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The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture1. The extent to which migration from continental Europe mediated these transitions is a matter of long-standing debate2–4. Here we study genome-wide ancient DNA from 460 medieval northwestern Europeans—including 278 individuals from England—alongside archaeological data, to infer contemporary population dynamics. We identify a substantial increase of continental northern European ancestry in early medieval England, which is closely related to the early medieval and present-day inhabitants of Germany and Denmark, implying large-scale substantial migration across the North Sea into Britain during the Early Middle Ages. As a result, the individuals who we analysed from eastern England derived up to 76% of their ancestry from the continental North Sea zone, albeit with substantial regional variation and heterogeneity within sites. We show that women with immigrant ancestry were more often furnished with grave goods than women with local ancestry, whereas men with weapons were as likely not to be of immigrant ancestry. A comparison with present-day Britain indicates that subsequent demographic events reduced the fraction of continental northern European ancestry while introducing further ancestry components into the English gene pool, including substantial southwestern European ancestry most closely related to that seen in Iron Age France

Due to postmortem DNA degradation, most ancient genomes sequenced to date have low depth of coverage, preventing the true underlying genotypes from being recovered. Genotype imputation has been put forward to improve genotyping accuracy for low-coverage genomes. However, it is unknown to what extent imputation of ancient genomes produces accurate genotypes and whether imputation introduces bias to downstream analyses. To address these questions, we downsampled 43 ancient genomes, 42 of which are high-coverage (above 10x) and three constitute a trio (mother, father and son), from different times and continents to simulate data with coverage in the range of 0.1x-2.0x and imputed these using state-of-the-art methods and reference panels. We assessed imputation accuracy across ancestries and depths of coverage. We found that ancient and modern DNA imputation accuracies were comparable. We imputed most of the 42 high-coverage genomes downsampled to 1x with low error rates (below 5%) and estimated higher error rates for African genomes, which are underrepresented in the reference panel. We used the ancient trio data to validate imputation and phasing results using an orthogonal approach based on Mendel’s rules of inheritance. This resulted in imputation and switch error rates of 1.9% and 2.0%, respectively, for 1x genomes. We further compared the results of downstream analyses between imputed and high-coverage genomes, notably principal component analysis (PCA), genetic clustering, and runs of homozygosity (ROH). For these three approaches, we observed similar results between imputed and high-coverage genomes using depths of coverage of at least 0.5x, except for African genomes, for which the decreased imputation accuracy impacted ROH estimates. Altogether, these results suggest that, for most populations and depths of coverage as low as 0.5x, imputation is a reliable method with potential to expand and improve ancient DNA studies.

The Caribbean was one of the last regions of the Americas to be settled by humans, but where they came from and how and when they reached the islands remain unclear. We generated genome-wide data for 93 ancient Caribbean islanders dating between 3200 and 400 calibrated years before the present and found evidence of at least three separate dispersals into the region, including two early dispersals into the Western Caribbean, one of which seems connected to radiation events in North America. This was followed by a later expansion from South America. We also detected genetic differences between the early settlers and the newcomers from South America, with almost no evidence of admixture. Our results add to our understanding of the initial peopling of the Caribbean and the movements of Archaic Age peoples in the Americas., The research was funded by the Max Planck Society and the European Research Council under the 7th Framework Program (grant agreement no. 319209, ERC Synergy Project NEXUS1492). H.S. was supported by the HERA (Humanities in the European Research Area) Joint Research Program “Uses of the Past” (CitiGen) and the European Union’s Horizon 2020 research and innovation program under grant agreement no. 649307. W.J.P. and M.A.N.-C. were supported by the National Science Foundation (BCS-0612727 and BCS1622479). C.L.-F. was supported by a grant from the Ministry of Science, Innovation and Universities (PGC2018-0955931-B-100, AEI/FEDER, UE). M.R. was supported by the Social Sciences and Humanities Research Council of Canada (435-2016-0529). M.R., Y.C.d.A., U.M.G.H., and S.T.H.G. were supported by the Social Sciences and Humanities Research Council of Canada (standard research grant SSHRC ‐ 410‐2011‐1179 and SSHRC postdoctoral fellowship ‐ 756‐2016‐0180) and several University of Winnipeg internal grants (Major grant 2017, 2018; Partnership Development grant 2017, 2018; and Discretionary grant 2017, 2018).

Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%–40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th–19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics., We acknowledge the following for funding our research: Carlsbergfondet grants CF14-0995 and Marie Skłodowska-Curie Actions grant 655732 (to S.G.), Danish National Research Foundation grant DNRF94, Lundbeckfonden grant R52-5062, Carlsbergfondet grant CF18-1109 and ERC Consolidator grant (681396-ExtinctionGenomics) (to M.T.P.G.), and MEDHEAL600 funded by the Research Council of Norway (FRIHUMSAM) project number is 262424. G.L.C. is supported by the Science Foundation Ireland under grant number 16/RC/3948. T.M.B. is supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 864203).

Objectives: To identify and characterize anthropogenic lead sources on a 17th/18th century Barbadian plantation and to test if lead isotope analyses can be used to identify the geographic origins of first‐generation African captives. Materials and Methods: We carried out lead (Pb) isotope analyses on dental enamel samples from 24 individuals from the Newton Plantation Cemetery in Barbados, which had previously been analyzed for strontium (Sr) and oxygen (O) isotope composition (Schroeder et al., American Journal of Physical Anthropology, 2009, 139:547–557) and Pb concentrations (Schroeder et al., American Journal of Physical Anthropology, 2013, 150:203–209. Results: We are able to identify British Pb sources, and more specifically Bristol/Mendips Pb, as the most likely source of anthropogenic Pb on the plantation, highlighting the impact of the British Atlantic economy on the lives of enslaved peoples in Barbados during the period of plantation slavery. Furthermore, we find that there is only one clear outlier among seven individuals who had previously been identified as African‐born based on their enamel Sr isotope composition (Schroeder et al., American Journal of Physical Anthropology, 2009, 139:547–557). All other individuals present a very homogenous Pb isotope composition, which overlaps with that of British Pb sources. Conclusion: Our results indicate that while Pb isotope analyses can help identify and further characterize the sources of anthropogenic Pb in plantation settings, they might not be suited for identifying the origins of African‐born individuals in diasporic contexts.

Significance We sequenced the genomes of 15 skeletons from a 5,000-y-old mass grave in Poland associated with the Globular Amphora culture. All individuals had been brutally killed by blows to the head, but buried with great care. Genome-wide analyses demonstrate that this was a large extended family and that the people who buried them knew them well: mothers are buried with their children, and siblings next to each other. From a population genetic viewpoint, the individuals are clearly distinct from neighboring Corded Ware groups because of their lack of steppe-related ancestry. Although the reason for the massacre is unknown, it is possible that it was connected with the expansion of Corded Ware groups, which may have resulted in violent conflict., The third millennium BCE was a period of major cultural and demographic changes in Europe that signaled the beginning of the Bronze Age. People from the Pontic steppe expanded westward, leading to the formation of the Corded Ware complex and transforming the genetic landscape of Europe. At the time, the Globular Amphora culture (3300–2700 BCE) existed over large parts of Central and Eastern Europe, but little is known about their interaction with neighboring Corded Ware groups and steppe societies. Here we present a detailed study of a Late Neolithic mass grave from southern Poland belonging to the Globular Amphora culture and containing the remains of 15 men, women, and children, all killed by blows to the head. We sequenced their genomes to between 1.1- and 3.9-fold coverage and performed kinship analyses that demonstrate that the individuals belonged to a large extended family. The bodies had been carefully laid out according to kin relationships by someone who evidently knew the deceased. From a population genetic viewpoint, the people from Koszyce are clearly distinct from neighboring Corded Ware groups because of their lack of steppe-related ancestry. Although the reason for the massacre is unknown, it is possible that it was connected with the expansion of Corded Ware groups, which may have resulted in competition for resources and violent conflict. Together with the archaeological evidence, these analyses provide an unprecedented level of insight into the kinship structure and social behavior of a Late Neolithic community.

Archaeologists often struggle with the challenge of linking historic-period artifact assemblages with specific communities. In particular, small home sites discovered on historic plantations are often difficult to identify as an African American or white tenant house since the material culture appears similar. The discipline also struggles with how to identify the expression of specific West African cultures in their archaeological assemblages. Here, we discuss how DNA was successfully extracted and analyzed from a clay tobacco pipe stem collected from an African American slave quarter in Maryland, USA, and what this information can and cannot reveal about the people present at the site. We successfully identified DNA from a woman, and genome-wide analyses revealed she was closely related to Mende living in present-day Sierra Leone, West Africa. The ability to recover genetic data from personal artifacts now provides archaeologists a viable tool to address questions about communities and ancestral origins. Furthermore, these findings hold the potential to connect living descendants with their ancestors’ homes.

Objectives Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. Materials and methods Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in-solution hybridization capture and high-throughput sequencing. Results Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four-fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on-target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum-level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off-target sequences in human genome-enriched calculus libraries may still be useful for oral microbiome reconstruction. Discussion While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples. H2020 European Research Council, Grant/Award Number: 319209; Horizon 2020 Framework Programme, Grant/Award Number: 649307DK-TAF 5662; National Science Foundation, Grant/Award Number: BCS 1516633, BCS-1528698

Objective This paper will review how different methods employed to study bone loss in the past were used to explore different questions and aspects of bone loss, how methodology has changed over time, and how these different approaches have informed our understanding of bone loss in the past. Materials and methods A review and discussion is conducted on research protocols and results of 84 paleopathology publications on bone loss in archaeological skeletal collections published between 1969 and 2021. Conclusions The variety in research protocols confounds accurate meta-analysis of previously published research; however, more recent publications incorporate a combination of bone mass and bone quality based methods. Biased sample selection has resulted in a predominance of European and Medieval publications, limiting more general observations on bone loss in the past. Collection of dietary or paleopathological covariables is underemployed in the effort to interpret bone loss patterns. Significance Paleopathology publications have demonstrated differences in bone loss between distinct archaeological populations, between sex and age groups, and have suggested factors underlying observed differences. However, a lack of a gold standard has encouraged the use of a wide range of methods. Understanding how this array of methods effects results is crucial in contextualizing our knowledge of bone loss in the past. Limitations The development of a research protocol is also influenced by available expertise, available equipment, restrictions imposed by the curator, and site-specific taphonomic aspects. These factors will likely continue to cause (minor) biases even if a best practice can be established. Suggestions for future research Greater effort to develop uniform terminology and operational definitions of osteoporosis in skeletal remains, as well as the expansion of time scale and geographical areas studied. The Next-Generation Sequencing revolution has also opened up the possibility of ancient DNA analyses to study genetic predisposition to bone loss in the past.

The extensive peat bogs of Southern Scandinavia have yielded rich Mesolithic archaeological assemblages, with one of the most iconic artefacts being the bone point. Although great in number they remain understudied. Here we present a combined investigation of the typology, protein-based species composition, and absolute chronology of Maglemosian bone points. The majority of the bone points are made from cervids and bovines. However, changes both in species composition and barb morphology can be directly linked to a paucity of finds lasting nearly 600 years in Southern Scandinavia around 10,300 cal BP. We hypothesize that this hiatus was climate-driven and forced hunter-gatherers to abandon the lakes. Furthermore, the marked change in bone points coincides with a change in lithic technology. We, therefore, propose that the Maglemose culture in Southern Scandinavia is fundamentally divided into an Early Complex and a Late Complex. Results - Bone points - Radiocarbon dating - Protein analysis Discussion Methods - Materials - Radiocarbon dating - Proteomics

Humans have a notable capacity to withstand the ravages of infectious diseases. Smallpox killed millions of people but drove Jenner's invention of vaccination, which eventually led to the annihilation of this virus, declared in 1980. To investigate the history of smallpox, Mühlemann et al. obtained high-throughput shotgun sequencing data from 1867 human remains ranging from >31,000 to 150 years ago (see the Perspective by Alcamí). Thirteen positive samples emerged, 11 of which were northern European Viking Age people (6th to 7th century CE). Although the sequences were patchy and incomplete, four could be used to infer a phylogenetic tree. This showed distinct Viking Age lineages with multiple gene inactivations. The analysis pushes back the date of the earliest variola infection in humans by ∼1000 years and reveals the existence of a previously unknown virus clade. This is the author’s version of the work. It is posted here by permission of the AAAS for personal use, not for redistribution.

In the field of human history, ancient DNA has provided answers to long-standing debates about major movements of people and has begun to inform on other important facets of the human experience. The field is now moving from mostly large-scale supraregional studies to a more local perspective, shedding light on socioeconomic processes, inheritance rules, marriage practices and technological diffusion. In this Review, we summarize recent studies showcasing these types of insights, focusing on methods used to infer sociocultural aspects of human behaviour. This approach often involves working across disciplines — such as anthropology, archaeology, linguistics and genetics — that have until recently evolved in separation. Multidisciplinary dialogue is important for an integrated reconstruction of human history, which can yield extraordinary insights about past societies, reproductive behaviours and even lifestyle habits that would not be possible to obtain otherwise., F.R. was funded by a Villum Fonden Young Investigator award (project no. 00025300). H.S. was supported by the Humanities in the European Research Area (HERA) Joint Research Programme “Uses of the Past” (CitiGen) and the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 649307. M.V.L. was supported by the European Research Council, funded under the European Union’s Seventh Framework Programme (FP/20072013; European Research Council grant agreement no. 313716). C.L.-F. was supported by a grant from Obra Social “La Caixa” (GRC2017-SGR880, Generalitat de Catalunya) and a grant from FEDER-MCIU-AEI (PGC2018-095931-B-100) of Spain.

The rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable samples. Here we present a complete ancient human genome and oral microbiome sequenced from a 5700 year-old piece of chewed birch pitch from Denmark. We sequence the human genome to an average depth of 2.3× and find that the individual who chewed the pitch was female and that she was genetically more closely related to western hunter-gatherers from mainland Europe than hunter-gatherers from central Scandinavia. We also find that she likely had dark skin, dark brown hair and blue eyes. In addition, we identify DNA fragments from several bacterial and viral taxa, including Epstein-Barr virus, as well as animal and plant DNA, which may have derived from a recent meal. The results highlight the potential of chewed birch pitch as a source of ancient DNA., Birch pitch is thought to have been used in prehistoric times as hafting material or antiseptic and tooth imprints suggest that it was chewed. Here, the authors report a 5,700 year-old piece of chewed birch pitch from Denmark from which they successfully recovered a complete ancient human genome and oral microbiome DNA.

Excavations in 2010 on the Black Sea island of Sveti Ivan (Bulgaria) revealed the remains of a miniature marble sarcophagus containing human and animal remains, along with an inscribed tufa ossuary, beneath a 4th to 5th-century church floor. We found that the tufa ossuary had strong links with Cappadocian rhyolite tuff. The inscriptions on its surface suggest links to John the Baptist since they refer to him by name and contain a reference to his nativity date of June 24. The ancient Greek text also mentions him in the genitive case, i.e. ‘of Saint John’. Here, we review the historical evidence pertaining to the relics and conclude that they most likely reached Sveti Ivan via Constantinople during the 4–5th century CE. To shed more light on the relics, we sampled three of the remains for radiocarbon dating and ancient DNA analysis. Radiocarbon dating of one of the bones (a metacarpal) yielded a first century AD date (5–75 cal AD, 68.2% probability). Ancient DNA analysis of this bone, as well as a rib fragment and a tooth, using shotgun sequencing yielded very little human DNA, ranging between 0 and 0.9% of sequenced reads. However, the DNA did not show any of the post-mortem damage patterns that are typical for ancient DNA. We conclude that the sequences we obtained are most likely the result of modern contamination.

In molecular anthropology, DNA is regarded as a kind of biological "archive" that can provide unprecedented insights into human histories. More recently, genetic analysis has been used to explore the origins of African-descendant populations in the Americas. This idea has also been adopted by a burgeoning DNA ancestry testing industry that portrays these technologies as a means of restoring ethnic links effaced by slavery. Despite the popularity of these tests, critics have raised persistent scientific and ethical concerns about how far genomic data can, or should, be used to reconstruct social identities. In this paper, we take stock of these developments, assessing the combined influence of scientists, businesses, and members of the public in defining the scope of genetics for restoring ethnic links between African and African American populations. Drawing on perspectives from social and molecular anthropology, we examine the challenges of translating genetic findings into historically significant terms without reifying the correspondence between genetic and social identities, and we explore how personalized DNA ancestry results are being negotiated and mobilized by test takers "on the ground." Finally, we consider the responsibilities of anthropologists in addressing ongoing biocolonial tendencies and power disparities in the production of genetic ancestry.

This study focuses on the origins and diet of the seafarers on Columbus’s second voyage, individuals whose mortal remains were buried in the churchyard of the settlement of La Isabela. This was the...

Fil: Drube, Hilton. Universidad Nacional de Catamarca. Facultad de Ciencias Exactas y Naturales; Argentina. Universidad Nacional de Santiago del Estero; Argentina

An insufficient number of archaeological surveys has been carried out to date on Harappan Civilization cemeteries. One case in point is the necropolis at Rakhigarhi site (Haryana, India), one of the largest cities of the Harappan Civilization, where most burials within the cemetery remained uninvestigated. Over the course of the past three seasons (2013 to 2016), we therefore conducted excavations in an attempt to remedy this data shortfall. In brief, we found different kinds of graves co-existing within the Rakhigarhi cemetery in varying proportions. Primary interment was most common, followed by the use of secondary, symbolic, and unused (empty) graves. Within the first category, the atypical burials appear to have been elaborately prepared. Prone-positioned internments also attracted our attention. Since those individuals are not likely to have been social deviants, it is necessary to reconsider our pre-conceptions about such prone-position burials in archaeology, at least in the context of the Harappan Civilization. The data presented in this report, albeit insufficient to provide a complete understanding of Harappan Civilization cemeteries, nevertheless does present new and significant information on the mortuary practices and anthropological features at that time. Indeed, the range of different kinds of burials at the Rakhigarhi cemetery do appear indicative of the differences in mortuary rituals seen within Harappan societies, therefore providing a vivid glimpse of how these people respected their dead.

DNA extraction and library preparation are crucial steps in any ancient DNA study. Although palaeogenomic researchers are facing a growing choice of DNA extraction and sequencing library preparation methods, how their performance varies with DNA preservation remains unclear. To help elucidate this question, we compared the performance of two common DNA extraction and Illumina library preparation methods on a set of archaeological human samples, considered to contain ancient DNA of intermediate to good preservation (5–50% endogenous DNA). Results indicate that while the levels of contamination and endogenous DNA recovered are comparable for both silica-in-solution and silica-column based extractions, the ability of the former to accommodate larger starting quantities of sample material confers notable benefits with regards to library complexity, and furthermore seems to aid with the recovery of shorter endogenous DNA molecules. While our observations gained from comparing the single-stranded with double-stranded DNA library construction methods largely replicate earlier observations, the combination of our data with previously published datasets demonstrate that the benefits gained using single-stranded methods are inversely proportional to the endogenous DNA content in the ancient sample. © 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Between the early 16th and late 19th centuries, an estimated 12 million Africans were transported to the Americas as part of the transatlantic slave trade. Following Britain’s abolition of slave trade in 1807, the Royal Navy patrolled the Atlantic and intercepted slave ships that continued to operate. During this period, the island of St Helena in the middle of the South Atlantic served as a depot for “liberated” Africans. Between 1840 and 1867, approximately 27,000 Africans were disembarked on the island. To investigate their origins, we generated genome-wide ancient DNA data for 20 individuals recovered from St Helena. The genetic data indicate that they came from West Central Africa, possibly the area of present-day Gabon and Angola. The data further suggest that they did not belong to a single population, confirming historical reports of cultural heterogeneity among the island’s African community. Our results shed new light on the origins of enslaved Africans during the final stages of the slave trade and illustrate how genetic data can be used to complement and validate existing historical sources.

Ancient DNA samples generally contain a mixture of both endogenous and exogenous (contaminant) DNA. The authentic endogenous DNA content varies widely between samples and substrates but usually constitutes only a small fraction of the total DNA, while the remainder comprises contamination deriving from bacteria, fungi, and other microorganisms and in some cases also modern human DNA. Recently, several protocols have been developed to improve access to the endogenous DNA fraction by decreasing the exogenous fraction prior to extraction. The most common of these involve pretreatment with single or multiple washes with weak sodium phosphate or sodium hypochlorite (bleach) solutions, as described in Chapter 2 . Here, we present an alternative, less aggressive pretreatment protocol that uses a brief predigestion step in an EDTA-based lysis buffer to increase the endogenous fraction prior to extraction.

Being at the Western fringe of Europe, Iberia had a peculiar prehistory and a complex pattern of Neolithization. A few studies, all based on modern popu- lations, reported the presence of DNA of likely African origin in this region, generally concluding it was the result of recent gene flow, probably during the Islamic period. Here, we provide evidence of much older gene flow from Africa to Iberia by sequencing whole genomes from four human remains from Northern Portugal and Southern Spain dated around 4000 years BP (from the Middle Neolithic to the Bronze Age). We found one of them to carry an unequi- vocal Sub-Saharan mitogenome of most probably West or West-Central African origin, never reported before in prehistoric remains outside Africa. Our analyses of ancient nuclear genomes show small but significant levels of Sub-Saharan African affinity in several ancient Iberian samples, which indicates that what we detected was not an occasional individual phenomenon, but an admixture event recognizable at the population level. We interpret this result as evidence of an early migration process from Africa into the Iberian Peninsula through a Western route, possibly across the Strait of Gibraltar., his research was supported by a Marie Sklodowska-CurieIndividual Fellowship to G.G.F (NeoGenHeritage, grant no. 655478); by the European Research Council (ERC) Advanced grant 295733-LanGeLin and the consolidator grant 310763 - GeneFlow toG.B. and M.H., respectively; by the research project BIOGEOS (CGL2014-57209-P) of the Spanish MINECO to A.G.; and by theresearch project HAR2010-21786/HIST of the Spanish MINECOand Xunta de Galicia to R.F., M.V., A.L.-H. and X.P.R.-A. A.M. was supported by the European Research Council Consolidator grant 647787—LocalAdaptation

Ancient DNA samples generally contain a mixture of both endogenous and exogenous (contaminant) DNA. The authentic endogenous DNA content varies widely between samples and substrates but usually constitutes only a small fraction of the total DNA, while the remainder comprises contamination deriving from bacteria, fungi, and other microorganisms and in some cases also modern human DNA. Recently, several protocols have been developed to improve access to the endogenous DNA fraction by decreasing the exogenous fraction prior to extraction. The most common of these involve pretreatment with single or multiple washes with weak sodium phosphate or sodium hypochlorite (bleach) solutions, as described in Chapter 2 . Here, we present an alternative, less aggressive pretreatment protocol that uses a brief predigestion step in an EDTA-based lysis buffer to increase the endogenous fraction prior to extraction.

We present a complete ancient human genome and oral microbiome sequenced from a piece of resinous "chewing gum" recovered from a Stone Age site on the island of Lolland, Denmark, and directly dated to 5,858-5,661 cal. BP (GrM-13305; 5,007+/-11). We sequenced the genome to an average depth-of-coverage of 2.3x and find that the individual who chewed the resin was female and genetically more closely related to western hunter-gatherers from mainland Europe, than hunter-gatherers from central Scandinavia. We use imputed genotypes to predict physical characteristics and find that she had dark skin and hair, and blue eyes. Lastly, we also recovered microbial DNA that is characteristic of an oral microbiome and faunal reads that likely associate with diet. The results highlight the potential for this type of sample material as a new source of ancient human and microbial DNA.

We present the analysis of an osseous finger ring from a predominantly early Neolithic context in Denmark. To characterize the artefact and identify the raw material used for its manufacture, we performed micro-computed tomography scanning, zooarchaeology by mass spectrometry (ZooMS) peptide mass fingerprinting, as well as protein sequencing by liquid chromatography tandem mass spectrometry (LC-MS/MS). We conclude that the ring was made from long bone or antler due to the presence of osteons (Haversian canals). Subsequent ZooMS analysis of collagen I and II indicated that it was made fromAlces alcesorCervus elaphusmaterial. We then used LC-MS/MS analysis to refine our species identification, confirming that the ring was made fromCervus elaphus, and to examine the rest of the proteome. This study demonstrates the potential of ancient proteomics for species identification of prehistoric artefacts made from osseous material.

Grey wolves (Canis lupus) are one of the few large terrestrial carnivores that maintained a wide geographic distribution across the Northern Hemisphere throughout the Pleistocene and Holocene. Recent genetic studies have suggested that, despite this continuous presence, major demographic changes occurred in wolf populations between the late Pleistocene and early Holocene, and that extant wolves trace their ancestry to a single late Pleistocene population. Both the geographic origin of this ancestral population and how it became widespread remain a mystery. Here we analyzed a large dataset of novel modern and ancient mitochondrial wolf genomes, spanning the last 50,000 years, using a spatially and temporally explicit modeling framework to show that contemporary wolf populations across the globe trace their ancestry to an expansion from Beringia at the end of the Last Glacial Maximum - a process most likely driven by the significant ecological changes that occurred across the Northern Hemisphere during this period. This study provides direct ancient genetic evidence that long-range migration has played an important role in the population history of a large carnivore and provides an insight into how wolves survived the wave of megafaunal extinctions at the end of the last glaciation. Moreover, because late Pleistocene grey wolves were the likely source from which all modern dogs trace their origins, the demographic history described in this study has fundamental implications for understanding the geographical origin of the dog.

Significance Ancient DNA has revolutionized the field of archaeology, but in the Caribbean and other tropical regions of the world, the work has been hampered by poor DNA preservation. We present an ancient human genome from the Caribbean and use it to shed light on the early peopling of the islands. We demonstrate that the ancestors of the so-called “Taino” who inhabited large parts of the Caribbean in pre-Columbian times originated in northern South America, and we find evidence that they had a comparatively large effective population size. We also show that the native components in some modern Caribbean genomes are closely related to the ancient Taino, suggesting that indigenous ancestry in the region has survived through the present day., The Caribbean was one of the last parts of the Americas to be settled by humans, but how and when the islands were first occupied remains a matter of debate. Ancient DNA can help answering these questions, but the work has been hampered by poor DNA preservation. We report the genome sequence of a 1,000-year-old Lucayan Taino individual recovered from the site of Preacher’s Cave in the Bahamas. We sequenced her genome to 12.4-fold coverage and show that she is genetically most closely related to present-day Arawakan speakers from northern South America, suggesting that the ancestors of the Lucayans originated there. Further, we find no evidence for recent inbreeding or isolation in the ancient genome, suggesting that the Lucayans had a relatively large effective population size. Finally, we show that the native American components in some present-day Caribbean genomes are closely related to the ancient Taino, demonstrating an element of continuity between precontact populations and present-day Latino populations in the Caribbean.

Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is microbial and originates from the oral microbiome; however, a small but consistent proportion of DNA (mean 0.08 ± 0.08%, range 0.007–0.47%) derives from the host genome. Host DNA content within dentin is variable (mean 13.70 ± 18.62%, range 0.003–70.14%), and for a subset of dentin samples (15.21%), oral bacteria contribute > 20% of total DNA. Human DNA in dental calculus is highly fragmented, and is consistently shorter than both microbial DNA in dental calculus and human DNA in paired dentin samples. Finally, we find that microbial DNA fragmentation patterns are associated with guanine-cytosine (GC) content, but not aspects of cellular structure.

Background As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach—in-solution capture-enrichment—retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC + YCC) versus non-enriched (pre-capture) libraries. Results The six samples show different levels of initial endogenous content, with very low (

Background As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach—in-solution capture-enrichment—retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC + YCC) versus non-enriched (pre-capture) libraries. Results The six samples show different levels of initial endogenous content, with very low (

The transatlantic slave trade was the largest forced migration in world history. However, the origins of the enslaved Africans and their admixture dynamics remain unclear. To investigate the demographic history of African-descendant Marron populations, we generated genome-wide data (4.3 million markers) from 107 individuals from three African-descendant populations in South America, as well as 124 individuals from six west African populations. Throughout the Americas, thousands of enslaved Africans managed to escape captivity and establish lasting communities, such as the Noir Marron. We find that this population has the highest proportion of African ancestry (∼98%) of any African-descendant population analyzed to date, presumably because of centuries of genetic isolation. By contrast, African-descendant populations in Brazil and Colombia harbor substantially more European and Native American ancestry as a result of their complex admixture histories. Using ancestry tract-length analysis, we detect different dates for the European admixture events in the African-Colombian (1749 CE; confidence interval [CI]: 1737-1764) and African-Brazilian (1796 CE; CI: 1789-1804) populations in our dataset, consistent with the historically attested earlier influx of Africans into Colombia. Furthermore, we find evidence for sex-specific admixture patterns, resulting from predominantly European paternal gene flow. Finally, we detect strong genetic links between the African-descendant populations and specific source populations in Africa on the basis of haplotype sharing patterns. Although the Noir Marron and African-Colombians show stronger affinities with African populations from the Bight of Benin and the Gold Coast, the African-Brazilian population from Rio de Janeiro has greater genetic affinity with Bantu-speaking populations from the Bight of Biafra and west central Africa.

This thematic collection of articles presents research that extends archaeological processes of investigation from the tangible to the intangible. These articles examine the ways in which contested landscapes, both physical and virtual, animate trans-Atlantic connections. Such terrains and places engage fraught memories of slavery. Each article attempts to navigate the residual pain of these histories in public spaces, while reflecting on how agencies and voices are negotiated.

Between 1500 and 1850, more than 12 million enslaved Africans were transported to the New World. The vast majority were shipped from West and West-Central Africa, but their precise origins are largely unknown. We used genome-wide ancient DNA analyses to investigate the genetic origins of three enslaved Africans whose remains were recovered on the Caribbean island of Saint Martin. We trace their origins to distinct subcontinental source populations within Africa, including Bantu-speaking groups from northern Cameroon and non-Bantu speakers living in present-day Nigeria and Ghana. To our knowledge, these findings provide the first direct evidence for the ethnic origins of enslaved Africans, at a time for which historical records are scarce, and demonstrate that genomic data provide another type of record that can shed new light on long-standing historical questions.

© 2015 Macmillan Publishers Limited. All rights reserved.The Bronze Age of Eurasia (around 3000-1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

Lead was ubiquitous on Caribbean sugar plantations, where it was used extensively in the production of sugar and rum. Previous studies suggest that skeletal lead contents can be used to identify African-born individuals (as opposed to Creoles) among slave burials found in the New World. To test this hypothesis, we measured lead concentrations in enamel samples from 26 individuals from the Newton Plantation cemetery in Barbados, which was in use from around 1660 to 1820, and compared the results with enamel (87) Sr/(86) Sr measurements that had been previously obtained for the same population. Results show a clear association between low (i.e., below 1 ppm) enamel lead concentrations and higher enamel (87) Sr/(86) Sr ratios which have previously been interpreted as being indicative of African birth, suggesting that individuals with low enamel lead levels were indeed born in Africa as opposed to the New World. Based on these results, we propose that enamel lead measurements provide an effective and inexpensive way to determine African birth from skeletal remains. Furthermore, the lead measurements can provide useful insights into the health status and childhood environment of enslaved Africans during the colonial period.

The question of the ultimate origin of African slaves is one of the most perplexing in the history of trans-Atlantic slavery. Here we present the results of a small, preliminary isotopic study that was conducted in order to determine the geographical origin of 25 enslaved Africans who were buried at the Newton plantation, Barbados, sometime between the late 17th and early 19th century. In order to gain a more nuanced understanding of the slaves' origin, we used a combination of carbon, nitrogen, oxygen, and strontium isotope analyses. Carbon and nitrogen isotope ratios were determined in bone and dentinal collagen; oxygen and strontium isotopes were measured in tooth enamel. Results suggest that the majority of individuals were born on the island, if not the estate itself. Seven individuals, however, yielded enamel oxygen and strontium ratios that are inconsistent with a Barbadian origin, which strongly suggests that we are dealing with first-generation captives who were brought to the island with the slave trade. This idea is also supported by the fact that their carbon and nitrogen stable isotope values differ markedly between their teeth and bones. These intra-skeletal shifts reflect major dietary changes that probably coincided with their enslavement and forced migration to Barbados. While it is impossible to determine their exact origins, the results clearly demonstrate that the slaves did not all grow up in the same part of Africa. Instead, the data seem to suggest that they originated from at least three different areas, possibly including the Gold Coast and the Senegambia.

Scientific Reports 5: Article number: 16498;10.1038/srep16498 Published online: November132015; Updated: June022016 The Acknowledgements section in this Article is incomplete. “This work was supported by the European Research Council (FP7 ERC-Synergy Nexus1492 project grant number 319209) and the US National Institutes of Health (R01 {"type":"entrez-nucleotide","attrs":{"text":"GM089886","term_id":"221304226","term_text":"GM089886"}}GM089886), the BBVA Foundation (I Ayudas a Investigadores, Innovadores y Creadores), the Generalitat Valenciana (VALi+d APOSTD/2014/123 and GV/2015/060), the European Union (EUROTAST FP7 PEOPLE-2010 MC ITN, Braudel-IFER-FMSH; FP7/2007-2013 - MSCA-COFUND, n°245743), and the Centre for Chronic Diseases and Disorders (C2D2) Research Priming Fund grant to CFS. C2D2 is part-funded by the Wellcome Trust (ref: 097829). The authors thank Joaquin Lomba for his assistance with obtaining samples; Amanda Henry for providing helpful comments on the manuscript; Jacqueline Eng for providing osteological data for the Samdzong sample; Maria Haber and Azucena Aviles for providing osteological data for the Camino del Molino sample; Malin Holst for providing osteological data for the Tickhill samples; and also Matthias Garn & Partner, the Parish Church Council for St. Mary’s Church, Tickhill, South Yorkshire, and Wiles & Maguire, Ltd., for assistance with sample provisioning.” should read: “This work was supported by the European Research Council (FP7 ERC-Synergy Nexus1492 project grant number 319209), the US National Science Foundation (BCS-1516633) and the US National Institutes of Health (R01 {"type":"entrez-nucleotide","attrs":{"text":"GM089886","term_id":"221304226","term_text":"GM089886"}}GM089886), the BBVA Foundation (I Ayudas a Investigadores, Innovadores y Creadores), the Generalitat Valenciana (VALi+d APOSTD/2014/123 and GV/2015/060), the European Union (EUROTAST FP7 PEOPLE-2010 MC ITN, Braudel-IFER-FMSH; FP7/2007-2013 - MSCA-COFUND, n°245743), and the Centre for Chronic Diseases and Disorders (C2D2) Research Priming Fund grant to CFS. C2D2 is part-funded by the Wellcome Trust (ref: 097829). The authors thank Joaquin Lomba for his assistance with obtaining samples; Amanda Henry for providing helpful comments on the manuscript; Jacqueline Eng for providing osteological data for the Samdzong sample; Maria Haber and Azucena Aviles for providing osteological data for the Camino del Molino sample; Malin Holst for providing osteological data for the Tickhill samples; and also Matthias Garn & Partner, the Parish Church Council for St. Mary’s Church, Tickhill, South Yorkshire, and Wiles & Maguire, Ltd., for assistance with sample provisioning.”

Dental modification was widely practiced in sub-Saharan Africa as a form of cultural expression, and during the era of the transatlantic slave trade, it was regularly identified in enslaved Africans who were transported to the Americas. Here, we report three new cases of African types of dental modification from the Caribbean island of Saint Martin that were recently encountered during construction activities in the Zoutsteeg area of Philipsburg, the capital of the Dutch half of the island. The artifacts associated with the burials indicate that they date to the late 17th century, prior to the foundation of the town of Philipsburg in 1735. The dental evidence further suggests that the three individuals were born in Africa, as opposed to the Americas. This could be confirmed by tooth enamel strontium isotope measurements which yielded values that are inconsistent with an origin in the Caribbean but consistent with an origin in Africa. Unfortunately, neither the dental patterns nor the strontium isotope values allow us to determine their specific origins in Africa. However, both the methods used to modify the teeth and the isotope ratios suggest that the ‘Zoutsteeg Three’ originated in different parts of Africa. Copyright © 2012 John Wiley & Sons, Ltd.

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.

This study uses stable isotope analyses (δ13C and δ15N) of human bone collagen to reconstruct the diet of three Romano-British (first to early fifth century AD) populations from Gloucestershire in South West England. Gloucestershire was an important part of Roman Britain with two major administrative centres at Gloucester (Glevum) and Cirencester (Corinium) and numerous smaller settlements and farmsteads. To investigate potential dietary differences between the rural and urban populations of Roman Gloucestershire, we compared human bone collagen stable isotope values from 32 individuals from urban Gloucester with those of 46 individuals from two rural cemeteries at Horcott Quarry and Cotswold Community, respectively. Seven individuals from urban Gloucester were buried in a mass grave; all others were buried in single inhumations. Results show small but significant differences in stable isotope ratios between the urban and rural populations which indicate that the urban population might have consumed slightly more marine and/or freshwater resources than the people living in the rural communities. We interpret this difference as a direct reflection of Rome’s influence on Gloucester’s population and the town’s economic status. Subtle differences in stable isotope ratios were also observed at the site level, as burial practice does correlate with diet in some cases. Overall, the results from this study demonstrate that diet, as reconstructed through stable isotope analysis, is a very sensitive, if settlement-specific, indicator of social differentiation and culture change.

Summary Understanding the peopling of the Americas remains an important and challenging question. Here, we present 14C dates, and morphological, isotopic and genomic sequence data from two human skulls from the state of Minas Gerais, Brazil, part of one of the indigenous groups known as 'Botocudos'. We find that their genomic ancestry is Polynesian, with no detectable Native American component. Radiocarbon analysis of the skulls shows that the individuals had died prior to the beginning of the 19th century. Our findings could either represent genomic evidence of Polynesians reaching South America during their Pacific expansion, or European-mediated transport. © 2014 Elsevier Ltd.