockhammer, C. Posth, W. Haak, C. Jeong, J. Krause.

Anatolia was home to some of the earliest farming communities. It has been long debated whether a migration of farming groups introduced agriculture to central Anatolia. In this study, we report the first genome-wide data from a 15,000-year-old Anatolian hunter-gatherer and from seven Anatolian and Levantine early farmers. We find high genetic continuity (~80–90%) between the hunter-gatherers and early farmers of Anatolia and detect two distinct incoming ancestries: an early Iranian/Caucasus-related one and a later one linked to the ancient Levant. Finally, we observe a genetic link between southern Europe and the Near East predating 15,000 years ago. Our results suggest a limited role of human migration in the emergence of agriculture in central Anatolia.

“Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750).” Proceedings of the National Academy of Sciences 116 (25) (2019): 12363-72. doi: 10.1073/pnas.1820447116.

M. Keller, M.A. Spyrou, C.L. Scheib, G.U. Neumann, A. Kröpelin, B. Haas-Gebhard, B. Päffgen, J. Haberstroh, A. Ribera i Lacomba, C. Raynaud, C. Cessford, R. Durand, P. Stadler, K. Nägele, J.S. Bates, B. Trautmann, S.A. Inskip, J. Peters, J.E. Robb, T. Kivisild, D. Castex, M. McCormick, K.I. Bos, M. Harbeck, A. Herbig, J. Krause.

We identify bubonic plague (Yersinia pestis) in eight new sites from Britain, France, Germany, and Spain, demonstrating the geographic range of plague during the Justinianic Pandemic (541-750 CE), its microdiversity in the late Roman and early medieval period, and documenting the first Mediterranean victims in Spain and southern France. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. To elucidate the microevolution of the bacterium during this time period, we reconstructed eight genomes. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics; we also identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.

“Ancient DNA sheds light on the genetic origins of early Iron Age Philistines.” Science Advances Vol. 5, no. 7, eaax0061 (2019). doi: 10.1126/sciadv.aax0061.

M. Feldman, D.M. Master, R.A. Bianco, M. Burri, P.W. Stockhammer, A. Mittnik, A.J. Aja, C. Jeong, J. Krause.

The ancient Mediterranean port city of Ashkelon, identified as “Philistine” during the Iron Age, underwent a dramatic cultural change between the Late Bronze- and the early Iron- Age. It has long been debated whether this change was driven by a substantial movement of people, possibly linked to a larger migration of the so-called “Sea Peoples.” In this study, we report genome-wide data of Bronze- and Iron- Age individuals from Ashkelon. We find that the early Iron Age population was genetically distinct due to a European-related admixture. Interestingly, this genetic signal is no longer detectible in the later Iron Age population. Our results support that a migration event occurred during the Bronze- to Iron- Age transition in Ashkelon but did not leave a long-lasting genetic signature.

“The genomic history of the Iberian Peninsula over the past 8000 years.” Science 363 (2019): 1230-4.

I. Olalde, S. Mallick, N. Patterson, N. Rohland, V. Villalba-Mouco, M. Silva, K. Dulias, C. Edwards, F. Gandini, M. Pala, P. Soares, M. Ferrando-Bernal, N. Adamski, N. Broomandkhoshbacht, O. Cheronet, B. Culleton, D. Fernandes, A.M. Lawson, M. Mah, J. Oppenheimer, K. Stewardson, Z. Zhang, J.M.J. Arenas, I.J.T. Moyano, D.C. Salazar-García, P. Castanyer, M. Santos, J. Tremoleda, M. Lozano, P.G. Borja, J. Fernández-Eraso, J.A. Mujika-Alustiza, C. Barroso, F.J. Bermúdez, E.V. Mínguez, J. Burch, N. Coromina, D. Vivó, A. Cebrià, J.M. Fullola, O. García-Puchol, J.I. Morales, F.X. Oms, T. Majó, J.M. Vergès, A. Díaz-Carvajal, I. Ollich-Castanyer, F.J. López-Cachero, A.M. Silva, C. Alonso-Fernández, G.D. de Castro, J.J. Echevarría, A. Moreno-Márquez, G.P. Berlanga, P. Ramos-García, J.R. Muñoz, E.V. Vila, G.A. Arzo, Á.E. Arroyo, K.T. Lillios, J. Mack, J. Velasco-Vázquez, A. Waterman, L.B. de Lugo Enrich, M.B. Sánchez, B. Agustí, F. Codina, G. de Prado, A. Estalrrich, Á.F. Flores, C. Finlayson, G. Finlayson, S. Finlayson, F. Giles-Guzmán, A. Rosas, V.B. González, G.G. Atiénzar, M.S.H. Pérez, A. Llanos, Y.C. Marco, I.C. Beneyto, D. López-Serrano, S.B. McClure, M.M. Pérez, A.O. Foix, M.S. Borràs, A.C. Sousa, J.M.V. Encinas, D.J. Kennett, M. Richards, K.W. Alt, W. Haak, R. Pinhasi, C. Lalueza-Fox, D. Reich.

In this article we assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia’s ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European–speaking regions but also into non-Indo-European–speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean.

“The formation of human populations in South and Central Asia.” Science 365 (2019): 7487.

V. Narasimhan, N. Patterson, P. Moorjani, N. Rohland, R. Bernardos, S. Mallick, I. Lazaridis, N. Nakatsuka, I. Olalde, M. Lipson, A.M. Kim, L.M. Olivieri, A. Coppa, M. Vidale, J. Mallory, V. Moiseyev, E. Kitov, J. Monge, N. Adamski, N. Alex, N. Broomandkhoshbacht, F. Candilio, K. Callan, O. Cheronet, B.J. Culleton, M. Ferry, D. Fernandes, S. Freilich, B. Gamarra, D. Gaudio, M. Hajdinjak, E. Harney, T.K. Harper, D. Keating, A.M. Lawson, M. Mah, K. Mandl, M. Michel, M. Novak, J. Oppenheimer, N. Rai, K. Sirak, V. Slon, K. Stewardson, F. Zalzala, Z. Zhang, G. Akhatov, A.N. Bagashev, A. Bagnera, B. Baitanayev, J. Bendezu-Sarmiento, A.A. Bissembaev, G.L. Bonara, T.T. Chargynov, T. Chikisheva, P.K. Dashkovskiy, A. Derevianko, M. Dobes, K. Douka, N. Dubova, M.N. Duisengali, D. Enshin, A. Epimakhov, A.V. Fribus, D. Fuller, A. Goryachev, A. Gromov, S.P. Grushin, B. Hanks, M. Judd, E. Kazizov, A. Khokhlov, A.P. Krygin, E. Kupriyanova, P. Kuznetsov, D. Luiselli, F. Maksudov, A.M. Mamedov, T.B. Mamirov, C. Meiklejohn, D.C. Merrett, R. Micheli, O. Mochalov, S. Mustafokulov, A. Nayak, D. Pettener, R. Potts, D. Razhev, M. Rykun, S. Sarno, T.M. Savenkova, K. Sikhymbaeva, S.M. Slepchenko, O.A. Soltobaev, N. Stepanova, S. Svyatko, K. Tabaldiev, M. Teschler-Nicola, A.A. Tishkin, V.V. Tkachev, S. Vasilyev, P. Veleminsky, D. Voyakin, A. Yermolayeva, M. Zahir, V.S. Zubkov, A. Zubova, V.S. Shinde, C. Lalueza-Fox, M. Meyer, D. Anthony, N. Boivin, K. Thangaraj, D.J. Kennett, M. Frachetti, R. Pinhasi, D. Reich.

By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization’s decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.

“Kinship-based social inequality in Bronze Age Europe.” Science, 10 (2019).

A. Mittnik, K. Massy, C. Knipper, F. Wittenborn, S. Pfrengle, N. Carlichi-Witjes, H. Deeg, A. Furtwängler, M. Harbeck, K. von Heyking, C. Kociumaka, I. Kucukkalipci, S. Lindauer, S. Metz, A. Staskiewicz, A. Thiel, J. Wahl, W. Haak, E. Pernicka, S. Schiffels, P.W. Stockhammer, J. Krause.

Archaeology has used analysis of the artifacts and remains of people to uncover their past behaviors and to infer their cultural practices. However, establishing genetic relationships has only recently become possible. Mittnik et al. examined the kinship and inheritance of the remains of people from the German Lech River Valley over a time period spanning the Late Neolithic Corded Ware Culture, the Bell Beaker Complex, the Early Bronze Age, and the Middle Bronze Age (see the “Perspective” in the same issue by Feinman and Neitzel). From genetic and archaeological analyses, it was revealed that the Early Bronze Age household's burials over multiple generations consisted of a high-status core family and unrelated low-status individuals. Furthermore, women were not related to the men within the household, suggesting that men stayed within their birth communities in this society, but women did not, and potentially served as cultural transmitters between different regions.

“Ancient DNA’s impact on archaeology: what has been learned and how to build strong relationships.” The SAA Archaeological Record 19 (2019): 26-32.

J.W. Sedig.

This article discusses how ancient DNA (aDNA) has the potential to provide powerful new insights into humanity’s past. It may seem odd for such comments to come from someone who considers himself an American Southwest archaeologist; however, the author's role in the Reich Laboratory of Medical and Population Genetics as a liaison between geneticists and archaeologists has allowed him to critically examine the relationship between these two fields and to explore how they work together.

“An ancient Harappan genome lacks ancestry from Steppe Pastoralists or Iranian Farmers.” Cell 179 (2019): 729-35.

V. Shinde, V. Narasimhan, N. Rohland, S. Mallick, M. Mah, M. Lipson, N. Nakatsuka, N. Adamski, N. Broomandkhoshbacht, M. Ferry, A.M. Lawson, M. Michel, J. Oppenheimer, K. Stewardson, N. Jadhav, Y.J. Kim, M. Chatterjee, A. Munshi, A. Panyam, P. Waghmare, Y. Yadav, H. Patel, A. Kaushik, K. Thangaraj, M. Meyer, N. Patterson, N. Rai, D. Reich.

We report an ancient genome from the Indus Valley Civilization (IVC). The individual we sequenced fits as a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers, a unique profile that matches ancient DNA from 11 genetic outliers from sites in Iran and Turkmenistan in cultural communication with the IVC. These individuals had little if any Steppe pastoralist-derived ancestry, showing that it was not ubiquitous in northwest South Asia during the IVC as it is today. The Iranian-related ancestry in the IVC derives from a lineage leading to early Iranian farmers, herders, and hunter-gatherers before their ancestors separated, contradicting the hypothesis that the shared ancestry between early Iranians and South Asians reflects a large-scale spread of western Iranian farmers east. Instead, sampled ancient genomes from the Iranian plateau and IVC descend from different groups of hunter-gatherers who began farming without being connected by substantial movement of people.

“Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India.” Nature Communications, Advance online publication (2019).

E. Harney, A. Nayak, N. Patterson, P. Joglekar, V. Mushrif-Tripathy, S. Mallick, N. Rohland, J. Sedig, N. Adamski, R. Bernardos, N. Broomandkhoshbacht, B.J. Culleton, M. Ferry, T.K. Harper, M. Michel, J. Oppenheimer, K. Stewardson, Z. Zhang, Harashawaradhana, M.S. Bartwal, S. Kumar, S.C. Diyundi, P. Roberts, N. Boivin, D.J. Kennett, K. Thangaraj, D. Reich, N. Rai.

Situated at over 5,000 meters above sea level in the Himalayan Mountains, Roopkund Lake is home to the scattered skeletal remains of several hundred individuals of unknown origin. We report genome-wide ancient DNA for 38 skeletons from Roopkund Lake, and find that they cluster into three distinct groups. A group of 23 individuals have ancestry that falls within the range of variation of present-day South Asians. A further 14 have ancestry typical of the eastern Mediterranean. We also identify one individual with Southeast Asian-related ancestry. Radiocarbon dating indicates that these remains were not deposited simultaneously. Instead, all of the individuals with South Asian-related ancestry date to ~800 CE (but with evidence of being deposited in more than one event), while all other individuals date to ~1800 CE. These differences are also reflected in stable isotope measurements, which reveal a distinct dietary profile for the two main groups.

“Plague before the pandemics: the Greek medical evidence for bubonic plague before the sixth century.” Bulletin of the History of Medicine 93.2 (2019): 151-79.

J. Mulhall.

Recent biomolecular evidence has proven that Yersinia pestis, the pathogen that causes bubonic plague, was infecting human hosts in Eurasia as early as the Bronze Age, far earlier than previously believed. It remains an open question, however, whether bubonic plague was affecting Mediterranean populations of classical antiquity. This article evaluates the textual evidence for bubonic plague in classical antiquity from medical sources and discusses methodologies for “retrospective diagnosis” in light of new developments in microbiology. A close study of Greek medical texts using digital and traditional approaches suggests that bubonic plague was unfamiliar to medical writers until sometime before the second century CE, when sources cited by Rufus of Ephesus report a disease that resembles bubonic plague. Rufus of Ephesus describes this disease around CE 100, and Aretaeus (fl. ca. CE 50 or 150) appears to describe the same disease as well.

“Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa.” Science 365, 6448 (2019).

M.E. Prendergast, M. Lipson, E.A. Sawchuk, I. Olalde, C.A. Ogola, N. Rohland, K.A. Sirak, N. Adamski, R. Bernardos, N. Broomandkhoshbacht, K. Callan, B.J. Culleton, L. Eccles, T.K. Harper, A.M. Lawson, M. Mah, J. Oppenheimer, K. Stewardson, F. Zalzala, S.H. Ambrose, G. Ayodo, H.L. Gates Jr., A.O. Gidna, M. Katongo, A. Kwekason, A.Z.P. Mabulla, G.S. Mudenda, E.K. Ndiema, C. Nelson, P. Robertshaw, D.J. Kennett, F.K. Manthi, D. Reich.

Cattle, sheep, and goats appeared in eastern Africa 5000 years ago, catalyzing the spread of herding throughout sub-Saharan Africa. Archaeologists have long debated the geographic origins of eastern Africa’s first herders, the extent to which people moved with livestock, and relationships among food-producing and foraging communities. In this work, we integrate ancient DNA with archaeological, linguistic, and genetic evidence to explore how pastoralism developed within this region, establishing the roots of one of Africa’s dominant economic strategies.

“Medieval women's early involvement in manuscript production suggested by lapis lazuli identification in dental calculus.” Science Advances 5 eaau7126 (2019). DOI: 10.1126/sciadv.aau7126.

A. Radini, M. Tromp, A. Beach, E. Tong, C. Speller, M. McCormick, J.V. Dudgeon, M.J. Collins, F. Rühli, R. Kröger, C. Warinner.

During the European Middle Ages, the opening of long-distance Asian trade routes introduced exotic goods, including ultramarine, a brilliant blue pigment produced from lapis lazuli stone mined only in Afghanistan. Rare and as expensive as gold, this pigment transformed the European color palette, but little is known about its early trade or use. Here, we report the discovery of lapis lazuli pigment preserved in the dental calculus of a religious woman in Germany radiocarbon-dated to the 11th or early 12th century. The early use of this pigment by a religious woman challenges widespread assumptions about its limited availability in medieval Europe and the gendered production of illuminated texts.

Travels of Our Genes: A Story about Us and Our Ancestors. (Die Reise unserer Gene. Eine Geschichte über uns und unsere Vorfahren). Berlin, Propyläen (2019).

J. Krause with T. Trappe.

Where do we come from? Who are we? How do we differ from others? These questions are more urgent than ever. Krause and Trappe reach back into Prehistory and use ancient DNA to explain how we became the Europeans that we are today.

2018

“Reconciling material cultures in archaeology with genetic data: The nomenclature of clusters emerging from archaeogenomic analysis.” Scientific Reports 8:13003 (2018). doi:10.1038/s41598-018-31123-z

S. Eisenmann, E. Banffy, P. van Dommelen, K.P. Hofmann, J. Maran, I. Lazaridis, A. Mittnik, M. McCormick, J. Krause, D. Reich, P.W. Stockhammer.

Genome-wide ancient DNA analysis of skeletons retrieved from archaeological excavations has provided a powerful new tool for investigating past populations and migrations. An important objective for the coming years is properly to integrate ancient genomics into archaeological research. Our article aims to contribute to developing a better understanding and cooperation between the two disciplines and beyond. It focuses on the question of how best to name clusters encountered when analyzing the genetic makeup of past human populations. Recent studies have frequently borrowed archaeological cultural designations to name these genetic groups, while neglecting the historically problematic nature of the concept of “cultures” in archaeology. After reviewing current practices in naming genetic clusters, we introduce three possible nomenclature systems along with their advantages and challenges.

“The genomic history of southeastern Europe.” Nature 555 (2018): 197-203.

I. Mathieson, S. Alpaslan-Roodenberg, C. Posth, A. Szécsényi-Nagy, N. Rohland, S. Mallick, I. Olalde, N. Broomandkhoshbacht, F. Candilio, O. Cheronet, D. Fernandes, M. Ferry, B. Gamarra, G.G. Fortes, W. Haak, E. Harney, E. Jones, D. Keating, B. Krause-Kyora, I. Kucukkalipci, M. Michel, A. Mittnik, K. Nägele, M. Novak, J. Oppenheimer, N. Patterson, S. Pfrengle, K. Sirak, K. Stewardson, S. Vai, S. Alexandrov, K.W. Alt, R. Andreescu, D. Antonovic, A. Ash, N. Atanassova, K. Bacvarov, M.B. Gusztáv, H. Bocherens, M. Bolus, A. Boroneant, Y. Boyadzhiev, A. Budnik, J. Burmaz, S. Chohadzhiev, N.J. Conard, R. Cottiaux, M. Cuka, C. Cupillard, D.G. Drucker, N. Elenski, M. Francken, B. Galabova, G. Ganetsovski, B. Gély, T. Hajdu, V. Handzhyiska, K. Harvati, T. Higham, S. Iliev, I. Jankovic, I. Karavanic, D.J. Kennett, D. Komšo, A. Kozak, D. Labuda, M. Lari, C. Lazar, M. Leppek, K. Leshtakov, D. Lo Vetro, D. Los, I. Lozanov, M. Malina, F. Martini, K. McSweeney, H. Meller, M. Mendušic, P. Mirea, V. Moiseyev, V. Petrova, T.D. Price, A. Simalcsik, L. Sineo, M. Šlaus, V. Slavchev, P. Stanev, A. Starovic, T. Szeniczey, S. Talamo, M. Teschler-Nicola, C. Thevenet, I. Valchev, F. Valentin, S. Vasilyev, F. Veljanovska, S. Venelinova, E. Veselovskaya, B. Viola, C. Virag, J. Zaninovic, S. Zäuner, P.W. Stockhammer, G. Catalano, R. Krauß, D. Caramelli, G. Zarina, B. Gaydarska, M. Lillie, A.G. Nikitin, I. Potekhina, A. Papathanasiou, D. Boric, C. Bonsall, J. Krause, R. Pinhasi, D. Reich.

In this article we document a west–east cline of ancestry in indigenous hunter-gatherers and, in eastern Europe, the early stages in the formation of Bronze Age steppe ancestry. We show that the first farmers of northern and western Europe dispersed through southeastern Europe with limited hunter-gatherer admixture, but that some early groups in the southeast mixed extensively with hunter-gatherers without the sex-biased admixture that prevailed later in the north and west. We also show that southeastern Europe continued to be a nexus between east and west after the arrival of farmers, with intermittent genetic contact with steppe populations occurring up to 2,000 years earlier than the migrations from the steppe that ultimately replaced much of the population of northern Europe.

“The Beaker phenomenon and the genomic transformation of northwest Europe.” Nature 555 (2018): 190-6.

I. Olalde, S. Brace, M.E. Allentoft, I. Armit, K. Kristiansen, T. Booth, N. Rohland, S. Mallick, A. Szécsényi-Nagy, A. Mittnik, E. Altena, M. Lipson, I. Lazaridis, T.K. Harper, N. Patterson, N. Broomandkhoshbacht, Y. Diekmann, Z. Faltyskova, D. Fernandes, M. Ferry, E. Harney, P. de Knijff, M. Michel, J. Oppenheimer, K. Stewardson, A. Barclay, K.W. Alt, C. Liesau, P. Ríos, C. Blasco, J.V. Miguel, R.M. García, A.A. Fernández, E. Bánffy, M. Bernabò-Brea, D. Billoin, C. Bonsall, L. Bonsall, T. Allen, L. Büster, S. Carver, L.C. Navarro, O.E. Craig, G.T. Cook, B. Cunliffe, A. Denaire, K.E. Dinwiddy, N. Dodwell, M. Ernée, C. Evans, M. Kucharík, J.F. Farré, C. Fowler, M. Gazenbeek, R.G. Pena, M. Haber-Uriarte, E. Haduch, G. Hey, N. Jowett, T. Knowles, K. Massy, S. Pfrengle, P. Lefranc, O. Lemercier, A. Lefebvre, C.H. Martínez, V.G. Olmo, A.B. Ramírez, J.L. Maurandi, T. Majó, J.I. McKinley, K. McSweeney, B.G. Mende, A. Mod, G. Kulcsár, V. Kiss, A. Czene, R. Patay, A. Endrodi, K. Köhler, T. Hajdu, T. Szeniczey, J. Dani, Z. Bernert, M. Hoole, O. Cheronet, D. Keating, P. Velemínský, M. Dobeš, F. Candilio, F. Brown, R.F. Fernández, A.M. Herrero-Corral, S. Tusa, E. Carnieri, L. Lentini, A. Valenti, A. Zanini, C. Waddington, G. Delibes, E. Guerra-Doce, B. Neil, M. Brittain, M. Luke, R. Mortimer, J. Desideri, M. Besse, G. Brücken, M. Furmanek, A. Hałuszko, M. Mackiewicz, A. Rapinski, S. Leach, I. Soriano, K.T. Lillios, J.L. Cardoso, M.P. Pearson, P. Włodarczak, T.D. Price, P. Pilar Prieto, P.J. Rey, R. Risch, M.A. Rojo Guerra, A. Schmitt, J. Serralongue, A.M. Silva, V. Smrcka, L. Vergnaud, J. Zilhão, D. Caramelli, T. Higham, M.G. Thomas, D.J. Kennett, H. Fokkens, V. Heyd, A. Sheridan, K.G. Sjögren, P.W. Stockhammer, J. Krause, R. Pinhasi, W. Haak, I. Barnes, C. Lalueza-Fox, D. Reich.

In this paper we present genome-wide data from 400 Neolithic, Copper Age and Bronze Age Europeans, including 226 individuals associated with Beaker-complex artefacts. We detected limited genetic affinity between Beaker-complex-associated individuals from Iberia and central Europe, and thus exclude migration as an important mechanism of spread between these two regions. However, migration had a key role in the further dissemination of the Beaker complex. We document this phenomenon most clearly in Britain, where the spread of the Beaker complex introduced high levels of steppe-related ancestry and was associated with the replacement of approximately 90% of Britain’s gene pool within a few hundred years, continuing the east-to-west expansion that had brought steppe-related ancestry into central and northern Europe over the previous centuries.

“Population turnover in remote Oceania shortly after initial settlement.” Current Biology 28 (2018): 1157-65.

M. Lipson, P. Skoglund, M. Spriggs, F. Valentin, S. Bedford, R. Shing, H. Buckley, I. Phillip, G.K. Ward, S. Mallick, N. Rohland, N. Broomandkhoshbacht, O. Cheronet, M. Ferry, T.K. Harper, M. Michel, J. Oppenheimer, K. Sirak, K. Stewardson, K. Auckland, A.V.S. Hill, K. Maitland, S.J. Oppenheimer, T. Parks, K. Robson, T.N. Williams, D.J. Kennett, A.J. Mentzer, R. Pinhasi, D. Reich.

In this paper we find that people of almost entirely Papuan ancestry arrived in Vanuatu by around 2300 BP, likely reflecting migrations a few hundred years earlier at the end of the Lapita period, when there is also evidence of changes in skeletal morphology and cessation of long-distance trade between Near and Remote Oceania. Papuan ancestry was subsequently diluted through admixture but remains at least 80–90% in most islands. Through a fine-grained analysis of ancestry profiles, we show that the Papuan ancestry in Vanuatu derives from the Bismarck Archipelago rather than the geographically closer Solomon Islands. However, the Papuan ancestry in Polynesia—the most remote Pacific islands—derives from different sources, documenting a third stream of migration from Near to Remote Oceania.

“Indirect evidence for the social impact of the Justinianic Pandemic: episcopal burial and conciliar legislation in Visigothic Hispania.” Journal of Late Antiquity 11 (2018): 193-215.

H. Gruber.

The Justinianic Plague, the first documented pandemic outbreak of the bubonic plague, struck the Mediterranean region in the 540s CE. Despite some surviving narrative accounts, however, there is little direct written evidence for its impact in much of the Mediterranean world. This is especially true for Visigothic Hispania. However, certain texts that are not explicit accounts of the plague may hint at its impact. One such text is the fourth canon of the Council of Valencia, held in 546. This canon reflects episcopal concerns about what to do when a bishop dies “a sudden death.” According to it, the bishop should not be buried at once but “placed with great care in a coffin apart from the others.” Comparative philology, the archaeology of sixth-century Valencia, and recent paleogenetic investigation into the bacterium that causes the disease all combine to suggest that within the broader context of episcopal funerary displays, the “sudden death” referred to is the plague and that the canon is a response to changes in burial customs—especially the newfound prevalence of mass inhumation—caused by the first wave of the pandemic.

“Biological sexing of a 4000-Year-Old Egyptian mummy head to assess the potential of nuclear DNA recovery from the most damaged and limited forensic specimens.” Genes 9 (2018): 135.

O. Loreille, S. Ratnayake, A.L. Bazinet, T.B. Stockwell, D.D. Sommer, N. Rohland, S. Mallick, P.L.F. Johnson, P. Skoglund, A.J. Onorato, N.H. Bergman, D. Reich, J.A. Irwin.

In this paper we describe the biological sexing of a ~4000-year-old Egyptian mummy using shotgun sequencing and two established methods of biological sex determination (RX and RY), by way of mitochondrial genome analysis as a means of sequence data authentication. This particular case of historical interest increases the potential utility of HTS techniques for forensic purposes by demonstrating that data from the more discriminatory nuclear genome can be recovered from the most damaged specimens, even in cases where mitochondrial DNA cannot be recovered with current PCR-based forensic technologies. Although additional work remains to be done before nuclear DNA recovered via these methods can be used routinely in operational casework for individual identification purposes, these results indicate substantial promise for the retrieval of probative individually identifying DNA data from the most limited and degraded forensic specimens.

Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, (2018) Pantheon Books, New York.

D. Reich

David Reich describes how the revolution in the ability to sequence ancient DNA has changed our understanding of the deep human past. This book tells the emerging story of our often surprising ancestry - the extraordinary ancient migrations and mixtures of populations that have made us who we are.

“Ancient DNA from Chalcolithic Israel reveals the role of population mixture in cultural transformation.” Nature Communications 9 (2018): 3336.

E. Harney, M. May, D. Shalem, N. Rohland, S. Mallick, I. Lazaridis, R. Sarig, K. Stewardson, S. Nordenfelt, N. Patterson, I. Hershkovitz, D. Reich.

The material culture of the Late Chalcolithic period in the southern Levant (4500–3900/3800 BCE) is qualitatively distinct from previous and subsequent periods. To test the hypothesis that the advent and decline of this culture was influenced by movements of people, in this article we generated genome-wide ancient DNA from 22 individuals from Peqi’in Cave, Israel. These individuals were part of a homogeneous population that can be modeled as deriving ~57% of its ancestry from groups related to those of the local Levant Neolithic, ~17% from groups related to those of the Iran Chalcolithic, and ~26% from groups related to those of the Anatolian Neolithic. The Peqi’in population also appears to have contributed differently to later Bronze Age groups, one of which we show cannot plausibly have descended from the same population as that of Peqi’in Cave. These results provide an example of how population movements propelled cultural changes in the deep past.

2017

“Genetic origins of the Minoans and Mycenaeans.” Nature, 548: 23310 (2017), pp. 214-18. doi:10.1038/nature23310

I. Lazaridis, A. Mittnik, N. Patterson, S. Mallick, N. Rohland, S. Pfrengle, A. Furtwängler, A. Peltzer, C. Posth, A. Vasilakis, P.J.P. McGeorge, E. Konsolaki-Yannopoulou, G. Korres, H. Martlew, M. Michalodimitrakis, M. Özsait, N. Özsait, A. Papathanasiou, M. Richards, S.A. Roodenberg, Y. Tzedakis, R. Arnott, D.M. Fernandes, J.R. Hughey, D.M. Lotakis, P.A. Navas, Y. Maniatis, J.A. Stamatoyannopoulos, K. Stewardson, P.W. Stockhammer, R. Pinhasi, D. Reich, J. Krause, G. Stamatoyannopoulos.

This paper demonstrates that in spite of the close cultural relation between the Southern Greek mainland and Crete, this rich intercultural contact did not go hand in hand with a large-scale exchange of genetic material, since both southern Greek mainland as well as Cretan Late Bronze Age populations can clearly be distinguished genetically in the 2nd millennium BCE. Moreover, this paper has for the first time provided genetic evidence for a migration from the steppe that reached the Greek mainland, but not Crete. As this migration has hitherto been linked with the spread of the Indo-European languages (Haak et al. 2015), it could possibly be correlated with the existence of an Indo-European language on the Greek mainland in the 2nd millennium BCE (i.e., Linear B) and a non-Indo-European language at the same time on Crete (i.e., Linear A).

“Reconstructing prehistoric African population structure.” Cell 171 (2017): 59-71.

P. Skoglund, J.C. Thompson, M.E. Prendergast, A. Mittnik, K. Sirak, M. Hajdinjak, T. Salie, N. Rohland, S. Mallick, A. Peltzer, A. Heinze, I. Olalde, M. Ferry, E. Harney, M. Michel, K. Stewardson, J.I. Cerezo-Roman, C. Chiumia, A. Crowther, E. Gomani-Chindebvu, A.O. Gidna, K.M. Grillo, I.T. Helenius, G. Hellenthal, R. Helm, M. Horton, S. Lopez, A.Z.P. Mabulla, J. Parkington, C. Shipton, M.G. Thomas, R. Tibesasa, M. Welling, V.M. Hayes, D.J. Kennett, R. Ramesar, M. Meyer, S. Paabo, N. Patterson, A.G. Morris, N. Boivin, R. Pinhasi, J. Krause, D. Reich.

In this paper we assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100-2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we tracked the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We leveraged ancient genomes to document episodes of natural selection in southern African populations.

“Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods.” Nature Communications 8: 15694 (2017).

V.J. Schuenemann, A. Peltzer, B. Welte, W.P. van Pelt, M. Molak, C. Wang, A. Furtwängler, C. Urban, E. Reiter, K. Nieselt, B. Teßmann, M. Francken, K. Harvati, W. Haak, S. Schiffels, J. Krause.

In this study we presented the first genome-wide data of ancient Egyptian mummies. Our analysis suggests an increase of Sub-Saharan African ancestry in post-Roman periods. We furthermore find genetic continuity of Egyptians from the Late Bronze Age to the Roman period, despite multiple episodes of foreign domination. Post-Roman migrations from sub-Saharan Africa seem to have shifted the gene pool of Egyptians; as a result modern Egyptians share more genetic ancestry with Sub-Saharan Africans than ancient Egyptians.

“Parallel palaeogenomic transects reveal complex genetic history of early European farmers.” Nature 551 (2017): 368-72.

M. Lipson, A. Szécsényi-Nagy, S. Mallick, A. Pósa, B. Stégmár, V. Keerl, N. Rohland, K. Stewardson, M. Ferry, M. Michel, J. Oppenheimer, N. Broomandkhoshbacht, E. Harney, S. Nordenfelt, B. Llamas, G.B. Mende, K. Köhler, K. Oross, M. Bondár, T. Marton, A. Osztás, J. Jakucs, T. Paluch, F. Horváth, P. Csengeri, J. Koós, K. Sebők, A. Anders, P. Raczky, J. Regenye, J.P. Barna, S. Fábián, G. Serlegi, Z. Toldi, E.G. Nagy, J. Dani, E. Molnár, G. Pálfi, L. Márk,

B. Melegh, Z. Bánfai, L. Domboróczki, J. Fernández-Eraso, J. Antonio Mujika-Alustiza, C.A. Fernández, J.J. Echevarría, R. Bollongino, J. Orschiedt, K. Schierhold, H. Meller, A. Cooper, J. Burger, E. Bánffy, K.W. Alt, C. Lalueza-Fox, W. Haak, D. Reich.

In this paper we investigate the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples, of which 130 are newly reported here, from the Neolithic and Chalcolithic periods of Hungary (6000–2900 BCE, n = 100), Germany (5500–3000 BCE, n = 42) and Spain (5500–2200 BCE, n = 38). We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways in which gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modelling approaches to elucidate multiple dimensions of historical population interactions.

2016

“A high-coverage yersinia pestis genome from a sixth-century Justinianic Plague victim.” Molecular Biology and Evolution, 33 (2016): 2911-23. doi: 10.1093/molbev/msw170.

M. Feldman, M. Harbeck, M. Keller, M.A. Spyrou, A. Rott, B. Trautmann, H.C. Scholz, B. Päffgen, J. Peters, M. McCormick, K. Bos, A. Herbig, J. Krause.

The Justinianic Plague (541-ca. 750 CE) is thought to be the first of three historically documented plague pandemics that caused massive casualties. Historical accounts and molecular data suggest the bacterium Yersinia pestis as its etiological agent. Here we presented a new high-coverage (17.9-fold) Y. pestis genome obtained from a sixth-century skeleton recovered from a southern German burial site close to Munich. The reconstructed genome enabled the detection of 30 unique substitutions as well as structural differences that have not been previously described. We report indels affecting a lacl family transcription regulator gene as well as nonsynonymous substitutions in the nrdE, fadJ, and pcp genes, that have been suggested as plague virulence determinants or have been shown to be upregulated in different models of plague infection. In addition, we identify 19 false positive substitutions in a previously published lower-coverage Y. pestis genome from another archaeological site of the same time period and geographical region that is otherwise genetically identical to the high-coverage genome sequence reported here, suggesting low-genetic diversity of the plague during the sixth century in rural southern Germany.

“Genomic insights into the origin of farming in the ancient Near East.” Nature 536 (2016): 419-24.

I. Lazaridis, D. Nadel, G. Rollefson, D.C. Merrett, N. Rohland, S. Mallick, D. Fernandes, M. Novak, B. Gamarra, K. Sirak, S. Connell, K. Stewardson, E. Harney, Q. Fu, G. Gonzalez-Fortes, E.R. Jones, S.A. Roodenberg, G. Lengyel, F. Bocquentin, B. Gasparian, J.M. Monge, M. Gregg, V. Eshed, A. Mizrahi, C. Meiklejohn, F. Gerritsen, L. Bejenaru, M. Blüher, A. Campbell, G. Cavalleri, D. Comas, P. Froguel, E. Gilbert, S.M. Kerr, P. Kovacs, J. Krause, D. McGettigan, M. Merrigan, D.A. Merriwether, S. O'Reilly, M.B. Richards, O. Semino, M. Shamoon-Pour, G. Stefanescu, M. Stumvoll, A. Tönjes, A. Torroni, J.F. Wilson, L. Yengo, N.A. Hovhannisyan, N. Patterson, R. Pinhasi, D. Reich.

In this paper we reported genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 BCE, from Natufian hunter–gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter–gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter–gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.

Ice Core Project Publications 2015 - 2020

2020

"Alpine ice reveals the yearly political economy of the Angevin Empire, from the death of Thomas Becket to Magna Carta, c. CE 117” Antiquity, 94.374 (2020): 473-90.

C.P. Loveluck, A.F. More, N.E. Spaulding, H. Clifford, M.J. Handley, L. Hartman, E.V.Korotkikh, A.V. Kurbatov, P.A. Mayewski, S.B. Sneed, M. McCormick.

In this study, ultra-high-resolution evidence from the new Colle Gnifetti ice core (Switzerland), textual and archaeological sources show that Bränvall et al. were correct in suggesting England as the major point of origin for lead pollution in the later twelfth and early thirteenth centuries CE. Detailed yearly analysis of the different sources indicates that between the mid 1160s and 1216, the Colle Gnifetti ice core provides a remarkable measurable record of the environmental impact and economic history of silver and lead production in England under the Angevin kings, Henry II, Richard the Lionheart and John. Key events linked to the political economy of the Angevin Empire and reflected in the royal archives and historical records are inscribed into the pollution record, from construction of castles and monasteries, to the deaths of monarchs.https://doi.org/10.15184/aqy.2019.202

"The Impact of a Six‐Year Climate Anomaly on the ‘Spanish Flu’ Pandemic and WWIAGU GeoHealth, 4:9 (2020). https://doi.org/10.1029/2020GH000277

A.F. More, C.P. Loveluck, H. Clifford, M.J. Handley, E.V. Korotkikh, A.V. Kurbatov, M. McCormick, P.A. Mayewski

The H1N1 “Spanish influenza” pandemic of 1918–1919 caused the highest known number of deaths recorded for a single pandemic in human history. Several theories have been offered to explain the virulence and spread of the disease, but the environmental context remains underexamined. In this study, we present a new environmental record from a European, Alpine ice core, showing a significant climate anomaly that affected the continent from 1914 to 1919. Incessant torrential rain and declining temperatures increased casualties in the battlefields of World War I (WWI), setting the stage for the spread of the pandemic at the end of the conflict. Multiple independent records of temperature, precipitation, and mortality corroborate these findings.

2019

“Climates of history, histories of climate: from history to archaeoscience.” Journal of Interdisciplinary History, L:1 (2019), 3–30. https://www.mitpressjournals.org/doi/full/10.1162/jinh_a_01374.

M. McCormick.

The discovery of how humans experienced ancient climates is part of a broader deployment of science to expand the frontiers of historical knowledge. Cascading breakthroughs characterize ancient studies—especially the last few years’ technological and intellectual advances of the genomic revolution that have unveiled humanity’s deep history—and biomolecular archaeology’s recovery of ancient biomes and molecules more generally. Paleoclimate science, too, is transforming our knowledge of the relations between human societies and past climates. By adducing new unanticipated data, the scientific revolution now affecting historical research promises to disrupt, creatively, what we thought we knew about the human past. But the challenges of integrating scientific evidence into historical analysis call for new approaches suited to a new historical discipline that we may broadly characterize as archaeoscience. This essay shows how knowledge of ancient environments has grown by studying nature through history and by studying history through nature.

“A 2000 year Saharan dust event proxy record from an ice core in the European Alps.” Journal of Geophysical Research: Atmospheres, 124 (2019).

https://doi.org/10.1029/2019JD030725.

H.M. Clifford, N.E. Spaulding, A.V. Kurbatov, A.F. More, E.V. Korotkikh, S.B. Sneed, M. Handley, K.A. Maasch, C. Loveluck, J. Chaplin, M. McCormick, P.A. Mayewski.

Plumes of dust from the Saharan desert transported across the Atlantic Ocean and Mediterranean Sea, influence land, ocean and atmospheric systems, yet we know relatively little about how these events varied before the instrumental record. Saharan dust transport can result in flourishing ecosystems, poor air quality and even changes in the frequency of North Atlantic hurricanes. In our study, we develop a summer Saharan dust event record with sub‐annual resolution from an ice core drilled in the European Alps, dating back 2000 years. The Saharan dust record shows increased dust transport is caused by a combination of enhanced high‐pressure systems over the Mediterranean and drier conditions in Northern Africa, along with other atmospheric influences. Our record indicates the past century has seen an increased amount of Saharan dust transport, comparable to large occurrences over the past 2000 years. Additionally, we discuss implications for using our sub‐annually resolved Saharan dust record in concert with historical records to improve interpretations of human-climate interactions.

2018

“Temperature and mineral dust variability recorded in two low-accumulation Alpine ice cores over the last millennium.” Climate of the Past, 14 (2018): 21-37. https://doi.org/10.5194/cp-14-21-2018.

P. Bohleber, T. Erhardt, N.E. Spaulding, H. Hoffmann, H. Fischer, P.A. Mayewski.

Among ice core drilling sites in the European Alps, Colle Gnifetti (CG) is the only non-temperate glacier to offer climate records dating back at least 1000 years. This unique long-term archive is the result of an exceptionally low net accumulation driven by wind erosion and rapid annual layer thinning. However, the full exploitation of the CG time series has been hampered by considerable dating uncertainties and the seasonal summer bias in snow preservation. Using a new core drilled in 2013 we extend annual layer counting, for the first time at CG, over the last 1000 years and add additional constraints to the resulting age scale from radiocarbon dating. Based on this improved age scale, and using a multi-core approach with a neighboring ice core, we explore the time series of stable water isotopes and the mineral dust proxies Ca²⁺ and insoluble particles. Also in our latest ice core we face the already known limitation to the quantitative use of the stable isotope variability based on a high and potentially non-stationary isotope/temperature sensitivity at CG. Decadal trends in Ca²⁺ reveal substantial agreement with instrumental temperature and are explored here as a potential site-specific supplement to the isotope-based temperature reconstruction. The observed coupling between temperature and Ca²⁺ trends likely results from snow preservation effects and the advection of dust-rich air masses coinciding with warm temperatures. We find that if calibrated against instrumental data, the Ca²⁺-based temperature reconstruction is in robust agreement with the latest proxy-based summer temperature reconstruction, including a “Little Ice Age” cold period as well as a medieval climate anomaly. Part of the medieval climate period around CE 1100–1200 clearly stands out through an increased occurrence of dust events, potentially resulting from a relative increase in meridional flow and/or dry conditions over the Mediterranean.

“The role of historical context in understanding past climate, pollution and health data in trans-disciplinary studies.” GeoHealth (AGU), 2 (2018): 162-70. doi:10.1029/2017GH000121.

A.F. More, N.E. Spaulding, P. Bohleber, M.J. Handley, H. Hoffmann, E.V. Korotkikh, A.V. Kurbatov, C.P. Loveluck, S.B. Sneed, M. McCormick, P.A. Mayewski.

This article highlights the crucial importance of historical and archaeoscientific data in trans‐disciplinary studies of planetary health, in the form of a reply to two comments to a previous article (More et al., 2017, https://doi.org/10.1002/2017GH000064). This reply emphasizes the crucial importance of geographic and historical context in assessing the significance and reach of scientific findings. The article also showcases the growing role of “Big‐Data” scale data sets of demographic, epidemiological, and historical records for understanding how past pollution and climate data affected populations, especially when cutting‐edge methods (e.g., laser ablation inductively coupled plasma mass spectrometry) in climate science provide an ever more detailed chronology of past crises and long‐term pollution trends.

“Alpine ice-core evidence for the transformation of the European monetary system, AD 640-670.”Antiquity (2018) https://doi.org/10.15184/aqy.2018.110

C.P. Loveluck, M. McCormick, N.E. Spaulding, H. Clifford, M.J. Handley, L. Hartman, H. Hoffmann, E.V. Korotkikh, A.V. Kurbatov, A.F. More, S.B. Sneed, P.A. Mayewski.

The seventh-century CE switch from gold to silver currencies transformed the socio-economic landscape of Northwest Europe. The source of silver, however, has proven elusive. Recent research, integrating ice-core data from the Colle Gnifetti drill site in the Swiss Alps, geoarchaeological records and numismatic and historical data, has provided new evidence for this transformation. Annual resolution ice-core data are combined with lead pollution analysis to demonstrate that significant new silver mining facilitated the change to silver coinage, and dates the introduction of such coinage to c. CE 660. Archaeological evidence and atmospheric modelling of lead pollution locates the probable source of the silver to mines at Melle, in France.

2017

“Next generation ice core technology reveals true minimum natural levels of lead (Pb) in the atmosphere: insights from the Black Death.” GeoHealth (AGU), 1 (2019): 211-19. doi: 10.1002/2017GH000064.

A.F. More, N.E. Spaulding, P. Bohleber, M.J. Handley, H. Hoffmann, E.V. Korotkikh, A.V. Kurbatov, C.P. Loveluck, S.B. Sneed, M. McCormick, P.A. Mayewski

Current policies to reduce lead pollution in the air are based on the assumption that preindustrial levels of lead in the air were negligible, safe, or nonexistent. This trans‐disciplinary article shows that this is not the case, using next‐generation laser technology in climate science, in combination with detailed historical and archaeological records in as many as seven languages from all over Europe. We show that lead levels in the air have been elevated for the past 2000 years, except for a single 4-year period. This 4-year period corresponds with the largest pandemic ever to ravage Western Europe (the Black Death), resulting in a 40–50% reduction in population and interrupting mining and smelting of lead in the European continent. This unprecedented population collapse and severe economic decline halted lead mining and smelting and related emissions of lead in the air. It uses next‐generation technology and expertise in history, climate science, archaeology, and toxicology, brought to bear in a detailed contribution of ancient evidence to planetary health, with crucial implications now for public health and environmental policy, and the history of human exposure to lead

“Possible Icelandic tephra found in European Colle Gnifetti Glacier.”

Geochemistry, Geophysics, Geosystems (AGU), 18.11 (2017). doi: 10.1002/2017GC007022.

M.T. Luongo, A.V. Kurbatov, T. Erhardt, P.A. Mayewski, M. McCormick, A.F. More, N.E. Spaulding, S.D. Wheatley, M.G. Yates, P.D. Bohleber

Volcanic ash (tephra) provides unique time markers (isochrons) that are often used as an independent age‐control tool for stratigraphic correlations of paleoclimate archives from ice cores. However, little credence has been given to the notion of finding tephra in ice cores collected in the European Alps because of the relatively large distance from volcanic sources and the presumed nature of regional atmospheric circulation patterns. We filtered particles from melted ice core drilling chips gathered roughly every meter during a 2013 drilling operation at Colle Gnifetti glacier in the Swiss‐Italian Alps (45°55.74′N, 7°52.58′E, 4450 m asl). One filter, preliminarily dated to the nineteenth century by annual layer counting, contained a group of six visually similar tephra particles. Analyzing their chemistry using a scanning electron microscope equipped with an energy‐dispersive x‐ray spectrometer established that the six particles were volcanic in origin and are very similar in composition (a distinctive geochemical signature), pointing to a single volcanic eruption source. We proposed that one of several massive nineteenth century Eastern Icelandic eruptions is a potential source given eruption timing, size, tephra dispersion area, and similarities in chemical composition. This first finding of tephra in an Alpine ice core contributes to a regional tephrochronological framework that can be adapted for future correlation among different paleoclimate sequences. The lead author was a Harvard undergraduates working with the Science of the Past in the Departments of Earth and Planetary Sciences and History.

“A new multielement method for LA-ICP-MS data acquisition from glacier ice cores.” Environmental Science and Technology, 51.22 (2017): 13282–87. doi: 10.1021/acs.est.7b03950.

N.E. Spaulding, S.B. Sneed, M.J. Handley, P.Bohleber, A.V. Kurbatov, N.J. Pearce, T. Erhardt, P.A. Mayewski.

To answer pressing new research questions about the rate and timing of abrupt climate transitions, a robust system for ultrahigh-resolution sampling of glacier ice is needed. Here, we present a multielement method of LA-ICP-MS analysis wherein an array of chemical elements is simultaneously measured from the same ablation area. Although multielement techniques are commonplace for high-concentration materials, prior to the development of this method, all LA-ICP-MS analyses of glacier ice involved a single element per ablation pass or spot. This new method, developed using the LA-ICP-MS system at the W.M. Keck Laser Ice Facility at the University of Maine Climate Change Institute, has already been used to shed light on our flawed understanding of natural levels of Pb in Earth’s atmosphere.

2015

“New LA-ICP-MS cryocell and calibration technique for sub-millimeter analysis of ice cores.” Journal of Glaciology, 61.226 (2015), 233-42. doi: 10.3189/2015JoG14J139.

S.B. Sneed, P.A. Mayewski, W.G. Sayre, M.J. Handley, A.V. Kurbatov, K.C. Taylor, P. Bohleber, D. Wagenbach, T. Erhardt, N.E. Spaulding.

Ice cores provide a robust reconstruction of past climate. However, development of timescales by annual-layer counting, essential to detailed climate reconstruction and interpretation, on ice cores collected at low-accumulation sites or in regions of compressed ice, is problematic due to closely spaced layers. Ice-core analysis by laser ablation–inductively coupled plasma–mass spectrometry (LA-ICP-MS) provides sub-millimeter-scale sampling resolution (on the order of 100 μm in this study) and the low detection limits (ng L−1) necessary to measure the chemical constituents preserved in ice cores. We present a newly developed cryocell that can hold a 1 m long section of ice core, and an alternative strategy for calibration. Using ice-core samples from central Greenland, we demonstrate the repeatability of multiple ablation passes, highlight the improved sampling resolution, verify the calibration technique and identify annual layers in the chemical profile in a deep section of an ice core where annual layers have not previously been identified using chemistry. In addition, using sections of cores from the Swiss/Italian Alps we illustrate the relationship between Ca, Na and Fe and particle concentration and conductivity, and validate the LA-ICP-MS Ca profile through a direct comparison with continuous flow analysis results.

Select Publications about the Science of the Human Past from
SoHP Steering Committee Members - 2019-22

Peter Huybers, Department of Earth and Planetary Sciences

“Correcting datasets leads to more homogeneous early-twentieth-century sea surface warming.” Nature 571 (2019): 393–7. https://doi.org/10.1038/s41586-019-1349-2

D. Chan, E.C. Kent, D.I. Berry, P. Huybers.

Existing estimates of sea surface temperatures (SSTs) indicate that, during the early twentieth century, the North Atlantic and northeast Pacific oceans warmed by twice the global average, whereas the northwest Pacific Ocean cooled by an amount equal to the global average. Such a heterogeneous pattern suggests first-order contributions from regional variations in forcing or in ocean–atmosphere heat fluxes. These older SST estimates are, however, derived from measurements of water temperatures in ship-board buckets, and must be corrected for substantial biases. Here we show that correcting for offsets among groups of bucket measurements leads to SST variations that correlate better with nearby land temperatures and are more homogeneous in their pattern of warming. Offsets are identified by systematically comparing nearby SST observations among different groups. Correcting for offsets in German measurements decreases warming rates in the North Atlantic, whereas correcting for Japanese measurement offsets leads to increased and more uniform warming in the North Pacific. Japanese measurement offsets in the 1930s primarily result from records having been truncated to whole degrees Celsius when the records were digitized in the 1960s. These findings underscore the fact that historical SST records reflect both physical and social dimensions in data collection, and suggest that further opportunities exist for improving the accuracy of historical SST records.

Michael McCormick, Department of History

"Recognising Bias in Common Era Temperature Reconstructions." Dendrochronologia 74: 125982 (2022).

U. Büntgen, D. Arseneault, É. Boucher, O.V. Churakova, F. Gennaretti, A. Crivellaro, M.K. Hughes, A.V. Kirdyanov, L. Klippel, P.J. Krusic, H.W. Linderholm, F.C. Ljungqvist, J. Ludescher, M. McCormick, V.S. Myglan, K. Nicolussi, A. Piermattei, C. Oppenheimer, F. Reinig, M. Sigl, E.A. Vaganov, J. Esper.

A steep decline in the quality and quantity of available climate proxy records before medieval times challenges any comparison of reconstructed temperature and hydroclimate trends and extremes between the first and second half of the Common Era. Understanding of the physical causes, ecological responses and societal consequences of past climatic changes, however, demands highly-resolved, spatially-explicit, seasonally-defined and absolutely-dated archives over the entire period in question. Continuous efforts to improve existing proxy records and reconstruction methods and to develop new ones, as well as clear communication of all uncertainties (within and beyond academia) must be central tasks for the paleoclimate community.

"Prominent Role of Volcanism in Common Era Climate Variability and Human History." Dendrochronologia 64: 125757 (2020).

Climate reconstructions for the Common Era are compromised by the paucity of annually-resolved and absolutely-dated proxy records prior to medieval times. Where reconstructions are based on combinations of different climate archive types (of varying spatiotemporal resolution, dating uncertainty, record length and predictive skill), it is challenging to estimate past amplitude ranges, disentangle the relative roles of natural and anthropogenic forcing, or probe deeper interrelationships between climate variability and human history. Here, we compile and analyse updated versions of all the existing summer temperature sensitive tree-ring width chronologies from the Northern Hemisphere that span the entire Common Era. We apply a novel ensemble approach to reconstruct extra-tropical summer temperatures from 1 to 2010 CE, and calculate uncertainties at continental to hemispheric scales. Peak warming in the 280s, 990s and 1020s, when volcanic forcing was low, was comparable to modern conditions until 2010 CE. The lowest June–August temperature anomaly in 536 not only marks the beginning of the coldest decade, but also defines the onset of the Late Antique Little Ice Age (LALIA). While prolonged warmth during Roman and medieval times roughly coincides with the tendency towards societal prosperity across much of the North Atlantic/European sector and East Asia, major episodes of volcanically-forced summer cooling often presaged widespread famines, plague outbreaks and political upheavals. Our study reveals a larger amplitude of spatially synchronized summer temperature variation during the first millennium of the Common Era than previously recognised.

“Establishing the provenance of the Nazareth Inscription: Using stable isotopes to resolve a historic controversy and trace ancient marble production.” Journal of Archaeological Science: Reports 30 (102228) (2020).

K. Harper, M. McCormick, M. Hamilton, C. Peiffert, R. Michels, M. Engel.

Stable oxygen and carbon isotope analyses are commonly used to attempt to establish the provenance of ancient marble artifacts such as statues and architectural elements. In this study we apply the technique for a novel purpose: establishing the provenance of an important and mysterious inscribed document from the Roman Empire known as the Nazareth Inscription. The stable isotope enrichment in ¹³C and substantial depletion in ¹⁸O provide a unique signature allowing the confident and unexpected identification of the upper quarry of the Greek island of Kos as the source of the marble. This information resolves a near century of debate among ancient historians about the significance of the inscription, hitherto most often connected with Roman reactions to early Christian reports of Jesus’ empty tomb. It is proposed that the edict was issued by Caesar Augustus in response to the desecration of the grave of a famous tyrant from Kos named Nikias, a theory which more logically fits with the provenance of the marble and the events of that time. Isotope analyses of dated and localized inscriptions will deliver vast new data for the high-resolution economic history of marble production and distribution around the ancient Mediterranean.

“Reccopolis revealed: the first geomagnetic mapping of the early medieval Visigothic royal town.” Antiquity 93 (369) (2019): 735-51.

J. Henning, M. McCormick, L. Olmo Enciso, K. Rassmann, E.F. Eyub.

Reccopolis, in central Iberia, is the only archaeologically identified town founded by Germanic newcomers on Roman soil during the challenging socio-political and environmental circumstances of the mid to late sixth century AD. Despite archaeological investigations, doubts have persisted concerning the nature and size of Reccopolis. Recent geomagnetic survey, however, has revealed a dense urban fabric, unexpected new royal palace buildings, an extramural suburb and one of the potentially earliest Islamic mosques in Iberia. Reccopolis now stands as an exceptional example of early medieval urbanism that challenges our perceptions of urban development in sixth-century Europe.

“Radiocarbon dating the end of urban services in a late Roman town.” PNAS Commentary 116 (17) (2019): 8096-8.

Michael McCormick.

“Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750).” See above, MHAAM.

“A 2000 year Saharan dust event proxy record from an ice core in the European Alps.” See above, HICP.

“Climates of history, histories of climate: from history to archaeoscience.” See above, HICP.

“Medieval women's early involvement in manuscript production suggested by lapis lazuli identification in dental calculus.” See below, SoHP.

“Alpine ice reveals the yearly political economy of the Angevin Empire, from the death of Thomas Becket to Magna Carta, c. CE 1170-1216.” See above, HICP .

David Reich, Department of Genetics

“The genomic history of the Iberian Peninsula over the past 8000 years.” See above, MHAAM .

“The formation of human populations in South and Central Asia.” See above, MHAAM .

“An ancient Harappan genome lacks ancestry from Steppe Pastoralists or Iranian Farmers.” See above, MHAAM .

“Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India.” See above, MHAAM .

“Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa.” See above, MHAAM .

Christina Warinner, Department of Anthropology

“HOPS: Automated detection and authentication of pathogen DNA in archaeological remains.” Genome Biology 20 (280) (2019). https://doi.org/10.1186/s13059-019-1903-

R. Huebler, F.M. Key, C. Warinner, K.I. Bos, J. Krause, A. Herbig.

High-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present-day samples and can also be applied to molecular data from archaeological remains. Investigations of ancient microbes can provide valuable information on past bacterial commensals and pathogens, but their molecular detection remains a challenge. Here, we present HOPS (Heuristic Operations for Pathogen Screening), an automated bacterial screening pipeline for ancient DNA sequences that provides detailed information on species identification and authenticity. HOPS is a versatile tool for high-throughput screening of DNA from archaeological material to identify candidates for genome-level analyses.

“The dead shall be raised: Multidisciplinary analysis of 19th century human skeletons reveals complexity in New Haven Connecticut immigrant socioeconomic history and identity.” PLoS ONE 14 (9) (2019): e0219279. DOI: 10.1371/journal.pone.0219279

G.P. Aronsen, L. Fehren-Schmitz, J. Krigbaum, G.D. Kamenov, G. Conlogue, C. Warinner, A. Ozga, K. Sankaranarayanan, A. Griego, D.W. DeLuca, H.T. Eckels, R. Byczkiewicz, T. Grurich, N. Pellatier, S. Brownlee, A. Marichal, K. Williamson, Y. Tonoike, N.F. Bellantoni.

In July 2011, renovations to Yale-New Haven Hospital inadvertently exposed the cemetery of Christ Church, New Haven, Connecticut’s first Catholic cemetery. While this cemetery was active between 1833 and 1851, both the church and its cemetery disappeared from public records, making the discovery serendipitous. Four relatively well-preserved adult skeletons were recovered with few artifacts. All four individuals show indicators of manual labor, health and disease stressors, and dental health issues. Two show indicators of trauma, with the possibility of judicial hanging in one individual. Musculoskeletal markings are consistent with physical stress, and two individuals have arthritic indicators of repetitive movement/specialized activities. Radiographic analyses show osteopenia, healed trauma, and other pathologies in several individuals. Dental calculus analysis did not identify any tuberculosis indicators, despite osteological markers. Isotopic analyses of teeth indicate that all four were likely recent immigrants to the Northeastern United States. Nuclear and mitochondrial DNA were recovered from three individuals, and these analyses identified ancestry, hair/eye color, and relatedness. Genetic and isotopic results upended our initial ancestry assessment based on burial context alone. These individuals provide biocultural evidence of New Haven’s Industrial Revolution and the plasticity of ethnic and religious identity in the immigrant experience. Their recovery and the multifaceted analyses described here illuminate a previously undescribed part of the city’s rich history. The collective expertise of biological, geochemical, archaeological, and historical researchers interprets socioeconomic and cultural identity better than any one could alone. Our combined efforts changed our initial assumptions of a poor urban Catholic cemetery’s membership, and provide a template for future discoveries and analyses.

“Relief food subsistence revealed by microparticle and proteomics analyses of dental calculus from victims of the Great Irish Famine.” PNAS 116 (39) (2019): 19380-5. DOI: 10.1073/pnas.1908839116.

J. Geber, M. Tromp, A. Scott, A. Bouwman, P. Nanni, J. Grossmann, J. Hendy, C. Warinner.

This study provides direct evidence of the dependency on relief food in Ireland around the time of the Great Famine (1845 to 1852) through dental calculus analysis of archaeological human remains. The findings show a dominance of corn (maize) and milk from the identified foodstuffs and corroborate the contemporaneous historical accounts of diet and subsistence. It shows that microparticle and proteomic analyses, even when based on small archaeological samples, can provide a valid snapshot of dietary patterns and food consumption. The occurrence of egg protein, generally only included in the diet for the better-off social classes, also highlights how these analytical techniques can provide unanticipated insights into the variability of diet in historical populations.

“Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage.” Microbiome 7 (102) (2019). DOI: 10.1186/s40168-019-0717-3.

I.M. Velsko, J.A. Fellows-Yates, F. Aron, R.W. Hagen, L.A.F. Frantz, L. Loe, J.B. Rodriguez Martinez, E. Chaves, C. Gosden, G. Larson, C. Warinner.

Background

Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates.

Results

Metagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins.

Conclusions

Overall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus.

“Ancient DNA 101: An introductory guide in the era of high-throughput sequencing.” SAA Record 19 (1) (2019):18-25.

C.A. Hofman, C. Warinner.

A great deal has changed in the field of ancient DNA (aDNA) over the past decade. High quality high-throughput sequencing (HTS) first became commercially available on a wide scale in the early 2010s, and since then, the application of this technology to archaeological questions has revolutionized our understanding of the past— upending previous narratives of human ancestry (Meyer et al. 2012; Prüfer et al. 2014), migration (Allentoft et al. 2015; Haak et al. 2015; Olalde et al. 2018; Posth et al. 2018), domestication (Daly et al. 2018; Gaunitz et al. 2018; Ní Leathlobhair et al. 2018), historical ecology (Star et al. 2017; Thomson et al. 2014), historical epidemics (Bos et al. 2014; Vågene et al. 2018), and the microbiome (Warinner et al. 2014). Because so much has changed so rapidly, it can be difficult to stay up to date on the latest techniques and terminology. Here we provide a brief guide to the basics of aDNA and explain some of the most important recent changes and new possibilities in the field of paleogenomics. To help the reader navigate the increasingly complex and jargon-laden methods sections typical of paleogenomics articles, we provide a list of commonly used DNA analysis tools, along with descriptions and links, at the end of this article (Box 1). Finally, for those looking to integrate paleogenomics approaches into their own research, we provide information on the costs and infrastructure required and offer advice on how to set up a successful collaboration with an aDNA laboratory.

“Data integration for prediction of weight loss in dietary cross-over studies.” Scientific Reports 76097 (2020). DOI: 10.1038/s41598-020-76097-z.

R.L. Nielsen, M. Helenius, S. Garcia, H.M. Roager, D. Aytan, L.B.S. Hansen, M.V. Lind, J. Vogt, M. Dalgaard, M.I. Dahl, C.B. Jensen, R. Muktupavela, C. Warinner, V. Appel, R. Gøbel, H. Vestergaard, H. Torben, K. Kristiansen, S.B. Pedersen, T.N. Petersen, L. Lauritzen, T.R. Licht, O. Pedersen, R. Gupta.

“Medieval women's early involvement in manuscript production suggested by lapis lazuli identification in dental calculus.” See above, MHAAM.

Initiative for the Science of the Human Past at Harvard

Bringing together scientists and humanists

Research

For the most recent panorama, please see our 2022 highlights:

Inventing a New Discipline: SoHP and MHAAM Annual Bulletin

Archive of previous Annual Bulletins

______________________________

MHAAM Publications 2016 - 2024

2022

2021

2020

2019

2018

2017

2016

Ice Core Project Publications 2015 - 2020

2020

2019

2018

2017

2015

Select Publications about the Science of the Human Past from
SoHP Steering Committee Members - 2019-22

The Initiative for the Science of the Human Past at Harvard
sohp@fas.harvard.edu

Initiative for the Science of the Human Past at Harvard

Bringing together scientists and humanists

For the most recent panorama, please see our 2022 highlights:

Inventing a New Discipline: SoHP and MHAAM Annual Bulletin

Archive of previous Annual Bulletins

______________________________

MHAAM Publications 2016 - 2024

2022

2021

2020

2019

2018

2017

2016

Ice Core Project Publications 2015 - 2020

2020

2019

2018

2017

2015

Select Publications about the Science of the Human Past fromSoHP Steering Committee Members - 2019-22

The Initiative for the Science of the Human Past at Harvard sohp@fas.harvard.edu

Select Publications about the Science of the Human Past from
SoHP Steering Committee Members - 2019-22

The Initiative for the Science of the Human Past at Harvard
sohp@fas.harvard.edu