Explore the vast range of titles available.

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

Background Principal Component Analysis (PCA) is widely used in population genetics to visualize genetic relationships and population structures. In ancient genomics, genotype information may in parts remain unresolved due to the low abundance and degraded quality of ancient DNA. While methods like SmartPCA allow the projection of ancient samples despite missing data, they do not quantify projection uncertainty. The reliability of PCA projections for often very sparse ancient genotype samples is not well understood. Ignoring this uncertainty may lead to overconfident conclusions about the observed genetic relationships and population structure. Results This study systematically investigates the impact of missing loci on PCA projections using both simulated and real ancient human genotype data. Through extensive simulations with high-coverage ancient samples, we demonstrate that increasing levels of missing data can lead to less accurate SmartPCA projections, highlighting the importance of considering uncertainty when interpreting PCA results from ancient samples. To address this, we developed a probabilistic framework to quantify the uncertainty in PCA projections due to missing data. By applying our methodology to modern and ancient West Eurasian genotype samples from the Allen Ancient DNA Resource database, we could show a high concordance between our predicted projection and empirically derived distributions. Applying this framework to real-world data, we demonstrate its utility in predicting and visualizing embedding uncertainties for ancient samples of varying SNP coverages. Conclusion Our results emphasize the importance of accounting for projection uncertainty in ancient population studies. We therefore make our probabilistic model available through TrustPCA, a user-friendly web tool that provides researchers with uncertainty estimates alongside PCA projections, facilitating data exploration in ancient human genomic studies and enhancing transparency in data quality reporting.

The general view is that Eurasians mostly descend from a single group of humans that dispersed outside of sub-Saharan Africa around 50,000 to 100,000 years ago. Present-day North Africans share a majority of their ancestry with present-day Near Easterners, but not with sub-Saharan Africans. To investigate this conundrum, Van de Loosdrecht et al. sequenced high-quality DNA obtained from bone samples of seven individuals from Taforalt in eastern Morocco dating from the Later Stone Age, about 15,000 years ago. The Taforalt individuals were found to be most closely related to populations from the Near East (Natufians), with a third of their ancestry from sub-Saharan Africa. No evidence was found for introgression with western Europeans, despite attribution to the Iberomaurusian culture. None of the present-day or ancient Holocene African groups are a good proxy for the sub-Saharan genetic component. Science , this issue p. 548 Ancient human genomes suggest dynamic interactions among Pleistocene African populations. North Africa is a key region for understanding human history, but the genetic history of its people is largely unknown. We present genomic data from seven 15,000-year-old modern humans, attributed to the Iberomaurusian culture, from Morocco. We find a genetic affinity with early Holocene Near Easterners, best represented by Levantine Natufians, suggesting a pre-agricultural connection between Africa and the Near East. We do not find evidence for gene flow from Paleolithic Europeans to Late Pleistocene North Africans. The Taforalt individuals derive one-third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West and East Africans. Thus, we provide direct evidence for genetic interactions between modern humans across Africa and Eurasia in the Pleistocene.

Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. Nuclear DNA indicated Neanderthals as a sister group of Denisovans after diverging from modern humans. However, the closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. Here we report the complete mtDNA of an archaic femur from the Hohlenstein–Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago, providing a lower boundary for the time of the putative mtDNA introgression event. We demonstrate that a complete Neanderthal mtDNA replacement is feasible over this time interval even with minimal hominin introgression. The highly divergent HST branch is indicative of greater mtDNA diversity during the Middle Pleistocene than in later periods. Ancient DNA keeps expanding our understanding of complex genetic relationships between Pleistocene hominins. Here, Posth and colleagues analyse the mitochondrial genome of an archaic human that diverged from other Neanderthals ∼270,000 years ago, providing the minimum age for an African introgression into Neanderthals.

Correlating cultural, technological and ecological aspects of both Upper Pleistocene modern humans (UPMHs) and Neandertals provides a useful approach for achieving robust predictions about what makes us human. Here we present ecological information for a period of special relevance in human evolution, the time of replacement of Neandertals by modern humans during the Late Pleistocene in Europe. Using the stable isotopic approach, we shed light on aspects of diet and mobility of the late Neandertals and UPMHs from the cave sites of the Troisième caverne of Goyet and Spy in Belgium. We demonstrate that their diet was essentially similar, relying on the same terrestrial herbivores, whereas mobility strategies indicate considerable differences between Neandertal groups, as well as in comparison to UPMHs. Our results indicate that UPMHs exploited their environment to a greater extent than Neandertals and support the hypothesis that UPMHs had a substantial impact not only on the population dynamics of large mammals but also on the whole structure of the ecosystem since their initial arrival in Europe.

During excavations in 2011, a peculiar archaeological feature representing a mass grave with seven completely preserved skeletons was discovered at the site of the Roman period city of Mursa (modern-day Osijek, Croatia). The archaeological context and direct radiocarbon dating indicate that the bodies were interred during the mid-3 rd century CE. Bioarchaeological analysis shows that all seven individuals are adult males exhibiting numerous pathological lesions (e.g., enthesopathies, injuries). Carbon and nitrogen stable isotopes analysis indicates they had a mixed C 3 /C 4 -based vegetal diet with limited amounts of terrestrial animal protein and a very limited marine protein consumption. Ancient DNA analysis shows that individuals from the Mursa mass grave had a heterogenous ancestry. None of them show genetic continuity with the preceding local Early Iron Age population. The presented multidisciplinary analyses of the Mursa mass grave strongly suggest that the studied individuals were Roman soldiers, victims of a catastrophic event occurring as the result of the ‘Crisis of the Third Century’, most probably the battle of Mursa from 260 CE.

Genetic similarity among late Neanderthals is predicted well by their geographical location, and although some of these Neanderthals were contemporaneous with early modern humans, their genomes show no evidence of recent gene flow from modern humans. Late Neanderthal relations Many questions remain about the relationship between populations of Neanderthals around the time of their final interactions with modern humans, and how this contributed to the evolution of modern humans. Janet Kelso, Svante Pääbo and colleagues sequenced the genomes of five Neanderthals that lived between 39,000 and 47,000 years ago, broadening the temporal and geographical range of available Neanderthal genomes. They analyse these genomes together with previously sequenced ancient genomes and find that relatedness among Neanderthals is related to geographic proximity. They find that the majority of gene flow into early modern humans originated from one or more Neanderthal populations that diverged from the late Neanderthals at least 70,000 years ago, but after their split from the Altai Neanderthal approximately 150,000 years ago. Although it has previously been shown that Neanderthals contributed DNA to modern humans 1 , 2 , not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared. Our ability to retrieve DNA from a larger number of Neanderthal individuals has been limited by poor preservation of endogenous DNA 3 and contamination of Neanderthal skeletal remains by large amounts of microbial and present-day human DNA 3 , 4 , 5 . Here we use hypochlorite treatment 6 of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five Neanderthals who lived around 39,000 to 47,000 years ago (that is, late Neanderthals), thereby doubling the number of Neanderthals for which genome sequences are available. Genetic similarity among late Neanderthals is well predicted by their geographical location, and comparison to the genome of an older Neanderthal from the Caucasus 2 , 7 indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neanderthal history. We find that the bulk of Neanderthal gene flow into early modern humans originated from one or more source populations that diverged from the Neanderthals that were studied here at least 70,000 years ago, but after they split from a previously sequenced Neanderthal from Siberia 2 around 150,000 years ago. Although four of the Neanderthals studied here post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.

Despite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies, we obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards, a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized around one large pedigree, suggesting that biological relationships played an important role in these early medieval societies. Moreover, we identified genetic structure in each cemetery involving at least two groups with different ancestry that were very distinct in terms of their funerary customs. Finally, our data are consistent with the proposed long-distance migration from Pannonia to Northern Italy. The Longobards invaded and conquered much of Italy after the fall of the Western Roman Empire. Here, the authors sequence and analyze ancient genomic DNA from 63 samples from two cemeteries associated with the Longobards and identify kinship networks and two distinct genetic and cultural groups in each.

New genome-wide data for ancient, Bronze Age individuals, including Minoans, Mycenaeans, and southwestern Anatolians, show that Minoans and Mycenaeans were genetically very similar yet distinct, supporting the idea of continuity but not isolation in the history of populations of the Aegean. Genetic ancestry of Bronze Age Europeans The most prominent civilizations that emerged during the Bronze Age in Europe include the Minoan culture on the island of Crete and the Mycenaean culture on mainland Greece, both in the Aegean region. Iosif Lazaridis, David Reich, Johannes Krause, George Stamatoyannopoulos and colleagues investigated the origins of these two archaeological cultures by analysing new genome-wide data from 19 ancient individuals, including Minoans, Mycenaeans and their eastern neighbours from southwestern Anatolia. While Minoans and Mycenaeans were genetically very similar, with shared ancestry from the western Anatolian and Aegean regions, they were also distinct, with Mycenaeans showing additional ancestry related to the Bronze Age inhabitants of the Eurasian steppe. The origins of the Bronze Age Minoan and Mycenaean cultures have puzzled archaeologists for more than a century. We have assembled genome-wide data from 19 ancient individuals, including Minoans from Crete, Mycenaeans from mainland Greece, and their eastern neighbours from southwestern Anatolia. Here we show that Minoans and Mycenaeans were genetically similar, having at least three-quarters of their ancestry from the first Neolithic farmers of western Anatolia and the Aegean 1 , 2 , and most of the remainder from ancient populations related to those of the Caucasus 3 and Iran 4 , 5 . However, the Mycenaeans differed from Minoans in deriving additional ancestry from an ultimate source related to the hunter–gatherers of eastern Europe and Siberia 6 , 7 , 8 , introduced via a proximal source related to the inhabitants of either the Eurasian steppe 1 , 6 , 9 or Armenia 4 , 9 . Modern Greeks resemble the Mycenaeans, but with some additional dilution of the Early Neolithic ancestry. Our results support the idea of continuity but not isolation in the history of populations of the Aegean, before and after the time of its earliest civilizations.

The Iron Age of highland Pang Mapha, northwestern Thailand, is characterised by a mortuary practice known as Log Coffin culture. Dating between 2300 and 1000 years ago, large coffins carved from individual teak trees have been discovered in over 40 caves and rock shelters. While previous studies focussed on the cultural development of the Log Coffin-associated sites, the origins of the practice, connections with other wooden coffin-using groups in Southeast Asia, and social structure within the region remain understudied. Here, we present genome-wide data from 33 individuals from five Log Coffin culture sites to study genetic ancestry profiles and genetic interconnectedness. The Log Coffin-associated genomes can be modelled as an admixture between Hòabìnhian hunter-gatherer-, Yangtze River farmer-, and Yellow River farmer-related ancestry. This indicates different influence spheres from Bronze and Iron Age individuals from northeastern Thailand as reflected by cultural practices. Our analyses also identify close genetic relationships within the sites and more distant connections between sites in the same and different river valleys. In combination with high mitochondrial haplogroup diversity and genome-wide homogeneity, the Log Coffin-associated groups from northwestern Thailand seem to have been a large, well-connected community, where genetic relatedness played a significant role in the mortuary ritual. Large log coffins placed on stilts in natural caves characterize the Iron Age of northwestern Thailand. Here, the authors conduct archaeogenetic analyses of 33 individuals, identifying a large, well-connected community, where genetic relatedness played a significant role in the mortuary ritual.