MHAAM Publications - 2016-2021
“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).
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 .
“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.
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.
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.
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.” 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 identified 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 identified 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 first evidence for lignite exploitation was likely connected to and at the same time enabled Late Bronze Age Aegean metal and pottery production, significantly 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 intensified 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.
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.
“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 6th 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.
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.
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.
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 2nd millennium 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.
“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.
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.
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.
“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.
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.
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.
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.
“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.
“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.
Historical Ice Core Project Publications - 2015-2021
“Alpine ice reveals the yearly political economy of the Angevin Empire, from the death of Thomas Becket to Magna Carta, c. CE 1170-1216.” Antiquity, 94.374 (2020): 473-90. https://doi.org/10.15184/aqy.2019.202.
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.
“The Impact of a Six‐Year Climate Anomaly on the ‘Spanish Flu’ Pandemic and WWI.” AGU 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.
“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.
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).
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.
“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.
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.
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.
“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
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.
“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 - 2019-20
Peter Huybers, Earth and Planetary Sciences
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, History
“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.
“Climates of history, histories of climate: from history to archaeoscience.” See above, HICP.
David Reich, 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, Anthropology/Archaeology
“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.
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.
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.
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.