Ancient Individuals Research Articles

A population history of indigenousBahamianislanders: Insights from ancientDNA

AbstractObjectivesThe Bahamas is an archipelago in the western Atlantic Ocean that stretches over 1000 km, just north of Cuba and east of the Florida Peninsula. Modern DNA studies show that contemporary Bahamians are genetic descendants of European and African ancestors, unlike Cuba, Dominican Republic, and Puerto Rico, where Indigenous descendancy is well documented. For The Bahamas little was known about the genetic ancestry of the Indigenous Lucayans (AD 700–1600) and their relationship to other Indigenous Caribbean populations. In this study, we investigated genetic diversity in Indigenous Lucayans from the Bahamas Archipelago to better understand the phylogeography of their genetic lineages, and to determine their relationship with other Indigenous Caribbean populations.Materials and methodsWe characterized genetic diversity across two uniparental markers in 31 ancient individuals from burial sites on seven Bahamian islands.ResultsWe observed significant homogeneity in Lucayan paternal lineages, with only two haplogroups (Q‐M902 and Q‐Z781) found among them. Mitochondrial lineages were more diverse, with individuals belonging to haplogroup A2, B2, C1b, and C1d1. Four were assigned to a previously unidentified C1d lineage. Of the B2 samples, 7 of 11 belonged to the rare South America/Caribbean haplogroup B2e. This haplogroup was the most prevalent in the Northwest Bahamas while C1, particularly C1d, was more prevalent in the Central and Southern Bahamas.DiscussionThese findings document a complex genetic history with an initial migration from Hispaniola beginning 1300 years ago, and possible gene flow from Cuba to Andros in late Bahamian prehistory.

Overview of the Americas' First Peopling from a Patrilineal Perspective: New Evidence from the Southern Continent.

Uniparental genetic systems are unique sex indicators and complement the study of autosomal diversity by providing landmarks of human migrations that repeatedly shaped the structure of extant populations. Our knowledge of the variation of the male-specific region of the Y chromosome in Native Americans is still rather scarce and scattered, but by merging sequence information from modern and ancient individuals, we here provide a comprehensive and updated phylogeny of the distinctive Native American branches of haplogroups C and Q. Our analyses confirm C-MPB373, C-P39, Q-Z780, Q-M848, and Q-Y4276 as the main founding haplogroups and identify traces of unsuccessful (pre-Q-F1096) or extinct (C-L1373*, Q-YP4010*) Y-chromosome lineages, indicating that haplogroup diversity of the founder populations that first entered the Americas was greater than that observed in the Indigenous component of modern populations. In addition, through a diachronic and phylogeographic dissection of newly identified Q-M848 branches, we provide the first Y-chromosome insights into the early peopling of the South American hinterland (Q-BY104773 and Q-BY15730) and on overlying inland migrations (Q-BY139813).

Genetic continuity of Indo-Iranian speakers since the Iron Age in southern Central Asia

Since prehistoric times, southern Central Asia has been at the crossroads of the movement of people, culture, and goods. Today, the Central Asian populations are divided into two cultural and linguistic groups: the Indo-Iranian and the Turko-Mongolian groups. Previous genetic studies unveiled that migrations from East Asia contributed to the spread of Turko-Mongolian populations in Central Asia and the partial replacement of the Indo-Iranian populations. However, little is known about the origin of the latters. To shed light on this, we compare the genetic data on two current-day Indo-Iranian populations — Yaghnobis and Tajiks — with genome-wide data from published ancient individuals. The present Indo-Iranian populations from Central Asia display a strong genetic continuity with Iron Age samples from Turkmenistan and Tajikistan. We model Yaghnobis as a mixture of 93% Iron Age individual from Turkmenistan and 7% from Baikal. For the Tajiks, we observe a higher Baikal ancestry and an additional admixture event with a South Asian population. Our results, therefore, suggest that in addition to a complex history, Central Asia shows a remarkable genetic continuity since the Iron Age, with only limited gene flow.

Large-scale migration into Britain during the Middle to Late Bronze Age.

Present-day people from England and Wales have more ancestry derived from early European farmers (EEF) than didpeople of the Early Bronze Age1. To understand this, here we generated genome-wide data from 793 individuals, increasing data from the Middle to the Late Bronze Age 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 people of England and Wales from the Iron Age, 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 the Late Bronze Age, coincident with archaeological evidence of intensified cultural exchange2-6. There was comparatively less gene flow from continental Europe during the Iron Age, and the independent genetic trajectory in Britain is also reflected in the rise of the allele conferring lactase persistence to approximately 50% by this time compared to approximately 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.

Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia

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.

Predicting skeletal stature using ancient DNA

ObjectivesAncient DNA provides an opportunity to separate the genetic and environmental bases of complex traits by allowing direct estimation of genetic values in ancient individuals. Here, we test whether genetic scores for height in ancient individuals are predictive of their actual height, as inferred from skeletal remains. We estimate the contributions of genetic and environmental variables to observed phenotypic variation as a first step towards quantifying individual sources of morphological variation.Materials and methodsWe collected stature estimates and femur lengths from West Eurasian skeletal remains with published genome‐wide ancient DNA data (n = 182, dating from 33,000–850 BP). We also recorded genetic sex, genetic ancestry, date and paleoclimate data for each individual, and δ13C and δ15N stable isotope values where available (n = 69). We tested different methods of calculating polygenic scores, using summary statistics from four different genome wide association studies (GWAS) for height, and three methods for imputing missing genotypes.ResultsA polygenic score for height predicts 6.3% of the variance in femur length in our data (n = 132, SD = 0.0069%, p = 0.001), controlling for sex, ancestry, and date. This is consistent with the predictive power of height PRS in present‐day populations and the low coverage of ancient samples. Comparatively, sex explains about 17% of the variance in femur length in our sample. Environmental effects also likely play a role in variation, independent of genetics, though with considerable uncertainty (longitude: R 2 = 0.033, SD = 0.008, p = 0.011). Genotype imputation did not improve polygenic prediction, and results varied based on the GWAS summary statistics we used.DiscussionPolygenic scores explain a small but significant proportion of the variance in height in ancient individuals, though not enough to make useful predictions of individual phenotypes. However, environmental variables also contribute to phenotypic outcomes and understanding their interaction with direct genetic predictions will provide a framework with which to model how plasticity and genetic changes ultimately combine to drive adaptation and evolution.

A 3,000-year-old, basal S. enterica lineage from Bronze Age Xinjiang suggests spread along the Proto-Silk Road.

Salmonella enterica (S. enterica) has infected humans for a long time, but its evolutionary history and geographic spread across Eurasia is still poorly understood. Here, we screened for pathogen DNA in 14 ancient individuals from the Bronze Age Quanergou cemetery (XBQ), Xinjiang, China. In 6 individuals we detected S. enterica. We reconstructed S. enterica genomes from those individuals, which form a previously undetected phylogenetic branch basal to Paratyphi C, Typhisuis and Choleraesuis–the so-called Para C lineage. Based on pseudogene frequency, our analysis suggests that the ancient S. enterica strains were not host adapted. One genome, however, harbors the Salmonella pathogenicity island 7 (SPI-7), which is thought to be involved in (para)typhoid disease in humans. This offers first evidence that SPI-7 was acquired prior to the emergence of human-adapted Paratyphi C around 1,000 years ago. Altogether, our results show that Salmonella enterica infected humans in Eastern Eurasia at least 3,000 years ago, and provide the first ancient DNA evidence for the spread of a pathogen along the Proto-Silk Road.

Parental relatedness through time revealed by runs of homozygosity in ancient DNA

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.

Peopling History of the Tibetan Plateau and Multiple Waves of Admixture of Tibetans Inferred From Both Ancient and Modern Genome-Wide Data.

Archeologically attested human occupation on the Tibetan Plateau (TP) can be traced back to 160 thousand years ago (kya) via the archaic Xiahe people and 30∼40 kya via the Nwya Devu anatomically modern human. However, the history of the Tibetan populations and their migration inferred from the ancient and modern DNA remains unclear. Here, we performed the first ancient and modern genomic meta-analysis among 3,017 Paleolithic to present-day Eastern Eurasian genomes (2,444 modern individuals from 183 populations and 573 ancient individuals). We identified a close genetic connection between the ancient-modern highland Tibetans and lowland island/coastal Neolithic Northern East Asians (NEA). This observed genetic affinity reflected the primary ancestry of high-altitude Tibeto-Burman speakers originated from the Neolithic farming populations in the Yellow River Basin. The identified pattern was consistent with the proposed common north-China origin hypothesis of the Sino-Tibetan languages and dispersal patterns of the northern millet farmers. We also observed the genetic differentiation between the highlanders and lowland NEAs. The former harbored more deeply diverged Hoabinhian/Onge-related ancestry and the latter possessed more Neolithic southern East Asian (SEA) or Siberian-related ancestry. Our reconstructed qpAdm and qpGraph models suggested the co-existence of Paleolithic and Neolithic ancestries in the Neolithic to modern East Asian highlanders. Additionally, we found that Tibetans from Ü-Tsang/Ando/Kham regions showed a strong population stratification consistent with their cultural background and geographic terrain. Ü-Tsang Tibetans possessed a stronger Chokhopani-affinity, Ando Tibetans had more Western Eurasian related ancestry and Kham Tibetans harbored greater Neolithic southern EA ancestry. Generally, ancient and modern genomes documented multiple waves of human migrations in the TP’s past. The first layer of local hunter-gatherers mixed with incoming millet farmers and arose the Chokhopani-associated Proto-Tibetan-Burman highlanders, which further respectively mixed with additional genetic contributors from the western Eurasian Steppe, Yellow River and Yangtze River and finally gave rise to the modern Ando, Ü-Tsang and Kham Tibetans.

Genetic Relationships between Mesoamerican Ancient Populations and with American Greater Southwest and Caribbean Populations Close to Mesoamerican Borders

abstract: Mesoamerica is a cultural and geographic region with a northern boundary adjacent to the American Greater Southwest and a southeastern boundary that includes the Maya area, which is adjacent to the Caribbean. These regions are of interest to analyze genetic structure, ancestry, and gene flow between the ancient populations. We identified the mitochondrial DNA haplogroups and haplotypes in 19 colonial and 10 pre-Columbian Maya from Xcaret and 6 Paquimé individuals. We analyzed our data together with 603 ancient individuals and with 95 colonial and 502 pre-Columbian individuals. The results show clear genetic differences among Mesoamerica, American Greater Southwest, and Caribbean regions. High frequency of haplogroup A in Paquimé and Mine Canyon and the distribution of its haplotypes in the networks suggest these populations are probably genetically related with both Mesoamerican and the American Greater Southwest populations. The genetic structure of the Maya is due to common ancestry, and it was maintained by geographic isolation and gene flow mostly between Mayan populations. The Spanish conquest did not change this structure in the Maya from Xcaret, Quintana Roo. Although populations from Central Mexico are not genetically homogeneous, they are clearly different from Maya. Teotihuacan and Cholula were contemporary cities that allied to control the region, but they show genetic differences that could be related to a distant common ancestry; they probably descended from the same group but separated very early, before their arrival in Central Mexico.

LINADMIX: evaluating the effect of ancient admixture events on modern populations.

The rise in the number of genotyped ancient individuals provides an opportunity to estimate population admixture models for many populations. However, in models describing modern populations as mixtures of ancient ones, it is typically difficult to estimate the model mixing coefficients and to evaluate its fit to the data. We present LINADMIX, designed to tackle this problem by solving a constrained linear model when both the ancient and the modern genotypes are represented in a low-dimensional space. LINADMIX estimates the mixing coefficients and their standard errors, and computes a P-value for testing the model fit to the data. We quantified the performance of LINADMIX using an extensive set of simulated studies. We show that LINADMIX can accurately estimate admixture coefficients, and is robust to factors such as population size, genetic drift, proportion of missing data and various types of model misspecification. LINADMIX is available as a python code at https://github.com/swidler/linadmix. Supplementary data are available at Bioinformatics online.

Social stratification during the Eastern Zhou Dynasty of China (771–476 bce): Mortuary and stable isotopic analyses of the Shangshihe cemetery

AbstractHistoric records for the Zhou Dynasty of China (1046–256 bce) defined distinct differentiation of social classes, in which ways of life and the afterlife were put into written form to regulate funerary and dietary practices. The presence of social stratification would suggest differences in nutrition during life and in ceremonial values for the afterlife. In this study, we examined grave goods and human skeletons from people of different social classes in the Guo State (虢) during the Spring–Autumn Period of the Eastern Zhou Dynasty (771–476 bce). Specimens were excavated from the Shangshihe cemetery in Yima County, Henan Province, China. Differences in total burial values and diet structure between different social ranks, sex, and age groups were assessed using mortuary and isotopic analyses. Our mortuary analysis indicated that there were significant differences in grave size, complexity, and values of grave goods between people of different social classes. The stable carbon and nitrogen isotopic analysis indicated a trend that people buried with two or three coffin layers consumed more animal‐derived, protein‐rich food than people who were buried with one layer of coffin. The elderly might have had better nutrition than younger people did. However, there was no sex‐based difference in nutrition between males and females. Results of these paralleled mortuary and isotopic analyses conform to historic records of social stratification in the Zhou Dynasty of China. Evidence of social stratification and its impact on nutrition and health should be considered while assessing the nutrition and health of ancient human individuals and communities.

Peopling of the Americas as inferred from ancient genomics.

In less than a decade, analyses of ancient genomes have transformed our understanding of the Indigenous peopling and population history of the Americas. These studies have shown that this history, which began in the late Pleistocene epoch and continued episodically into the Holocene epoch, was far more complex than previously thought. It is now evident that the initial dispersal involved the movement from northeast Asia of distinct and previously unknown populations, including some for whom there are no currently known descendants. The first peoples, once south of the continental ice sheets, spread widely, expanded rapidly and branched into multiple populations. Their descendants-over the next fifteen millennia-experienced varying degrees of isolation, admixture, continuity and replacement, and their genomes help to illuminate the relationships among major subgroups of Native American populations. Notably, all ancient individuals in the Americas, save for later-arriving Arctic peoples, are more closely related to contemporary Indigenous American individuals than to any other population elsewhere, which challenges the claim-which is based on anatomical evidence-that there was an early, non-Native American population in the Americas. Here we review the patterns revealed by ancient genomics that help to shed light on the past peoples who created the archaeological landscape, and together lead to deeper insights into the population and cultural history of the Americas.

Fine‐scale north‐to‐south genetic admixture profile in Shaanxi Han Chinese revealed by genome‐wide demographic history reconstruction

AbstractThe Han Chinese are the world's largest ethnic group residing across China. Shaanxi province in northern China was a pastoral–agricultural interlacing region sensitive to climate change since Neolithic times, which makes it a vital place for studying population dynamics. However, genetic studies of Shaanxi Han are underrepresented due to the lack of high‐density sampling and genome‐wide data. Here, we genotyped 700 000 single nucleotide polymorphisms (SNPs) in 200 Han individuals from nine populations in Shaanxi and compared with available modern and ancient Eurasian individuals. We revealed a north–south genetic cline in Han Chinese with Shaanxi Han locating at the northern side of the cline. We detected the western Eurasian‐related admixture in Shaanxi populations, especially in Guanzhong and Shanbei Han Chinese in proportions of 2%–4.6%. Shaanxi Han were suggested to derive a large part of ancestry (39%–69%) from a lineage that also contributed largely to ancient and present‐day Tibetans (85%) as well as southern Han, supporting the common northern China origin of modern Sino‐Tibetan‐speaking populations and southwestward expansion of millet farmers from the middle‐upper Yellow River Basin to the Tibetan Plateau and to southern China. The rest of the ancestry of Shaanxi Han was from a lineage closely related to ancient and present‐day Austronesian and Tai‐Kadai speaking populations in southern China and Southeast Asia. We also observed a genetic substructure in Shaanxi Han in terms of north–south‐related ancestry corresponding well to the latitudes. Maternal mitochondrial DNA and paternal Y‐chromosome lineages further demonstrated the aforementioned admixture pattern of Han Chinese in Shaanxi province.

Palaeopathology and amino acid δ13C analysis: Investigating pre-Columbian individuals with tuberculosis at Pica 8, northern Chile (1050-500 BP)

Bulk δ15N and δ13C values of proteinaceous tissues are being increasingly used in bioarchaeological studies to elucidate the physio-pathological status of ancient individuals. This method has not always been successful.The present study aims to explore the novel use of single amino acid carbon isotope analysis in palaeopathology by investigating the effect of a serious infectious disease, tuberculosis (TB), on the isotope composition of two collagenous tissues (tendon, rib). This is achieved by comparing the bulk and amino acid stable isotope compositions of collagenous tissues collected from human remains with and without TB-like bone lesions. The sample set comprises twelve adult individuals (males = 6, females = 6), who were buried at Pica 8, an inland oasis situated on the mid-elevation plains of northern Chile (Late Intermediate Period, ~1050-500 BP). Similarity and consistency in the diet of these individuals are explored using amino acid carbon isotope analysis of 1-cm hair segments longitudinally cut along a single hair fibre.The results show that there is a difference between collagen δ13C serine values measured in the rib collagen of five individuals presenting TB-like bone lesions (3 males and 2 females) and in those five without lesions (3 males and 2 females; control individuals). The rib collagen δ13C serine values of pathological individuals are lower (more negative) than those of the control individuals. Within the group of pathological individuals, lower δ13C serine values in rib collagen are correlated with higher (more positive) δ15N values. Since only individuals (N = 10) with similar dietary intakes were included in the statistical analyses, it appears that the δ13C serine values could be linked to altered carbon metabolism, rather than induced by dietary factors. Serine accounts for less than 3% of the total carbon in bone collagen, and thus an altered serine metabolism would be masked within the averaged bulk carbon isotope value. In future studies, it is advised to undertake stable carbon isotope analysis of non-essential amino acids as a means of characterising pathologically altered body tissues.

Unraveling a fine-scale high genetic heterogeneity and recent continental connections of an Arabian Peninsula population

Recent studies have showed the diverse genetic architecture of the highly consanguineous populations inhabiting the Arabian Peninsula. Consanguinity coupled with heterogeneity is complex and makes it difficult to understand the bases of population-specific genetic diseases in the region. Therefore, comprehensive genetic characterization of the populations at the finest scale is warranted. Here, we revisit the genetic structure of the Kuwait population by analyzing genome-wide single nucleotide polymorphisms data from 583 Kuwaiti individuals sorted into three subgroups. We envisage a diverse demographic genetic history among the three subgroups based on drift and allelic sharing with modern and ancient individuals. Furthermore, our comprehensive haplotype-based analyses disclose a high genetic heterogeneity among the Kuwaiti populations. We infer the major sources of ancestry within the newly defined groups; one with an obvious predominance of sub-Saharan/Western Africa mostly comprising Kuwait-B individuals, and other with West Eurasia including Kuwait-P and Kuwait-S individuals. Overall, our results recapitulate the historical population movements and reaffirm the genetic imprints of the legacy of continental trading in the region. Such deciphering of fine-scale population structure and their regional genetic heterogeneity would provide clues to the uncharted areas of disease-gene discovery and related associations in populations inhabiting the Arabian Peninsula.

A population history of Tokelau – genetic variation and change in atoll populations

Tokelau is a remote archipelago of atolls in western Polynesia, located approximately 500 km north of Samoa. It is thought to have been settled as part of the Austronesian expansion(s). However, its exact role in this population dispersal is not completely understood. Here we describe the results of complete mitochondrial genome sequencing for both the current inhabitants and ancient individuals from the archipelago in addition to an assessment of Y-chromosome diversity among the present population. We find relatively little genetic diversity compared with other western Polynesian populations, most likely due to historically reported bottleneck events. However, the presence of rare mitochondrial lineages hints at prehistoric occupation by peoples from the northwest (e.g., Tuvalu and Micronesia). Ancient DNA data from Atafu, the northernmost Tokelauan atoll, is further consistent with abandonment and later resettlement of the island from a Samoan or Samoan-derived source population. Moreover, the ancient and modern mitogenomes also suggest links with other atoll populations in the western Pacific.

DNA Markers Reveal Genetic Associations among 11,000-Year-Old Scots Pine (Pinus sylvestris L.) Found in the Baltic Sea with the Present-Day Gene Pools in Lithuania

We aimed to extract DNA and amplify PCR fragments at the mitochondrial DNA Nad7.1 locus and 11 nuclear microsatellite loci in nine circa 11,000-year-old individuals of Scots pine found at the bottom of the Baltic sea and test the genetic associations with the present-day gene pool of Scots pine in Lithuania. We followed a strict anticontamination protocol in the lab and, simultaneously with the aDNA specimens, tested DNA-free controls. The DNA was extracted by an ATMAB protocol from the ancient wood specimens sampled underwater from Scots pine stumps located circa 20–30 m deep and circa 12 km ashore in western Lithuania. As the references, we used 30 present-day Lithuanian populations of Scots pine with 25–50 individuals each. The aDNA yield was 11–41 ng/μL. The PCR amplification for the mtDNA Nad7.1 locus and the nDNA loci yielded reliable aDNA fragments for three and seven out of nine ancient pines, respectively. The electrophoresis profiles of all the PCR tested DNA-free controls contained the sizing standard only, indicating low likelihood for contamination. At the mtDNA Nad7.1 locus, all three ancient Scots pine individuals had the type A (300 bp) allele, indicating postglacial migration from the refugia in Balkan peninsula. The GENECLASS Bayesian assignment tests revealed relatively stringer and consistent genetic associations between the ancient Scots pine trees and the present-day southern Lithuanian populations (assignment probability 0.37–0.55) and several wetlands in Lithuania. Our study shows that salty sea water efficiently preserves ancient DNA in wood at the quality levels suitable for genetic testing of trees dated back as far as 11,000 years before present.

Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups.

Previous studies show that the indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting ~400 years ago and their descendants are today mixed with Europeans and Asians. To gain insight on the occupants of the Vaalkrans Shelter located at the southernmost tip of Africa, we investigated the genetic make-up of an individual who lived there about 200 years ago. We further contextualize the genetic ancestry of this individual among prehistoric and current groups. From a hair sample excavated at the shelter, which was indirectly dated to about 200 years old, we sequenced the genome (1.01 times coverage) of a Later Stone Age individual. We analyzed the Vaalkrans genome together with genetic data from 10 ancient (pre-colonial) individuals from southern Africa spanning the last 2000 years. We show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter-gatherers and ~20% to a mixed East African-Eurasian source. This genetic make-up is similar to modern-day Khoekhoe individuals from the Northern Cape Province (South Africa) and Namibia, but in the southern Cape, the Vaalkrans man's descendants have likely been assimilated into mixed-ancestry "Coloured" groups. The Vaalkrans man's genome reveals that Khoekhoe pastoralist groups/individuals lived in the southern Cape as late as 200 years ago, without mixing with non-African colonists or Bantu-speaking farmers. Our findings are also consistent with the model of a Holocene pastoralist migration, originating in Eastern Africa, shaping the genomic landscape of historic and current southern African populations.

Ancient proteins provide evidence of dairy consumption in eastern Africa

Consuming the milk of other species is a unique adaptation of Homo sapiens, with implications for health, birth spacing and evolution. Key questions nonetheless remain regarding the origins of dairying and its relationship to the genetically-determined ability to drink milk into adulthood through lactase persistence (LP). As a major centre of LP diversity, Africa is of significant interest to the evolution of dairying. Here we report proteomic evidence for milk consumption in ancient Africa. Using liquid chromatography tandem mass spectrometry (LC-MS/MS) we identify dairy proteins in human dental calculus from northeastern Africa, directly demonstrating milk consumption at least six millennia ago. Our findings indicate that pastoralist groups were drinking milk as soon as herding spread into eastern Africa, at a time when the genetic adaptation for milk digestion was absent or rare. Our study links LP status in specific ancient individuals with direct evidence for their consumption of dairy products.