Steering Committee Publications

Select Publications by SoHP Steering Committee Members - 2019-22

Peter Huybers, Department of Earth and Planetary Sciences

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

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

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

Michael McCormick, Department of History

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

David Reich, Department of Genetics

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

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

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

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

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

Christina Warinner, Department of Anthropology

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

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

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

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

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

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

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

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

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

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

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

Background

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

Results

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

Conclusions

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

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

C.A. Hofman, C. Warinner.

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

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

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

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