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The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show the same patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10 000 years ago. We also found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4 000 years, from the Mesolithic to the end of Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River.

The southern African indigenous Khoe-San populations harbor the most divergent lineages of all living peoples. Exploring their genomes is key to understanding deep human history. We sequenced 25 full genomes from five Khoe-San populations, revealing many novel variants, that 25% of variants are unique to the Khoe-San, and that the Khoe-San group harbors the greatest level of diversity across the globe. In line with previous studies, we found several gene regions with extreme values in genome-wide scans for selection, potentially caused by natural selection in the lineage leading to Homo sapiens and more recent in time. These gene regions included immunity-, sperm-, brain-, diet-, and muscle-related genes. When accounting for recent admixture, all Khoe-San groups display genetic diversity approaching the levels in other African groups and a reduction in effective population size starting around 100,000 years ago. Hence, all human groups show a reduction in effective population size commencing around the time of the Out-of-Africa migrations, which coincides with changes in the paleoclimate records, changes that potentially impacted all humans at the time.

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).

Central Asia has been an important region connecting the different parts of Eurasia throughout history and prehistory, with large states developing in this region during the Iron Age. Archaeogenomics is a powerful addition to the zooarchaeological toolkit for understanding the relation of these societies to animals. Here, we present the genetic identification of a goitered gazelle specimen (Gazella subgutturosa) at the site Gazimulla-Tepa, in modern-day Uzbekistan, confirming hunting of the species in the region during the Iron Age. The sample was directly radiocarbon dated to 2724-2439 calBP. A phylogenetic analysis of the mitochondrial genome places the individual into the modern variation of G. subgutturosa. Our data does represent both the first ancient DNA and the first nuclear DNA sequences of this species. The lack of genomic resources available for this gazelle and related species prevented us from performing a more in-depth analysis of the nuclear sequences generated. Therefore, we are making our sequence data available to the research community to facilitate other research of this nowadays threatened species which has been subject to human hunting for several millennia across its entire range on the Asian continent.

We have sampled five out of the eleven previously identified human specimens and some faunal remains from the Plovers Lake site in the Cradle of Humankind, South Africa, for ancient DNA. We were successful in obtaining positive results for three of the human individuals and three ‘buffalo’ teeth. Based on ages obtained for flowstone and one bovid tooth, the site was interpreted previously as a hominin-bearing Middle Stone Age site of more than 60 000 years old. Our work, however, revealed that not all the material accumulated during the Pleistocene. Instead, the sampled humans and bovids most likely represent a Bantu-speaking Iron Age population (mtDNA haplogroup L3d) and their Nguni cattle. Newly obtained radiocarbon dates confirmed that these remains are probably no older than the last 500 years bp. This study demonstrates the usefulness of inter-disciplinary investigation into the human past, and the depositional and stratigraphic complexities that researchers in the Cradle of Humankind need to contend with before interpreting their assemblages.

Summary The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic,1 mainly because material culture studies provide limited insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings,2 household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from Aşıklı Höyük and Çatalhöyük. We infer pedigree relationships by simultaneously analyzing multiple types of information, including autosomal and X chromosome kinship coefficients, maternal markers, and radiocarbon dating. In two early Neolithic villages dating to the 9th and 8th millennia BCE, Aşıklı Höyük and Boncuklu, we discover that siblings and parent-offspring pairings were frequent within domestic structures, which provides the first direct indication of close genetic relationships among co-burials. In contrast, in the 7th millennium BCE sites of Çatalhöyük and Barcın, where we study subadults interred within and around houses, we find close genetic relatives to be rare. Hence, genetic relatedness may not have played a major role in the choice of burial location at these latter two sites, at least for subadults. This supports the hypothesis that in Çatalhöyük,3, 4, 5 and possibly in some other Neolithic communities, domestic structures may have served as burial location for social units incorporating biologically unrelated individuals. Our results underscore the diversity of kin structures in Neolithic communities during this important phase of sociocultural development., Highlights • Genetic kinship estimated from co-buried individuals’ genomes in Neolithic Anatolia • Close relatives are common among co-burials in Aşıklı and Boncuklu • Many unrelated infants found buried in the same building in Çatalhöyük and Barcın • Neolithic societies in Southwest Asia may have held diverse concepts of kinship, Yaka et al. use ancient genomes from Neolithic Anatolia and present evidence for diverse concepts of social kinship in Neolithic societies. In some communities, like Çatalhöyük, many genetically unrelated infants were buried together inside the same buildings, whereas in other sites, people buried together were frequently close biological kin.

A recommendation of: Alba Refoyo-Martinez, Siyang Liu, Anja Moltke Jorgensen, Xin Jin, Anders Albrechtsen, Alicia R. Martin, Fernando Racimo How robust are cross-population signatures of polygenic adaptation in humans? 10.1101/2020.07.13.200030

In this paper, we investigate population dynamics in the Scandinavian Neolithic and Early Bronze Age in southwestern Sweden. Human mobility patterns in Falbygden were studied by applying strontium isotope analysis combined with archaeological and bioarchaeological data, including mtDNA and sex assessment on a large dataset encompassing 141 individuals from 21 megalithic graves. In combination with other archaeological and anthropological records, we investigated the temporal and spatial scale of individual movement, mobility patterns of specific categories of people and possible social drivers behind them. Our results of strontium and biomolecular analyses suggest that mobility increased in the Late Neolithic and Early Bronze Age compared to the earlier parts of the Neolithic. The data indicate individuals moving both into and away from Falbygden. Mobility patterns and contact networks also shift over time.

Identifying local adaptation in bottlenecked species is essential for effective conservation management. Selection detection methods are often applied to bottlenecked species and have an important role in species management plans, assessments of the species’ adaptive capacity, and looking for responses to major threats like climate change. Yet, the allele frequency changes driven by selection and exploited in selection detection methods, are similar to those caused by the strong neutral genetic drift expected during a bottleneck. Consequently, it is often unclear what accuracy selection detection methods may offer within bottlenecked populations. In this study, we used simulations to explore if signals of selection could be confidently distinguished from genetic drift across 23 bottlenecked and reintroduced populations of Alpine ibex (Capra ibex). We used the meticulously recorded demographic history of the Alpine ibex to generate a comprehensive simulated SNP data. The simulated SNPs were then used to benchmark the confidence we could place in putative outliers identified through selection scans on empirical Alpine ibex SNP data. Within the simulated dataset, the false positive rates were high for all selection detection methods but fell substantially when two or more selection detection methods were combined. However, the true positive rates were consistently low and became essentially negligible after this increased stringency. Despite the detection of many putative outlier loci in the empirical Alpine ibex RADseq data, none met the threshold needed to distinguish them from genetic drift-driven false positives. Unfortunately, the low true positive rate also creates a paradox, by preventing the exclusion of recent local adaptation within the Alpine ibex.

[EN] Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from ‘‘Pesxtera Muierii,’’ Romania who lived 34,000 years ago to 13.53 coverage. The genome shows similarities to modern- day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture ( 3.1%) to most EUP humans but only half compared to the 40,000-year-old Pesxtera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans. The computations were performed on resources provided by SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX). Sequencing was performed by the SNP&SEQ Technology Platform in Uppsala. T.G. was supported by a grant from the Swedish Research Council Vetenskapsra° det (2017-05267). M.G.N. was supported by a Spinoza grant of the Netherlands Organisation for Scientific Research and an ERC Advanced Grant (no. 833247). M.J. was supported by an ERC Starting Grant and the Knut and Alice Wallenberg Foundation. C.R. was supported by a Basque Government Grant to Research Groups of the Basque University System (IT1138-16).

Sheep were among the first domesticated animals, but their demographic history is little understood. Here we analyzed nuclear polymorphism and mitochondrial data (mtDNA) from ancient central and west Anatolian sheep dating from Epipaleolithic to late Neolithic, comparatively with modern-day breeds and central Asian Neolithic/Bronze Age sheep (OBI). Analyzing ancient nuclear data, we found that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds relative to Asian breeds, a conclusion supported by mtDNA haplogroup frequencies. In contrast, OBI showed higher genetic affinity to present-day Asian breeds. These results suggest that the east-west genetic structure observed in present-day breeds had already emerged by 6000 BCE, hinting at multiple sheep domestication episodes or early wild introgression in southwest Asia. Furthermore, we found that ANS are genetically distinct from all modern breeds. Our results suggest that European and Anatolian domestic sheep gene pools have been strongly remolded since the Neolithic., Yurtman, Özer, Yüncü et al. provide an ancient DNA data set to demonstrate the impact of human activity on the demographic history of domestic sheep. The authors demonstrate that there may have been multiple domestication events with notable changes to the gene pool of European and Anatolian sheep since the Neolithic.

Estimates of individual-level genomic ancestry are routinely used in human genetics, and related fields. The analysis of population structure and genomic ancestry can yield insights in terms of modern and ancient populations, allowing us to address questions regarding admixture, and the numbers and identities of the parental source populations. Unrecognized population structure is also an important confounder to correct for in genome-wide association studies. However, it remains challenging to work with heterogeneous datasets from multiple studies collected by different laboratories with diverse genotyping and imputation protocols. This work presents a new approach and an accompanying open-source toolbox that facilitates a robust integrative analysis for population structure and genomic ancestry estimates for heterogeneous datasets. We show robustness against individual outliers and different protocols for the projection of new samples into a reference ancestry space, and the ability to reveal and adjust for population structure in a simulated case-control admixed population. Given that visually evident and easily recognizable patterns of human facial characteristics co-vary with genomic ancestry, and based on the integration of three different sources of genome data, we generate average 3D faces to illustrate genomic ancestry variations within the 1,000 Genome project and for eight ancient-DNA profiles, respectively. ispartof: Scientific Reports vol:10 issue:1 ispartof: location:England status: published

The Middle East plays a central role in human history harbouring a vast diversity of ethnic, cultural and religious groups. However, much remains to be understood about past and present genomic diversity in this region. Here, we present for the first time, a multidisciplinary bioarchaeological analysis of two individuals dated to late 7th and early 8th centuries from Tell Qarassa, an open-air site in modern-day Syria. Radiocarbon dates, religious and cultural burial evidence indicate that this site represents one of the earliest Islamic Arab burials in the Levant during the Late Antiquity period. Interestingly, we found genomic similarity to a genotyped group of modern-day Bedouins and Saudi rather than to most neighbouring Levantine groups. This is highlighted through substantial Neolithic Levant ancestry in our samples, inviting an alternative scenario of long-term continuity in this region. This raises questions about the influence of ancient populations and historical migrations to genetic structure in the Middle East. As our study represents the first genomic analysis of an early Islamic burial in the Levant, we discuss our findings and possible historic scenarios in light of forces such as genetic drift and their possible interaction with religious and cultural processes., This work was funded by a grant from the Royal Physiographic Society of Lund (Nilsson-Ehle Endowments) to TG and CV and the La Trobe Internal Research grants to CV. MS was part of the Erasmus Mundus Master Programme in Evolutionary Biology (MEME). TG is supported by a grant from the Swedish Research Council Vetenskapsrådet (2017-05267). MJ and AG were supported by grants from the Swedish Research Council Vetenskapsrådet and the Knut and AliceWallenberg foundation. JS is supported by a grant from Marie Skłodowska-Curie Actions (European Commission, no. GA 750460; H2020-MSCA-IF-2016). The archaeological research at Tell Qarassa was supported by the Spanish Ministry of Economy and Competitiveness (grant HAR2016-74999-P) and the Palarq Foundation.We thank Arielle R. Munters for initial data processing, Phillip Edwards for fruitful discussionand Frank Braemer for comments on an early draft of the manuscript. The computations wereperformed on resources provided by SNIC through Uppsala Multidisciplinary Center forAdvanced Computational Science (UPPMAX) under projects sllstore2017020 and 2019/8-150.Shotgun sequencing was performed at the National Genomics Infrastructure (NGI) Stockholm.

Objectives In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub‐Neolithic hunter‐gatherer Pitted Ware culture. By investigating the genetic make‐up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture‐influenced burials), we could determine the impact of migration and the impact of cultural influences. Methods We sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene‐pools. Results The genomic data show that all individuals belonged to one genetic population—a population associated with the Pitted Ware culture—irrespective of the burial style. Conclusion We conclude that the Pitted Ware culture communities were not impacted by gene‐flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange. Title in thesis list of papers: The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe cultureDe två sista författarna delar sistaförfattarskapet

Accurate inference of genomic ancestry is critically important in human genetics, epidemiology, and related fields. Geneticists today have access to multiple heterogeneous population-based datasets from studies collected under different protocols. Therefore, joint analyses of these datasets require robust and consistent inference of ancestry, where a common strategy is to yield an ancestry space generated by a reference dataset. However, such a strategy is sensitive to batch artefacts introduced by different protocols. In this work, we propose a novel robust genome-wide ancestry inference method; referred to as SUGIBS, based on an unnormalized genomic (UG) relationship matrix whose spectral (S) decomposition is generalized by an Identity-by-State (IBS) similarity degree matrix. SUGIBS robustly constructs an ancestry space from a single reference dataset, and provides a robust projection of new samples, from different studies. In experiments and simulations, we show that, SUGIBS is robust against individual outliers and batch artifacts introduced by different genotyping protocols. The performance of SUGIBS is equivalent to the widely used principal component analysis (PCA) on normalized genotype data in revealing the underlying structure of an admixed population and in adjusting for false positive findings in a case-control admixed GWAS. We applied SUGIBS on the 1000 Genome project, as a reference, in combination with a large heterogeneous dataset containing auxiliary 3D facial images, to predict population stratified average or ancestry faces. In addition, we projected eight ancient DNA profiles into the 1000 Genome ancestry space and reconstructed their ancestry face. Based on the visually strong and recognizable human facial phenotype, comprehensive facial illustrations of the populations embedded in the 1000 Genome project are provided. Furthermore, ancestry facial imaging has important applications in personalized and precision medicine along with forensic and archeological DNA phenotyping.Author SummaryEstimates of individual-level genomic ancestry are routinely used in human genetics, epidemiology, and related fields. The analysis of population structure and genomic ancestry can yield significant insights in terms of modern and ancient population dynamics, allowing us to address questions regarding the timing of the admixture events, and the numbers and identities of the parental source populations. Unrecognized or cryptic population structure is also an important confounder to correct for in genome-wide association studies (GWAS). However, to date, it remains challenging to work with heterogeneous datasets from multiple studies collected by different laboratories with diverse genotyping and imputation protocols. This work presents a new approach and an accompanying open-source software toolbox that facilitates a robust integrative analysis for population structure and genomic ancestry estimates for heterogeneous datasets. Given that visually evident and easily recognizable patterns of human facial characteristics covary with genomic ancestry, we can generate predicted ancestry faces on both the population and individual levels as we illustrate for the 26 1000 Genome populations and for eight eminent ancient-DNA profiles, respectively.

Anatolia and the Near East have long been recognized as the epicenter of the Neolithic expansion through archaeological evidence. Recent archaeogenetic studies on Neolithic European human remains have shown that the Neolithic expansion in Europe was driven westward and northward by migration from a supposed Near Eastern origin [1-5]. However, this expansion and the establishment of numerous culture complexes in the Aegean and Balkans did not occur until 8,500 before present (BP), over 2,000 years after the initial settlements in the Neolithic core area [6-9]. We present ancient genome-wide sequence data from 6,700-year-old human remains excavated from a Neolithic context in Kumtepe, located in northwestern Anatolia near the well-known (and younger) site Troy [10]. Kumtepe is one of the settlements that emerged around 7,000 BP, after the initial expansion wave brought Neolithic practices to Europe. We show that this individual displays genetic similarities to the early European Neolithic gene pool and modern-day Sardinians, as well as a genetic affinity to modern-day populations from the Near East and the Caucasus. Furthermore, modern-day Anatolians carry signatures of several admixture events from different populations that have diluted this early Neolithic farmer component, explaining why modern-day Sardinian populations, instead of modern-day Anatolian populations, are genetically more similar to the people that drove the Neolithic expansion into Europe. Anatolia's central geographic location appears to have served as a connecting point, allowing a complex contact network with other areas of the Near East and Europe throughout, and after, the Neolithic.

The impact of human mobility on the northern European urban populations during the Viking and Early Middle Ages and its repercussions in Scandinavia itself are still largely unexplored. Our study of the demographics in the final phase of the Viking era is the first comprehensive multidisciplinary investigation that includes genetics, isotopes, archaeology, and osteology on a larger scale. This early Christian dataset is particularly important as the earlier common pagan burial tradition during the Iron Age was cremation, hindering large-scale DNA analyses. We present genome-wide sequence data from 23 individuals from the 10

Archaeogenomic research has proven to be a valuable tool to trace migrations of historic and prehistoric individuals and groups, whereas relationships within a group or burial site have not been investigated to a large extent. Knowing the genetic kinship of historic and prehistoric individuals would give important insights into social structures of ancient and historic cultures. Most archaeogenetic research concerning kinship has been restricted to uniparental markers, while studies using genome-wide information were mainly focused on comparisons between populations. Applications which infer the degree of relationship based on modern-day DNA information typically require diploid genotype data. Low concentration of endogenous DNA, fragmentation and other post-mortem damage to ancient DNA (aDNA) makes the application of such tools unfeasible for most archaeological samples. To infer family relationships for degraded samples, we developed the software READ (Relationship Estimation from Ancient DNA). We show that our heuristic approach can successfully infer up to second degree relationships with as little as 0.1x shotgun coverage per genome for pairs of individuals. We uncover previously unknown relationships among prehistoric individuals by applying READ to published aDNA data from several human remains excavated from different cultural contexts. In particular, we find a group of five closely related males from the same Corded Ware culture site in modern-day Germany, suggesting patrilocality, which highlights the possibility to uncover social structures of ancient populations by applying READ to genome-wide aDNA data. READ is publicly available from https://bitbucket.org/tguenther/read.

The consequences of the Neolithic transition in Europe--one of the most important cultural changes in human prehistory--is a subject of great interest. However, its effect on prehistoric and modern-day people in Iberia, the westernmost frontier of the European continent, remains unresolved. We present, to our knowledge, the first genome-wide sequence data from eight human remains, dated to between 5,500 and 3,500 years before present, excavated in the El Portalón cave at Sierra de Atapuerca, Spain. We show that these individuals emerged from the same ancestral gene pool as early farmers in other parts of Europe, suggesting that migration was the dominant mode of transferring farming practices throughout western Eurasia. In contrast to central and northern early European farmers, the Chalcolithic El Portalón individuals additionally mixed with local southwestern hunter-gatherers. The proportion of hunter-gatherer-related admixture into early farmers also increased over the course of two millennia. The Chalcolithic El Portalón individuals showed greatest genetic affinity to modern-day Basques, who have long been considered linguistic and genetic isolates linked to the Mesolithic whereas all other European early farmers show greater genetic similarity to modern-day Sardinians. These genetic links suggest that Basques and their language may be linked with the spread of agriculture during the Neolithic. Furthermore, all modern-day Iberian groups except the Basques display distinct admixture with Caucasus/Central Asian and North African groups, possibly related to historical migration events. The El Portalón genomes uncover important pieces of the demographic history of Iberia and Europe and reveal how prehistoric groups relate to modern-day people.

Genome-wide association studies (GWAS) became a widely used method to map qualitative and quantitative traits in plants. We compared existing single-marker and haplotype-based methods for GWAS with a focus on barley. Based on German winter barley cultivars, four different single-marker and haplotype-based methods were tested for their power to detect significant associations in a large genome with a limited number of markers. We identified significant associations for yield and quality-related traits using the iSelect array with 3886 mapped single nucleotide polymorphism (SNP) markers in a structured population consisting of 109 genotypes. Genome simulations with different numbers of genotypes, marker densities and marker effects were used to compare different GWAS methods. Results of simulations revealed a higher power in detecting significant associations for haplotype- than for single-marker approaches, but showed a higher false discovery rate for SNP detection, due to lack of correction for population structure. Our simulations revealed that a population size of about 500 individuals is required to detect QTLs explaining a small trait variance (

Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens . We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. The remains of three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, and those of four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record.

Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the last glaciation. However, the origin(s) of the first colonizers and their migration routes remain unclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavated across Scandinavia and dated to 9,500-6,000 years before present. Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. This result suggests that Scandinavia was initially colonized following two different routes: one from the south, the other from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These adaptations include high frequencies of low pigmentation variants and a gene-region associated with physical performance, which shows strong continuity into modern-day northern Europeans.

Southern Africa is consistently placed as one of the potential regions for the evolution of Homo sapiens. To examine the region’s human prehistory prior to the arrival of migrants from East and West Africa or Eurasia in the last 1,700 years, we generated and analyzed genome sequence data from seven ancient individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherers date to ~2,000 years ago, and we show that they were related to current-day southern San groups such as the Karretjie People. Four Iron Age farmers (300–500 years old) have genetic signatures similar to present day Bantu-speakers. The genome sequence (13x coverage) of a juvenile boy from Ballito Bay, who lived ~2,000 years ago, demonstrates that southern African Stone Age hunter-gatherers were not impacted by recent admixture; however, we estimate that all modern-day Khoekhoe and San groups have been influenced by 9–22% genetic admixture from East African/Eurasian pastoralist groups arriving >1,000 years ago, including the Ju|‘hoansi San, previously thought to have very low levels of admixture. Using traditional and new approaches, we estimate the population divergence time between the Ballito Bay boy and other groups to beyond 260,000 years ago. These estimates dramatically increases the deepest divergence amongst modern humans, coincide with the onset of the Middle Stone Age in sub-Saharan Africa, and coincide with anatomical developments of archaic humans into modern humans as represented in the local fossil record. Cumulatively, cross-disciplinary records increasingly point to southern Africa as a potential (not necessarily exclusive) ‘hot spot’ for the evolution of our species.

Objectives The objective of this study has been to confirm the sex and the affinity of an individual buried in a well‐furnished warrior grave (Bj 581) in the Viking Age town of Birka, Sweden. Previously, based on the material and historical records, the male sex has been associated with the gender of the warrior and such was the case with Bj 581. An earlier osteological classification of the individual as female was considered controversial in a historical and archaeological context. A genomic confirmation of the biological sex of the individual was considered necessary to solve the issue. Materials and methods Genome‐wide sequence data was generated in order to confirm the biological sex, to support skeletal integrity, and to investigate the genetic relationship of the individual to ancient individuals as well as modern‐day groups. Additionally, a strontium isotope analysis was conducted to highlight the mobility of the individual. Results The genomic results revealed the lack of a Y‐chromosome and thus a female biological sex, and the mtDNA analyses support a single‐individual origin of sampled elements. The genetic affinity is close to present‐day North Europeans, and within Sweden to the southern and south‐central region. Nevertheless, the Sr values are not conclusive as to whether she was of local or nonlocal origin. Discussion The identification of a female Viking warrior provides a unique insight into the Viking society, social constructions, and exceptions to the norm in the Viking time‐period. The results call for caution against generalizations regarding social orders in past societies.

Comparing the sex-specifically inherited X chromosome to the autosomes in ancient genetic samples, we (1) studied sex-specific admixture for two prehistoric migrations. For each migration, we used several admixture estimation procedures, including ADMIXTURE model-based clustering (2), comparing X-chromosomal and autosomal ancestry in contemporaneous Central Europeans, interpreting greater admixture from the migrating population on the autosomes as male-biased migration. For migration into late Neolithic/Bronze Age Central Europeans (BA) from the Pontic-Caspian steppe (SP), we inferred male-biased admixture at 5-14 males per migrating female. Lazaridis & Reich (3) contest this male-biased migration claim. For simulated individuals, they claim that ADMIXTURE provides biased X-chromosomal ancestry estimates. They argue that if the bias is taken into account, then X-chromosomal steppe ancestry is similar to our autosomal ancestry estimate, and that hence, steppe male and female contributions are similar. We conduct simulations of ancient and modern data under a range of conditions. We conclude that our inference of male-biased Pontic-Caspian steppe migration, seen using ADMIXTURE, STRUCTURE, mechanistic simulations, and X/autosomal FST, is robust. Our analysis further illuminates the impact of small haploid reference samples on ADMIXTURE; we look forward to refining sex-specific migration estimates as larger, higher-coverage ancient samples become available.

Significance The gene pool of modern Europeans was shaped through prehistoric migrations that reached the Western Mediterranean last. Obtaining biomolecular data has been challenging due to poor preservation related to adverse climatic conditions in this region. Here, we study the impact of prehistoric (Neolithic–Bronze Age) migrations in Iberia by analyzing genomic and dietary data, demonstrating that farming practices were introduced by a population genetically distinct from the first farmers in central and northern Europe. After recovering from a founder bottleneck, these first farmers mixed with local hunter-gatherers. Finally, post-Neolithic migrations had a much smaller impact on the Iberian gene pool than they had in other parts of Europe. Stable isotope analysis reveals a homogenous terrestrial diet throughout this period., Population genomic studies of ancient human remains have shown how modern-day European population structure has been shaped by a number of prehistoric migrations. The Neolithization of Europe has been associated with large-scale migrations from Anatolia, which was followed by migrations of herders from the Pontic steppe at the onset of the Bronze Age. Southwestern Europe was one of the last parts of the continent reached by these migrations, and modern-day populations from this region show intriguing similarities to the initial Neolithic migrants. Partly due to climatic conditions that are unfavorable for DNA preservation, regional studies on the Mediterranean remain challenging. Here, we present genome-wide sequence data from 13 individuals combined with stable isotope analysis from the north and south of Iberia covering a four-millennial temporal transect (7,500–3,500 BP). Early Iberian farmers and Early Central European farmers exhibit significant genetic differences, suggesting two independent fronts of the Neolithic expansion. The first Neolithic migrants that arrived in Iberia had low levels of genetic diversity, potentially reflecting a small number of individuals; this diversity gradually increased over time from mixing with local hunter-gatherers and potential population expansion. The impact of post-Neolithic migrations on Iberia was much smaller than for the rest of the continent, showing little external influence from the Neolithic to the Bronze Age. Paleodietary reconstruction shows that these populations have a remarkable degree of dietary homogeneity across space and time, suggesting a strong reliance on terrestrial food resources despite changing culture and genetic make-up.

Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gate-way out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of northeast Africa by genotyping ~3.9 million SNPs in 221 individuals from 18 populations sampled in Sudan and South Sudan and combine this data with published genome-wide data from surrounding areas. We find a strong genetic divide between the populations from the northeastern parts of the region (Nubians, central Arab populations, and the Beja) and populations towards the west and south (Nilotes, Darfur and Kordofan populations). This differentiation is mainly caused by a large Eurasian ancestry component of the northeast populations likely driven by migration of Middle Eastern groups followed by admixture that affected the local populations in a north-to-south succession of events. Genetic evidence points to an early admixture event in the Nubians, concurrent with historical contact between North Sudanese and Arab groups. We estimate the admixture in current-day Sudanese Arab populations to about 700 years ago, coinciding with the fall of Dongola in 1315/1316 AD, a wave of admixture that reached the Darfurian/Kordofanian populations some 400–200 years ago. In contrast to the northeastern populations, the current-day Nilotic populations from the south of the region display little or no admixture from Eurasian groups indicating long-term isolation and population continuity in these areas of northeast Africa., Author summary Northeast Africa has geographic and historical links to Eurasia via the Middle East and the Arabian Peninsula, but the demographic history of the region itself has been more elusive. We investigate genomic diversity of northeast African populations and found a clear bimodal distribution of variation, correlated with geography, and likely driven by Eurasian admixture in the wake of migrations along the Nile. This admixture process largely coincides with the time of the Arab conquest, spreading in a southbound direction along the Nile and the Blue Nile. Nilotic populations occupying the region around the White Nile show long-term continuity, genetic isolation and genetic links to ancestral East African people. Compared to current times, groups that are ancestral to the current-day Nilotes likely inhabited a larger area of northeast Africa prior to the migration from the Middle East as their ancestry component can still be found in a large area. Our findings reveal the genetic history of Sudanese and South Sudanese people, broaden our knowledge on demographic history of humans, and quantify the impact of large-scale historic migration events in northeast Africa.

Dramatic events in human prehistory, such as the spread of agriculture to Europe from Anatolia and the Late Neolithic/Bronze Age (LNBA) migration from the Pontic-Caspian steppe, can be investigated using patterns of genetic variation among the people that lived in those times. In particular, studies of differing female and male demographic histories on the basis of ancient genomes can provide information about complexities of social structures and cultural interactions in prehistoric populations. We use a mechanistic admixture model to compare the sex-specifically-inherited X chromosome to the autosomes in 20 early Neolithic and 16 LNBA human remains. Contrary to previous hypotheses suggested by the patrilocality of many agricultural populations, we find no evidence of sex-biased admixture during the migration that spread farming across Europe during the early Neolithic. For later migrations from the Pontic steppe during the LNBA, however, we estimate a dramatic male bias, with ~5-14 migrating males for every migrating female. We find evidence of ongoing, primarily male, migration from the steppe to central Europe over a period of multiple generations, with a level of sex bias that excludes a pulse migration during a single generation. The contrasting patterns of sex-specific migration during these two migrations suggest a view of differing cultural histories in which the Neolithic transition was driven by mass migration of both males and females in roughly equal numbers, perhaps whole families, whereas the later Bronze Age migration and cultural shift were instead driven by male migration, potentially connected to new technology and conquest.

After the dispersal of modern humans (Homo sapiens) Out of Africa, hominins with a similar morphology to that of present-day humans initiated the gradual demographic expansion into Eurasia. The mitogenome (33-fold coverage) of the Peştera Muierii 1 individual (PM1) from Romania (35 ky cal BP) we present in this article corresponds fully to Homo sapiens, whilst exhibiting a mosaic of morphological features related to both modern humans and Neandertals. We have identified the PM1 mitogenome as a basal haplogroup U6*, not previously found in any ancient or present-day humans. The derived U6 haplotypes are predominantly found in present-day North-Western African populations. Concomitantly, those found in Europe have been attributed to recent gene-flow from North Africa. The presence of the basal haplogroup U6* in South East Europe (Romania) at 35 ky BP confirms a Eurasian origin of the U6 mitochondrial lineage. Consequently, we propose that the PM1 lineage is an offshoot to South East Europe that can be traced to the Early Upper Paleolithic back migration from Western Asia to North Africa, during which the U6 lineage diversified, until the emergence of the present-day U6 African lineages.

Genomic information from ancient human remains is beginning to show its full potential for learning about human prehistory. We review the last few years' dramatic finds about European prehistory based on genomic data from humans that lived many millennia ago and relate it to modern-day patterns of genomic variation. The early times, the Upper Palaeolithic, appears to contain several population turn-overs followed by more stable populations after the Last Glacial Maximum and during the Mesolithic. Some 11,000 years ago the migrations driving the Neolithic transition start from around Anatolia and reach the north and the west of Europe millennia later followed by major migrations during the Bronze age. These findings show that culture and lifestyle were major determinants of genomic differentiation and similarity in pre-historic Europe rather than geography as is the case today.

The transcriptome and proteome of Arabidopsis thaliana are reduced in nitrogen content when compared with other taxa, which may result from ecological nitrogen limitation. We hypothesized that if the A. thaliana transcriptome is selected for a low nitrogen content, nitrogen-reducing derived alleles of single nucleotide polymorphisms (SNPs) should segregate at higher frequencies than nitrogen-increasing alleles. This pattern should be stronger in populations with a larger effective population size (N(e)) if natural selection is more efficient in large than in small populations. We analyzed variation in the nitrogen content in the transcriptome of 80 natural accessions of A. thaliana. In contrast to our expectations, derived alleles increase the nitrogen content in all accessions, and there is a positive correlation between nitrogen difference and derived allele frequency, which is strongest with nonsynonymous SNPs (nsSNPs). Also, there is a positive correlation between nitrogen difference and N(e) that was mainly caused by nsSNPs. These observations led us to reject the hypothesis that the transcriptome of A. thaliana is currently under selection to reduce nitrogen content. Instead, we show that a change in nitrogen content is a side effect of interacting evolutionary factors that influence base composition and include mutational bias, purifying selection of functionally deleterious alleles, and GC-biased gene conversion. We provide strong evidence that GC-biased gene conversion may play an important role for base composition in the highly selfing plant A. thaliana.

The domestication of plants frequently results in a high level of genetic differentiation between domesticated plants and their wild progenitors. This process is counteracted by gene flow between wild and domesticated plants because they are usually able to inter-mate and to exchange genes. We investigated the extent of gene flow between wild barley Hordeum spontaneum and cultivated barley Hordeum vulgare, and its effect on population structure in wild barley by analysing a collection of 896 wild barley accessions (Barley1K) from Israel and all available Israeli H. vulgare accessions from the Israeli gene bank. We compared the performance of simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) marker data genotyped over a core collection in estimating population parameters. Estimates of gene flow rates with SSR markers indicated a high level of introgression from cultivated barley into wild barley. After removing accessions from the wild barley sample that were recently admixed with cultivated barley, the inference of population structure improved significantly. Both SSR and SNP markers showed that the genetic population structure of wild barley in Israel corresponds to the three major ecogeographic regions: the coast, the Mediterranean north and the deserts in the Jordan valley and the South. Gene flow rates were estimated to be higher from north to south than in the opposite direction. As has been observed in other crop species, there is a significant exchange of alleles between the wild species and domesticated varieties that needs to be accounted for in the population genetic analysis of domestication.

The plant Arabidopsis thaliana occurs naturally in many different habitats throughout Eurasia. As a foundation for identifying genetic variation contributing to adaptation to diverse environments, a 1001 Genomes Project to sequence geographically diverse A. thaliana strains has been initiated. Here we present the first phase of this project, based on population-scale sequencing of 80 strains drawn from eight regions throughout the species' native range. We describe the majority of common small-scale polymorphisms as well as many larger insertions and deletions in the A. thaliana pan-genome, their effects on gene function, and the patterns of local and global linkage among these variants. The action of processes other than spontaneous mutation is identified by comparing the spectrum of mutations that have accumulated since A. thaliana diverged from its closest relative 10 million years ago with the spectrum observed in the laboratory. Recent species-wide selective sweeps are rare, and potentially deleterious mutations are more common in marginal populations.

Plant genetic diversity has been mainly investigated with neutral markers, but large-scale DNA sequencing projects now enable the identification and analysis of different classes of genetic polymorphisms, such as non-synonymous single nucleotide polymorphisms (nsSNPs) in protein coding sequences. Using the SIFT and MAPP programs to predict whether nsSNPs are tolerated (i.e., effectively neutral) or deleterious for protein function, genome-wide nsSNP data from Arabidopsis thaliana and rice were analyzed. In both species, about 20% of polymorphic sites with nsSNPs were classified as deleterious; they segregate at lower allele frequencies than tolerated nsSNPs due to purifying selection. Furthermore, A. thaliana accessions from marginal populations show a higher relative proportion of deleterious nsSNPs, which likely reflects differential selection or demographic effects in subpopulations. To evaluate the sensitivity of predictions, genes from model and crop plants with known functional effects of nsSNPs were inferred with the algorithms. The programs predicted about 70% of nsSNPs correctly as tolerated or deleterious, i.e., as having a functional effect. Forward-in-time simulations of bottleneck and domestication models indicated a high power to detect demographic effects on nsSNP frequencies in sufficiently large datasets. The results indicate that nsSNPs are useful markers for analyzing genetic diversity in plant genetic resources and breeding populations to infer natural/artificial selection and genetic drift.

Altitudinal gradients in mountain regions are short-range clines of different environmental parameters such as temperature or radiation. We investigated genomic and phenotypic signatures of adaptation to such gradients in five Arabidopsis thaliana populations from the North Italian Alps that originated from 580 to 2350 m altitude by resequencing pools of 19-29 individuals from each population. The sample includes two pairs of low- and high-altitude populations from two different valleys. High-altitude populations showed a lower nucleotide diversity and negative Tajima's D values and were more closely related to each other than to low-altitude populations from the same valley. Despite their close geographic proximity, demographic analysis revealed that low- and high-altitude populations split between 260 000 and 15 000 years before present. Single nucleotide polymorphisms whose allele frequencies were highly differentiated between low- and high-altitude populations identified genomic regions of up to 50 kb length where patterns of genetic diversity are consistent with signatures of local selective sweeps. These regions harbour multiple genes involved in stress response. Variation among populations in two putative adaptive phenotypic traits, frost tolerance and response to light/UV stress was not correlated with altitude. Taken together, the spatial distribution of genetic diversity reflects a potentially adaptive differentiation between low- and high-altitude populations, whereas the phenotypic differentiation in the two traits investigated does not. It may resemble an interaction between adaptation to the local microhabitat and demographic history influenced by historical glaciation cycles, recent seed dispersal and genetic drift in local populations.