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  • 1.
    Ausmees, Kristiina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Sanchez-Quinto, Federico
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    An empirical evaluation of genotype imputation of ancient DNA2019Report (Other academic)
  • 2.
    Babiker, Hiba
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Schlebusch, Carina M
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Hassan, Hisham Y
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci.2011In: Investigative Genetics, ISSN 2041-2223, E-ISSN 2041-2223, Vol. 2, no 1Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: There is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region.

    RESULT: We report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE) was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia.

    CONCLUSION: We show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.

  • 3. Blum, Michael G. B.
    et al.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Deep Divergences of Human Gene Trees and Models of Human Origins2011In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 28, no 2, p. 889-898Article in journal (Refereed)
    Abstract [en]

    Two competing hypotheses are at the forefront of the debate on modern human origins. In the first scenario, known as the recent Out-of-Africa hypothesis, modern humans arose in Africa about 100,000-200,000 years ago and spread throughout the world by replacing the local archaic human populations. By contrast, the second hypothesis posits substantial gene flow between archaic and emerging modern humans. In the last two decades, the young time estimates-between 100,000 and 200,000 years-of the most recent common ancestors for the mitochondrion and the Y chromosome provided evidence in favor of a recent African origin of modern humans. However, the presence of very old lineages for autosonnal and X-linked genes has often been claimed to be incompatible with a simple, single origin of modern humans. Through the analysis of a public DNA sequence database, we find, similar to previous estimates, that the common ancestors of autosomal and X-linked genes are indeed very old, living, on average, respectively, 1,500,000 and 1,000,000 years ago. However, contrary to previous conclusions, we find that these deep gene genealogies are consistent with the Out-of-Africa scenario provided that the ancestral effective population size was approximately 14,000 individuals. We show that an ancient bottleneck in the Middle Pleistocene, possibly arising from an ancestral structured population, can reconcile the contradictory findings from the mitochondrion on the one hand, with the autosomes and the X chromosome on the other hand.

  • 4.
    Breton, Gwenna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Schlebusch, Carina M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University.
    Lombard, Marlize
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Soodyall, Himla
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Lactase Persistence Alleles Reveal Partial East African Ancestry of Southern African Khoe Pastoralists2014In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 24, no 8, p. 852-858Article in journal (Refereed)
    Abstract [en]

    The ability to digest milk into adulthood, lactase persistence (LP), as well as specific genetic variants associated with LP, is heterogeneously distributed in global populations [1-4]. These variants were most likely targets of selection when some populations converted from hunter-gatherer to pastoralist or farming lifestyles [5-7]. Specific LP polymorphisms are associated with particular geographic regions and populations [1-4, 8-10]; however, they have not been extensively studied in southern Africa. We investigate the LP-regulatory region in 267 individuals from 13 southern African populations (including descendants of hunter-gatherers, pastoralists, and agropastoralists), providing the first comprehensive study of the LP-regulatory region in a large group of southern Africans. The "East African" LP single-nucleotide polymorphism (SNP) (14010G>C) was found at high frequency (>20%) in a strict pastoralist Khoe population, the Nama of Namibia, suggesting a connection to East Africa, whereas the "European" LP SNP (13910C>T) was found in populations of mixed ancestry. Using genome-wide data from various African populations, we identify admixture (13%) in the Nama, from an Afro-Asiatic group dating to >1,300 years ago, with the remaining fraction of their genomes being from San hunter-gatherers. We also find evidence of selection around the LCT gene among Khoe-speaking groups, and the substantial frequency of the 14010C variant among the Nama is best explained by adaptation to digesting milk. These genome-local and genome-wide results support a model in which an East African group brought pastoralist practices to southern Africa and admixed with local hunter-gatherers to form the ancestors of Khoe people.

  • 5.
    Chylenski, Maciej
    et al.
    Adam Mickiewicz Univ, Fac Hist, Inst Archaeol, Umultowska 89D, PL-61614 Poznan, Poland..
    Juras, Anna
    Adam Mickiewicz Univ, Fac Biol, Inst Anthropol, Dept Human Evolutionary Biol, Umultowska 89, PL-61614 Poznan, Poland..
    Ehler, Edvard
    Adam Mickiewicz Univ, Fac Biol, Inst Anthropol, Dept Human Evolutionary Biol, Umultowska 89, PL-61614 Poznan, Poland.;Charles Univ Prague, Fac Educ, Dept Biol & Environm Studies, Magdaleny Rettigove 4, Prague 11639, Czech Republic..
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Piontek, Janusz
    Adam Mickiewicz Univ, Fac Biol, Inst Anthropol, Dept Human Evolutionary Biol, Umultowska 89, PL-61614 Poznan, Poland..
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Marciniak, Arkadiusz
    Adam Mickiewicz Univ, Fac Hist, Inst Archaeol, Umultowska 89D, PL-61614 Poznan, Poland..
    Dabert, Miroslawa
    Adam Mickiewicz Univ, Fac Biol, Mol Biol Techn Lab, Umultowska 89, PL-61614 Poznan, Poland..
    Late Danubian mitochondrial genomes shed light into the Neolithisation of Central Europe in the 5th millennium BC2017In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 17, article id 80Article in journal (Refereed)
    Abstract [en]

    Background: Recent aDNA studies are progressively focusing on various Neolithic and Hunter-Gatherer (HG) populations, providing arguments in favor of major migrations accompanying European Neolithisation. The major focus was so far on the Linear Pottery Culture (LBK), which introduced the Neolithic way of life in Central Europe in the second half of 6th millennium BC. It is widely agreed that people of this culture were genetically different from local HGs and no genetic exchange is seen between the two groups. From the other hand some degree of resurgence of HGs genetic component is seen in late Neolithic groups belonging to the complex of the Funnel Beaker Cultures (TRB). Less attention is brought to various middle Neolithic cultures belonging to Late Danubian sequence which chronologically fall in between those two abovementioned groups. We suspected that genetic influx from HG to farming communities might have happened in Late Danubian cultures since archaeologists see extensive contacts between those two communities. Results: Here we address this issue by presenting 5 complete mitochondrial genomes of various late Danubian individuals from modern-day Poland and combining it with available published data. Our data show that Late Danubian cultures are maternally closely related to Funnel Beaker groups instead of culturally similar LBK. Conclusions: We assume that it is an effect of the presence of individuals belonging to U5 haplogroup both in Late Danubians and the TRB. The U5 haplogroup is thought to be a typical for HGs of Europe and therefore we argue that it is an additional evidence of genetic exchange between farming and HG groups taking place at least as far back as in middle Neolithic, in the Late Danubian communities.

  • 6.
    Coutinho, Alexandra
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Edlund, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Henshilwood, Christopher
    Institutt for arkeologi, historie, kultur- og religionsvitenskap, Universitetet i Bergen.
    van Niekerk, Karen
    Department of Archaeology, History, Cultural Studies and Religion, Universitetet i Bergen.
    Lombard, Marlize
    Department of Anthropology and Development Studies, University of Johannesburg.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groupsManuscript (preprint) (Other academic)
    Abstract [en]

    The indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting to arrive some 400 years ago and their descendants are today mixed with Europeans and Asians. Here we sequence and analyze the genome (1.01 times coverage) of a Later Stone Age individual, who lived about 200 years ago, obtained from a hair sample excavated at Vaalkrans Shelter southern Cape, South Africa. We analyzed this genome, along with genetic data from 10 prehistoric individuals from southern Africa spanning the last 2000 years. Our results show that the individual from Vaalkrans was a man who traced ~80% of his ancestry to local southern San hunter-gatherer populations, and ~20% to a mixed East African-Eurasian source. This genetic make-up is very similar to modern-day Khoekhoe individuals from South Africa and Namibia. The Vaalkrans man’s genome reveals how the Holocene pastoralist migration event shaped the genomic landscape of historic and current southern African populations and shows that Khoekhoe groups lived in the southern Cape as late as 200 years ago.

  • 7.
    Coutinho, Alexandra
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Munters, Arielle
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Svensson, Emma
    Area Offices, Office of Technology and Science; The Student Service Unit.
    Götherström, Anders
    Department of Archaeology and Classical Studies, Stockholm University.
    Storå, Jan
    Department of Archaeology and Classical Studies, Stockholm University.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herdersManuscript (preprint) (Other academic)
    Abstract [en]

    The 3rd millennium BCE was a period of marked cultural and demographic developments in Europe. Here we sequence genome data from human skeletal remains to study the interaction between two Scandinavian cultures; the hunter-gatherer Pitted Ware culture (PWC, 3400-2400 BCE) and the farmer/herder Battle Axe culture (BAC, 2800-2300 BCE), two cultures who have been found to be represented by distinct gene-pools in northern Europe. We focus on the Baltic island of Gotland that presents Scandinavia’s richest record of PWC gravesites where the majority of individuals are buried in typical PWC manner (supine position), but with some burials indicating BAC influences (either hocker position burial or burials with BAC associated artifacts). We sequenced and analyzed the genomes of 25 individuals of both types of burials excavated in three gravesites in order to determine if the different burial styles were associated with the different gene-pools (PWC or BAC) at the time. The genomic data show that all individuals belonged to one genetic population – that of the PWC – irrespective of the burial style. We conclude that the PWC communities on the island of Gotland were culturally influenced by the BAC society, without any signs of gene-flow.

  • 8.
    Coutinho, Alexandra
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    The Evolution of Adaptive traits in Indigenous human populations in Sub-Saharan AfricaManuscript (preprint) (Other academic)
    Abstract [en]

    Several well-known genetic variants that confer disease resistance or other adaptive advantages have been investigated in modern-day populations across the globe. In particular, sub-Saharan African populations display variation for many of these loci. In this study, we investigate allele frequencies underlying functional variants of interest in sub-Saharan African populations. By also investigating sequence data from ancient human remains from excavated sites in sub-Saharan Africa, we can start to get an indication of the allele frequency trajectories of adaptive variants, how they have diffused through the African genetic landscape, and how much migration and admixture played a role in the distribution of these variants in modern-day African populations. Our results show that as well as selection, migration has had a large influence on changing allele frequency through time in variants associated with disease resistance, salt sensitivity and metabolism. Yet in other variants, such as some associated with skin pigmentation, allele frequencies have changed little over time. Lastly, this study emphasizes the need for continued study of African populations, as due to the sheer genetic diversity present in Africa, different functional variants may confer similar means of adaptation than those we know for out-of-Africa populations. This study is the first to comprehensively investigate adaptive variants in both ancient and modern Africans, and further research will continue to reveal how the genetic landscape of modern humans has changed, and continues to change through time.

  • 9.
    da Fonseca, Rute R.
    et al.
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark.;Univ Copenhagen, Bioinformat Ctr, DK-2200 Copenhagen, Denmark..
    Smith, Bruce D.
    Smithsonian Inst, Natl Museum Nat Hist, Dept Anthropol, Program Human Ecol & Archaeobiol, Washington, DC 20560 USA..
    Wales, Nathan
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark..
    Cappellini, Enrico
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark..
    Skoglund, Pontus
    Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA..
    Fumagalli, Matteo
    Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA..
    Samaniego, Jose Alfredo
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark..
    Caroe, Christian
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark..
    Avila-Arcos, Mara C.
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark.;Stanford Univ, Dept Genet, Sch Med, Stanford, CA 94305 USA..
    Hufnagel, David E.
    Iowa State Univ, Dept Ecol Evolut & Organismal Biol, Ames, IA 50011 USA..
    Korneliussen, Thorfinn Sand
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark..
    Vieira, Filipe Garrett
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark.;Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA..
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Arriaza, Bernardo
    Univ Tarapaca, Inst Alta Invest, Arica 15101, Chile..
    Willerslev, Eske
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark..
    Nielsen, Rasmus
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark.;Univ Calif Berkeley, Dept Integrat Biol & Stat, Berkeley, CA 94720 USA..
    Hufford, Matthew B.
    Iowa State Univ, Dept Ecol Evolut & Organismal Biol, Ames, IA 50011 USA..
    Albrechtsen, Anders
    Univ Copenhagen, Bioinformat Ctr, DK-2200 Copenhagen, Denmark..
    Ross-Ibarra, Jeffrey
    Univ Calif Davis, Dept Plant Sci, Ctr Populat Biol, Davis, CA 95616 USA.;Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA..
    Gilbert, M. Thomas P.
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark.;Curtin Univ, Trace & Environm DNA Lab, Dept Environm & Agr, Perth, WA 6102, Australia..
    The origin and evolution of maize in the Southwestern United States2015In: Nature Plants, ISSN 2055-026X, Vol. 1, no 1, article id UNSP 14003Article in journal (Refereed)
    Abstract [en]

    The origin of maize (Zea mays mays) in the US Southwest remains contentious, with conflicting archaeological data supporting either coastal(1-4) or highland(5,6) routes of diffusion of maize into the United States. Furthermore, the genetics of adaptation to the new environmental and cultural context of the Southwest is largely uncharacterized(7). To address these issues, we compared nuclear DNA from 32 archaeological maize samples spanning 6,000 years of evolution to modern landraces. We found that the initial diffusion of maize into the Southwest about 4,000 years ago is likely to have occurred along a highland route, followed by gene flow from a lowland coastal maize beginning at least 2,000 years ago. Our population genetic analysis also enabled us to differentiate selection during domestication for adaptation to the climatic and cultural environment of the Southwest, identifying adaptation loci relevant to drought tolerance and sugar content.

  • 10. DeGiorgio, Michael
    et al.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Rosenberg, Noah A.
    Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa2009In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, no 38, p. 16057-16062Article in journal (Refereed)
    Abstract [en]

    Studies of worldwide human variation have discovered three trends in summary statistics as a function of increasing geographic distance from East Africa: a decrease in heterozygosity, an increase in linkage disequilibrium (LD), and a decrease in the slope of the ancestral allele frequency spectrum. Forward simulations of unlinked loci have shown that the decline in heterozygosity can be described by a serial founder model, in which populations migrate outward from Africa through a process where each of a series of populations is formed from a subset of the previous population in the outward expansion. Here, we extend this approach by developing a retrospective coalescent-based serial founder model that incorporates linked loci. Our model both recovers the observed decline in heterozygosity with increasing distance from Africa and produces the patterns observed in LD and the ancestral allele frequency spectrum. Surprisingly, although migration between neighboring populations and limited admixture between modern and archaic humans can be accommodated in the model while continuing to explain the three trends, a competing model in which a wave of outward modern human migration expands into a series of preexisting archaic populations produces nearly opposite patterns to those observed in the data. We conclude by developing a simpler model to illustrate that the feature that permits the serial founder model but not the archaic persistence model to explain the three trends observed with increasing distance from Africa is its incorporation of a cumulative effect of genetic drift as humans colonized the world.

  • 11. Duforet-Frebourg, Nicolas
    et al.
    Gattepaille, Lucie M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Blum, Michael G. B.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    HaploPOP: a software that improves population assignment by combining markers into haplotypes2015In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 16, article id 242Article in journal (Refereed)
    Abstract [en]

    Background: In ecology and forensics, some population assignment techniques use molecular markers to assign individuals to known groups. However, assigning individuals to known populations can be difficult if the level of genetic differentiation among populations is small. Most assignment studies handle independent markers, often by pruning markers in Linkage Disequilibrium (LD), ignoring the information contained in the correlation among markers due to LD. Results: To improve the accuracy of population assignment, we present an algorithm, implemented in the HaploPOP software, that combines markers into haplotypes, without requiring independence. The algorithm is based on the Gain of Informativeness for Assignment that provides a measure to decide if a pair of markers should be combined into haplotypes, or not, in order to improve assignment. Because complete exploration of all possible solutions for constructing haplotypes is computationally prohibitive, our approach uses a greedy algorithm based on windows of fixed sizes. We evaluate the performance of HaploPOP to assign individuals to populations using a split-validation approach. We investigate both simulated SNPs data and dense genotype data from individuals from Spain and Portugal. Conclusions: Our results show that constructing haplotypes with HaploPOP can substantially reduce assignment error. The HaploPOP software is freely available as a command-line software at www.ieg.uu.se/Jakobsson/software/HaploPOP/.

  • 12.
    Fraser, Magdalena
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Sanchez-Quinto, Federico
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Evans, Jane
    Natural Environment Research Council, Isotope Geosciences Laboratory, British Geological Survey, Keyworth, Nottingham NG12 5GG, UK.
    Storå, Jan
    Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91 Stockholm, Sweden.
    Götherström, Anders
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91 Stockholm, Sweden.
    Wallin, Paul
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Knutsson, Kjel
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    New insights on cultural dualism and population structure in the MiddleNeolithic Funnel Beaker culture on the island of Gotland2018In: Journal of Archaeological Science: Reports, ISSN 2352-409X, E-ISSN 2352-4103, Vol. 17, p. 325-334Article in journal (Refereed)
    Abstract [en]

    In recent years it has been shown that the Neolithization of Europe was partly driven by migration of farming groups admixing with local hunter-gatherer groups as they dispersed across the continent. However, little research has been done on the cultural duality of contemporaneous foragers and farming populations in the same region. Here we investigate the demographic history of the Funnel Beaker culture [Trichterbecherkultur or TRB, c. 4000–2800 cal BCE], and the sub-Neolithic Pitted Ware culture complex [PWC, c. 3300–2300 cal BCE] during the Nordic Middle Neolithic period on the island of Gotland, Sweden. We use a multidisciplinary approach to investigate individuals buried in the Ansarve dolmen, the only confirmed TRB burial on the island. We present new radiocarbon dating, isotopic analyses for diet and mobility, and mitochondrial DNA haplogroup data to infer maternal inheritance. We also present a new Sr-baseline of 0.71208 ± 0.0016 for the local isotope variation. We compare and discuss our findings together with that of contemporaneous populations in Sweden and the North European mainland.

    The radiocarbon dating and Strontium isotopic ratios show that the dolmen was used between c. 3300–2700 cal BCE by a population which displayed local Sr-signals. Mitochondrial data show that the individuals buried in the Ansarve dolmen had maternal genetic affinity to that of other Early and Middle Neolithic farming cultures in Europe, distinct from that of the contemporaneous PWC on the island. Furthermore, they exhibited a strict terrestrial and/or slightly varied diet in contrast to the strict marine diet of the PWC. The findings indicate that two different contemporary groups coexisted on the same island for several hundred years with separate cultural identity, lifestyles, as well as dietary patterns.

  • 13.
    Fraser, Magdalena
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Sanchez-Quinto, Federico
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Evans, Jane
    Natural Environment Research Council, Isotope Geosciences Laboratory, British Geological Survey, Keyworth, Nottingham NG12 5GG, UK.
    Svedjemo, Gustaf
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Knutsson, Kjel
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Götherström, Anders
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91 Stockholm, Sweden.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Wallin, Paul
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Storå, Jan
    Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, SE-106 91 Stockholm, Sweden.
    The Stone Cist Conundrum: A multidisciplinary approach to investigate Late Neolithic/ Early Bronze Age population demography on the Island of Gotland2018In: Journal of Archaeological Science: Reports, ISSN 2352-409X, E-ISSN 2001-1199, Vol. 20, p. 324-337Article in journal (Refereed)
    Abstract [en]

    The Late Neolithic period in Scandinavia [LN, c. 2350-1700 cal BCE] marks a time of considerable changes in settlement patterns, economy, and material culture. This shift also lays the foundation for the demographic developments in the Early Bronze Age [EBA, c. 1700-1100 cal BCE]. However, little is presently known regarding the developments from these time-periods on the island of Gotland in the Baltic Sea. During the Middle Neolithic period [MN, c. 3300-2350 cal BCE], Gotland was inhabited by groups associated with the Funnel Beaker culture [TRB, c. 4000-2700 cal BCE], and the sub-Neolithic Pitted Ware culture [PWC, c. 3300-2300 cal BCE]. Some indications of connections with the Bathe Axe/Corded Ware cultures [BAC/CWC, c. 2800-2300 cal BCE] have also been found, but no typical BAC/CWC burials have been located on the island to date. Here, we investigate the chronological and internal relationship of twenty-three individuals buried in four LN/EBA stone cist burials; Haffinds, Hagur, Suderkvie, and Utalskog on Gotland. We present eleven mitochondrial genomes [from 23 X to 1271 X coverage], and twenty-three new radiocarbon dates, as well as stable isotope data for diet. We examine the local Sr-baseline range for Gotland, and present new Sr-data to discuss mobility patterns of the individuals. The genetic results are compared and discussed in light of earlier cultural periods from Gotland [TRB and PWC], and CWC from the European continent, as well as contemporaneous LN secondary burials in the MN Ansarve dolmen. We find that all burials were used into the EBA, but only two of the cists showed activity already during the LN. We also see some mobility to Gotland during the LN/EBA period based on Strontium and mitochondrial data. We see a shift in the dietary pattern compared to the preceding period on the island [TRB and PWC], and the two LN individuals from the Ansarve dolmen exhibited different dietary and mobility patterns compared to the individuals from the LN/EBA stone cist burials. We find that most of the cist burials were used by individuals local to the area of the burials, with the exception of the large LN/EBA Haffinds cist burial which showed higher levels of mobility. Our modeling of ancestral mitochondrial contribution from chronologically older individuals recovered in the cultural contexts of TRB, PWC and CWC show that the best model is a 55/45 mix of CWC and TRB individuals. A 3-way model with a slight influx from PWC [5%] also had a good fit. This is difficult to reconcile with the current archaeological evidence on the island. We suggest that the maternal CWC/TRB contribution we see in the local LN/EBA individuals derives from migrants after the Scandinavian MN period, which possible also admixed with smaller local groups connected with the PWC. Further genomic analyses of these groups on Gotland will help to clarify the demographic history during the MN to EBA time periods.

  • 14.
    Gattepaille, Lucie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Inferring Past Effective Population Size from Distributions of Coalescent Times2016In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 204, no 3, p. 1191-1206Article in journal (Refereed)
    Abstract [en]

    Inferring and understanding changes in effective population size over time is a major challenge for population genetics. Here we investigate some theoretical properties of random-mating populations with varying size over time. In particular, we present an exact solution to compute the population size as a function of time, N-e(t), based on distributions of coalescent times of samples of any size. This result reduces the problem of population size inference to a problem of estimating coalescent time distributions. To illustrate the analytic results, we design a heuristic method using a tree-inference algorithm and investigate simulated and empirical population-genetic data. We investigate the effects of a range of conditions associated with empirical data, for instance number of loci, sample size, mutation rate, and cryptic recombination. We show that our approach performs well with genomic data ( 10,000 loci) and that increasing the sample size from 2 to 10 greatly improves the inference of Ne(t) whereas further increase in sample size results in modest improvements, even under a scenario of exponential growth. We also investigate the impact of recombination and characterize the potential biases in inference of Ne(t). The approach can handle large sample sizes and the computations are fast. We apply our method to human genomes from four populations and reconstruct population size profiles that are coherent with previous finds, including the Out-of-Africa bottleneck. Additionally, we uncover a potential difference in population size between African and non-African populations as early as 400 KYA. In summary, we provide an analytic relationship between distributions of coalescent times and Ne(t), which can be incorporated into powerful approaches for inferring past population sizes from population-genomic data.

  • 15.
    Gattepaille, Lucie M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Combining Markers into Haplotypes Can Improve Population Structure Inference2012In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 190, no 1, p. 159-174Article in journal (Refereed)
    Abstract [en]

    High-throughput genotyping and sequencing technologies can generate dense sets of genetic markers for large numbers of individuals. For most species, these data will contain many markers in linkage disequilibrium (LD). To utilize such data for population structure inference, we investigate the use of haplotypes constructed by combining the alleles at single-nucleotide polymorphisms (SNPs). We introduce a statistic derived from information theory, the gain of informativeness for assignment (GIA), which quantifies the additional information for assigning individuals to populations using haplotype data compared to using individual loci separately. Using a two-loci-two-allele model, we demonstrate that combining markers in linkage equilibrium into haplotypes always leads to non-positive GIA, suggesting that combining the two markers is not advantageous for ancestry inference. However, for loci in LD, GIA is often positive, suggesting that assignment can be improved by combining markers into haplotypes. Using GIA as a criterion for combining markers into haplotypes, we demonstrate for simulated data a significant improvement of assigning individuals to candidate populations. For the many cases that we investigate, incorrect assignment was reduced between 26% and 97% using haplotype data. For empirical data from French and German individuals, the incorrectly assigned individuals can, for example, be decreased by 73% using haplotypes. Our results can be useful for challenging population structure and assignment problems, in particular for studies where large-scale population-genomic data are available.

  • 16.
    Gattepaille, Lucie M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Blum, M. G. B.
    Inferring population size changes with sequence and SNP data: lessons from human bottlenecks2013In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 110, no 5, p. 409-419Article, review/survey (Refereed)
    Abstract [en]

    Reconstructing historical variation of population size from sequence and single-nucleotide polymorphism (SNP) data is valuable for understanding the evolutionary history of species. Changes in the population size of humans have been thoroughly investigated, and we review different methodologies of demographic reconstruction, specifically focusing on human bottlenecks. In addition to the classical approaches based on the site-frequency spectrum (SFS) or based on linkage disequilibrium, we also review more recent approaches that utilize atypical shared genomic fragments, such as identical by descent or homozygous segments between or within individuals. Compared with methods based on the SFS, these methods are well suited for detecting recent bottlenecks. In general, all these various methods suffer from bias and dependencies on confounding factors such as population structure or poor specification of the mutational and recombination processes, which can affect the demographic reconstruction. With the exception of SFS-based methods, the effects of confounding factors on the inference methods remain poorly investigated. We conclude that an important step when investigating population size changes rests on validating the demographic model by investigating to what extent the fitted demographic model can reproduce the main features of the polymorphism data. 

  • 17.
    Goldberg, Amy
    et al.
    Stanford Univ, Dept Biol, Stanford, CA 94305 USA..
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Rosenberg, Noah A.
    Stanford Univ, Dept Biol, Stanford, CA 94305 USA..
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ancient X chromosomes reveal contrasting sex bias in Neolithic and Bronze Age Eurasian migrations2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 10, p. 2657-2662Article in journal (Refereed)
    Abstract [en]

    Dramatic events in human prehistory, such as the spread of agriculture to Europe from Anatolia and the late Neolithic/Bronze Age migration from the Pontic-Caspian Steppe, can be investigated using patterns of genetic variation among the people who 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 with the autosomes in 20 early Neolithic and 16 late Neolithic/Bronze Age 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 late Neolithic/Bronze Age, however, we estimate a dramatic male bias, with approximately five to 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.

  • 18.
    Goldberg, Amy
    et al.
    Stanford Univ, Dept Biol, Stanford, CA, USA.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Rosenberg, Noah A.
    Stanford Univ, Dept Biol, Stanford, CA, USA.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Neolithic familial migration contrasts Bronze Age male migration inferred from ancient X chromosomes2017In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 162, no S64, p. 196-196Article in journal (Other academic)
  • 19.
    Goldberg, Amy
    et al.
    Stanford Univ, Dept Biol, Stanford, CA 94305 USA..
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala Univ, Dept Organismal Biol, S-75236 Uppsala, Sweden..
    Rosenberg, Noah A.
    Stanford Univ, Dept Biol, Stanford, CA 94305 USA..
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Robust model-based inference of male-biased admixture during Bronze Age migration from the Pontic-Caspian Steppe: Reply to Lazaridis and Reich2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 20, p. E3875-E3877Article in journal (Other academic)
  • 20.
    Günther, Torsten
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Genes mirror migrations and cultures in prehistoric Europe - a population genomic perspective2016In: Current Opinion in Genetics and Development, ISSN 0959-437X, E-ISSN 1879-0380, Vol. 41, p. 115-123Article, review/survey (Refereed)
    Abstract [en]

    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 Paleolithic, 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.

  • 21.
    Günther, Torsten
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Svensson, Emma
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Omrak, Ayca
    Stockholm Univ, Dept Archaeol & Class Studies.
    Sanchez-Quinto, Federico
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Kilinc, Gülsah Merve
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.; Middle East Tech Univ, Dept Biol Sci, Ankara.
    Krzewińska, Maja
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.
    Eriksson, Gunilla
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.
    Fraser, Magdalena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Edlund, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Munters, Arielle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Coutinho, Alexandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Simões, Luciana G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Vicente, Mário
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Sjölander, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Sellevold, Berit Jansen
    Norwegian Inst Cultural Heritage Res, Oslo.
    Jørgensen, Roger
    Arctic Univ Norway, Univ Tromsø, Tromsø Univ Museum, Tromsø.
    Claes, Peter
    Katholieke Univ Leuven, Dept Elect Engn, Ctr Proc Speech & Images, Leuven.
    Shriver, Mark D.
    Penn State Univ, Dept Anthropol, State Coll, Pennsylvania.
    Valdiosera, Cristina
    La Trobe Univ, Dept Archaeol & Hist, Melbourne.
    Netea, Mihai G.
    Radboud Univ Nijmegen, Med Ctr, Dept Internal Med, Nijmegen; Radboud Univ Nijmegen, Med Ctr, Radboud Ctr Infect Dis, Nijmegen.
    Apel, Jan
    Lund Univ, Dept Archaeol & Ancient Hist, Lund.
    Liden, Kerstin
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.
    Skar, Birgitte
    Norwegian Univ Sci & Technol Univ Museum, Trondheim.
    Storå, Jan
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.
    Götherström, Anders
    Uppsala University, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.; SciLifeLab, Stockholm.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. SciLifeLab, Stockholm.
    Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation2018In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 16, no 1, article id e2003703Article in journal (Refereed)
    Abstract [en]

    Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500-6,000 years before present (BP). 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. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, 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 potential 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.

  • 22.
    Günther, Torsten
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Valdiosera, Cristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. La Trobe Univ, Dept Archaeol & Hist, Melbourne, Vic 3086, Australia.;Univ Complutense Madrid, Inst Salud Carlos Evoluc & Comportamiento Human 3, Ctr Mixto, Madrid 28029, Spain..
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Urena, Irene
    Univ Complutense Madrid, Inst Salud Carlos Evoluc & Comportamiento Human 3, Ctr Mixto, Madrid 28029, Spain.;Univ Complutense Madrid, Fac Ciencias Geol, Dept Paleontol, E-28040 Madrid, Spain..
    Rodriguez-Varela, Ricardo
    Univ Complutense Madrid, Inst Salud Carlos Evoluc & Comportamiento Human 3, Ctr Mixto, Madrid 28029, Spain.;Univ Complutense Madrid, Fac Ciencias Geol, Dept Paleontol, E-28040 Madrid, Spain..
    Sverrisdóttir, Oddný Ósk
    Uppsala University, University Administration, Student Affairs and Academic Registry Division.
    Daskalaki, Evangelia A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Stockholm Univ, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden..
    Skoglund, Pontus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Stockholm Univ, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden.;Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA..
    Naidoo, Thijessen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Svensson, Emma M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden..
    Maria Bermudez de Castro, Jose
    Ctr Nacl Invest Evoluc Humana, Burgos 09002, Spain..
    Carbonell, Eudald
    Inst Catala Paleoecol Humana & Evolucio Social, CEIP Marcelli Domingo, Tarragona 43007, Spain..
    Dunn, Michael
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Languages, Department of Linguistics and Philology.
    Storå, Jan
    Stockholm Univ, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden..
    Iriarte, Eneko
    Univ Burgos, Dept Ciencias Hist & Geog, Burgos 09001, Spain..
    Arsuaga, Juan Luis
    Univ Complutense Madrid, Inst Salud Carlos Evoluc & Comportamiento Human 3, Ctr Mixto, Madrid 28029, Spain.;Univ Complutense Madrid, Fac Ciencias Geol, Dept Paleontol, E-28040 Madrid, Spain..
    Carretero, Jose-Miguel
    Univ Complutense Madrid, Inst Salud Carlos Evoluc & Comportamiento Human 3, Ctr Mixto, Madrid 28029, Spain.;Univ Burgos, Dept Ciencias Hist & Geog, Burgos 09001, Spain..
    Gotherstrom, Anders
    Stockholm Univ, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden..
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 38, p. 11917-11922Article in journal (Refereed)
    Abstract [en]

    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 Portalon 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 Portalon 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 Portalon 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 Portalon genomes uncover important pieces of the demographic history of Iberia and Europe and reveal how prehistoric groups relate to modern-day people.

  • 23.
    Hedenstierna-Jonson, Charlotte
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology. Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Kjellström, Anna
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden; Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden .
    Zachrisson, Torun
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Krzewińska, Maja
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Sobrado, Veronica
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Price, Neil
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Götherström, Anders
    Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    Storå, Jan
    Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
    A female Viking warrior confirmed by genomics2017In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 164, no 4, p. 853-860Article in journal (Refereed)
    Abstract [en]

    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.

  • 24.
    Hervella, M.
    et al.
    Univ Basque Country UPV EHU, Dept Genet Phys Anthropol & Anim Physiol, Barrio Sarriena S-N, Leioa 48940, Bizkaia, Spain..
    Svensson, Emma M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Alberdi, A.
    Univ Copenhagen, Nat Hist Museum Denmark, Oster Voldgade 5-7, DK-1350 Copenhagen, Denmark..
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Izagirre, N.
    Univ Basque Country UPV EHU, Dept Genet Phys Anthropol & Anim Physiol, Barrio Sarriena S-N, Leioa 48940, Bizkaia, Spain..
    Munters, Arielle R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Alonso, S.
    Univ Basque Country UPV EHU, Dept Genet Phys Anthropol & Anim Physiol, Barrio Sarriena S-N, Leioa 48940, Bizkaia, Spain..
    Ioana, M.
    Univ Med & Pharm Craiova, Human Genom Lab, Bvd 1 Mai 66, Craiova, Romania.;Radboud Univ Nijmegen, Med Ctr, Dept Internal Med, NL-6525 ED Nijmegen, Netherlands.;Radboud Univ Nijmegen, Med Ctr, Radboud Ctr Infect Dis, NL-6525 ED Nijmegen, Netherlands..
    Ridiche, F.
    Museum Oltenia, Hist & Archaeol Dept, Madona Dudu Str 14, Craiova, Romania..
    Soficaru, A.
    Romanian Acad, Fr J Rainer Inst Anthropol, Eroii Sanitari 8,POB 35-13, Bucharest, Romania..
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Netea, M. G.
    Radboud Univ Nijmegen, Med Ctr, Dept Internal Med, NL-6525 ED Nijmegen, Netherlands.;Radboud Univ Nijmegen, Med Ctr, Radboud Ctr Infect Dis, NL-6525 ED Nijmegen, Netherlands..
    de-la-Rua, C.
    Univ Basque Country UPV EHU, Dept Genet Phys Anthropol & Anim Physiol, Barrio Sarriena S-N, Leioa 48940, Bizkaia, Spain..
    The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 25501Article in journal (Refereed)
    Abstract [en]

    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 Pestera 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.

  • 25.
    Hollfelder, Nina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Schlebusch, Carina M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Babiker, Hiba
    Dept. of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany..
    Hassan, Hisham Y.
    Banoon ART and Cytogenetics Centre, Bahrain Defense Force Hospital, Manama, Kingdom of Bahrain..
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations2017In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 13, no 8, article id e1006976Article in journal (Refereed)
    Abstract [en]

    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 gateway 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 similar to 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.

  • 26. Huang, Lucy
    et al.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Pemberton, Trevor J.
    Ibrahim, Muntaser
    Nyambo, Thomas
    Omar, Sabah
    Pritchard, Jonathan K.
    Tishkoff, Sarah A.
    Rosenberg, Noah A.
    Haplotype variation and genotype imputation in African populations2011In: Genetic Epidemiology, ISSN 0741-0395, E-ISSN 1098-2272, Vol. 35, no 8, p. 766-780Article in journal (Refereed)
    Abstract [en]

    Sub-Saharan Africa has been identified as the part of the world with the greatest human genetic diversity. This high level of diversity causes difficulties for genome-wide association (GWA) studies in African populationsfor example, by reducing the accuracy of genotype imputation in African populations compared to non-African populations. Here, we investigate haplotype variation and imputation in Africa, using 253 unrelated individuals from 15 Sub-Saharan African populations. We identify the populations that provide the greatest potential for serving as reference panels for imputing genotypes in the remaining groups. Considering reference panels comprising samples of recent African descent in Phase 3 of the HapMap Project, we identify mixtures of reference groups that produce the maximal imputation accuracy in each of the sampled populations. We find that optimal HapMap mixtures and maximal imputation accuracies identified in detailed tests of imputation procedures can instead be predicted by using simple summary statistics that measure relationships between the pattern of genetic variation in a target population and the patterns in potential reference panels. Our results provide an empirical basis for facilitating the selection of reference panels in GWA studies of diverse human populations, especially those of African ancestry.

  • 27.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    COMPASS: a program for generating serial samples under an infinite sites model2009In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 25, no 21, p. 2845-2847Article in journal (Refereed)
    Abstract [en]

    The program COMPASS can generate samples that have been collected at various points in time from a population that is evolving according to a Wright-Fisher model. The samples are generated using coalescence simulations permitting various demographic scenarios and the program uses an infinite sites model to generate polymorphism data for the samples. By generating serially sampled population-genetic data, COMPASS allows investigating properties of polymorphism data that has been collected at different time points, and aid in making inference from ancient polymorphism data.

  • 28.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    The genomic footprints of Stone-Age Europeans2016In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 159, no Suppl. 62, p. 184-184Article in journal (Other academic)
  • 29.
    Jakobsson, Mattias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Edge, Michael D.
    Rosenberg, Noah A.
    The Relationship Between F-ST and the Frequency of the Most Frequent Allele2013In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 193, no 2, p. 515-528Article in journal (Refereed)
    Abstract [en]

    F-ST is frequently used as a summary of genetic differentiation among groups. It has been suggested that F-ST depends on the allele frequencies at a locus, as it exhibits a variety of peculiar properties related to genetic diversity: higher values for biallelic single-nucleotide polymorphisms (SNPs) than for multiallelic microsatellites, low values among high-diversity populations viewed as substantially distinct, and low values for populations that differ primarily in their profiles of rare alleles. A full mathematical understanding of the dependence of F-ST on allele frequencies, however, has been elusive. Here, we examine the relationship between F-ST and the frequency of the most frequent allele, demonstrating that the range of values that F-ST can take is restricted considerably by the allele-frequency distribution. For a two-population model, we derive strict bounds on F-ST as a function of the frequency M of the allele with highest mean frequency between the pair of populations. Using these bounds, we show that for a value of M chosen uniformly between 0 and 1 at a multiallelic locus whose number of alleles is left unspecified, the mean maximum F-ST is similar to 0.3585. Further, F-ST is restricted to values much less than 1 when M is low or high, and the contribution to the maximum F-ST made by the most frequent allele is on average similar to 0.4485. Using bounds on homozygosity that we have previously derived as functions of M, we describe strict bounds on F-ST in terms of the homozygosity of the total population, finding that the mean maximum F-ST given this homozygosity is 1 - In 2 approximate to 0.3069. Our results provide a conceptual basis for understanding the dependence of F-ST on allele frequencies and genetic diversity and for interpreting the roles of these quantities in computations of F-ST from population-genetic data. Further, our analysis suggests that many unusual observations of F-ST, including the relatively low F-ST values in high-diversity human populations from Africa and the relatively low estimates of F-ST for microsatellites compared to SNPs, can be understood not as biological phenomena associated with different groups of populations or classes of markers but rather as consequences of the intrinsic mathematical dependence of F-ST on the properties of allele-frequency distributions.

  • 30. Jay, Flora
    et al.
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Blum, Michael G. B.
    Anisotropic Isolation by Distance: The Main Orientations of Human Genetic Differentiation2013In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 30, no 3, p. 513-525Article in journal (Refereed)
    Abstract [en]

    Genetic differentiation among human populations is greatly influenced by geography due to the accumulation of local allele frequency differences. However, little is known about the possibly different increment of genetic differentiation along the different geographical axes (north-south, east-west, etc.). Here, we provide new methods to examine the asymmetrical patterns of genetic differentiation. We analyzed genome-wide polymorphism data from populations in Africa (n = 29), Asia (n = 26), America (n = 9), and Europe (n = 38), and we found that the major orientations of genetic differentiation are north-south in Europe and Africa, and east-west in Asia, but no preferential orientation was found in the Americas. Additionally, we showed that the localization of the individual geographic origins based on single nucleotide polymorphism data was not equally precise along all orientations. Confirming our findings, we obtained that, in each continent, the orientation along which the precision is maximal corresponds to the orientation of maximum differentiation. Our results have implications for interpreting human genetic variation in terms of isolation by distance and spatial range expansion processes. In Europe, for instance, the precise northnorthwest-southsoutheast axis of main European differentiation cannot be explained by a simple Neolithic demic diffusion model without admixture with the local populations because in that case the orientation of greatest differentiation should be perpendicular to the direction of expansion. In addition to humans, anisotropic analyses can guide the description of genetic differentiation for other organisms and provide information on expansions of invasive species or the processes of plant dispersal.

  • 31.
    Jeong, Choongwon
    et al.
    Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA.
    Ozga, Andrew T.
    Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA.
    Witonsky, David B.
    Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala Univ, Dept Organismal Biol, SE-75236 Uppsala, Sweden.
    Edlund, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala Univ, Dept Organismal Biol, SE-75236 Uppsala, Sweden.
    Hofman, Courtney A.
    Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA.
    Hagan, Richard W.
    Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala Univ, Dept Organismal Biol, SE-75236 Uppsala, Sweden.
    Lewis, Cecil M.
    Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA.
    Aldenderfer, Mark S.
    Univ Calif Merced, Sch Social Sci Humanities & Arts, Merced, CA 95343 USA.
    Di Rienzo, Anna
    Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA.
    Warinner, Christina
    Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA;Univ Zurich, Inst Evolut Med, CH-8057 Zurich, Switzerland.
    Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc2016In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, no 27, p. 7485-7490Article in journal (Refereed)
    Abstract [en]

    The high-altitude transverse valleys [>3,000 m above sea level (masl)] of the Himalayan arc from Arunachal Pradesh to Ladahk were among the last habitable places permanently colonized by prehistoric humans due to the challenges of resource scarcity, cold stress, and hypoxia. The modern populations of these valleys, who share cultural and linguistic affinities with peoples found today on the Tibetan plateau, are commonly assumed to be the descendants of the earliest inhabitants of the Himalayan arc. However, this assumption has been challenged by archaeological and osteological evidence suggesting that these valleys may have been originally populated from areas other than the Tibetan plateau, including those at low elevation. To investigate the peopling and early population history of this dynamic high-altitude contact zone, we sequenced the genomes (0.04x-7.25x, mean 2.16x) and mitochondrial genomes (20.8x-1,311.0x, mean 482.1x) of eight individuals dating to three periods with distinct material culture in the Annapurna Conservation Area (ACA) of Nepal, spanning 3,150-1,250 y before present (yBP). We demonstrate that the region is characterized by long-term stability of the population genetic make-up despite marked changes in material culture. The ancient genomes, uniparental haplotypes, and high-altitude adaptive alleles suggest a high-altitude East Asian origin for prehistoric Himalayan populations.

  • 32.
    Jeong, Choongwon
    et al.
    Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA..
    Ozga, Andrew T.
    Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA..
    Witonsky, David
    Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA..
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Lewis, Cecil M.
    Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA..
    Aldenderfer, Mark
    Univ Calif Merced, Dept Anthropol, Merced, CA USA..
    Di Rienzo, Anna
    Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA..
    Warinner, Christina
    Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA..
    Long-term genetic stability and a high altitude East Asian origin for the peoples of the high valleys of the Himalayan arc2016In: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 159, no Suppl. 62, p. 185-185Article in journal (Other academic)
  • 33.
    Juras, Anna
    et al.
    Adam Mickiewicz Univ, Dept Human Evolutionary Biol, Inst Anthropol, Fac Biol, Umultowska 89, PL-61614 Poznan, Poland..
    Chylenski, Maciej
    Adam Mickiewicz Univ, Inst Archaeol, Fac Hist, Umultowska 89D, PL-61614 Poznan, Poland..
    Ehler, Edvard
    Adam Mickiewicz Univ, Dept Human Evolutionary Biol, Inst Anthropol, Fac Biol, Umultowska 89, PL-61614 Poznan, Poland.;ASCR, Lab Genom & Bioinformat, Inst Mol Genet, Vvi, Videnska 1083, Prague 14220 4, Czech Republic..
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Zurkiewicz, Danuta
    Adam Mickiewicz Univ, Inst Archaeol, Fac Hist, Umultowska 89D, PL-61614 Poznan, Poland..
    Wlodarczak, Piotr
    Polish Acad Sci, Inst Archaeol & Ethnol, Slawkowska Str 17, PL-31016 Krakow, Poland..
    Wilk, Stanislaw
    Jagiellonian Univ, Inst Archaeol, Golebia 11, PL-31007 Krakow, Poland..
    Peska, Jaroslav
    Archaeol Ctr Olomouc, U Hradiska 42-6, Olomouc 77900, Czech Republic.;Palacky Univ Olomouc, Philosoph Fac, Sect Archaeol, Dept Hist, Hrade 5, Olomouc 77180, Czech Republic..
    Fojtik, Pavel
    Inst Archaeol Heritage Brno, Vvi, Kaloudova 30, Brno 61400, Czech Republic..
    Kralik, Miroslav
    Masaryk Univ, Fac Sci, Lab Morphol & Forens Anthropol LaMorFA, Dept Anthropol, Kotlarska 267-2, CS-61137 Brno, Czech Republic..
    Libera, Jerzy
    Marie Curie Sklodowska Univ, Inst Archaeol, Maria Curie Sklodowska Sq 4, PL-20031 Lublin, Poland..
    Baginska, Jolanta
    Muzeum Reg Janusza Petera, Ul Zamojska 2, PL-22600 Tomaszow Lubelski, Poland..
    Tunia, Krzysztof
    Polish Acad Sci, Inst Archaeol & Ethnol, Slawkowska Str 17, PL-31016 Krakow, Poland..
    Klochko, Viktor I.
    Natl Univ Kyiv Mohyla Acad, Inst Archaeol, Hryhoriya Skovorody St 2, UA-04655 Kiev, Ukraine..
    Dabert, Miroslawa
    Adam Mickiewicz Univ, Fac Biol, Mol Biol Tech Lab, Umultowska 89, PL-61614 Poznan, Poland..
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Johannesburg, Ctr Anthropol Res, Auckland Pk, ZA-2006 Johannesburg, South Africa..
    Kosko, Aleksander
    Adam Mickiewicz Univ, Inst Archaeol, Fac Hist, Umultowska 89D, PL-61614 Poznan, Poland..
    Mitochondrial genomes reveal an east to west cline of steppe ancestry in Corded Ware populations2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 11603Article in journal (Refereed)
    Abstract [en]

    From around 4,000 to 2,000 BC the forest-steppe north-western Pontic region was occupied by people who shared a nomadic lifestyle, pastoral economy and barrow burial rituals. It has been shown that these groups, especially those associated with the Yamnaya culture, played an important role in shaping the gene pool of Bronze Age Europeans, which extends into present-day patterns of genetic variation in Europe. Although the genetic impact of these migrations from the forest-steppe Pontic region into central Europe have previously been addressed in several studies, the contribution of mitochondrial lineages to the people associated with the Corded Ware culture in the eastern part of the North European Plain remains contentious. In this study, we present mitochondrial genomes from 23 Late Eneolithic and Bronze Age individuals, including representatives of the north-western Pontic region and the Corded Ware culture from the eastern part of the North European Plain. We identified, for the first time in ancient populations, the rare mitochondrial haplogroup X4 in two Bronze Age Catacomb culture-associated individuals. Genetic similarity analyses show close maternal genetic affinities between populations associated with both eastern and Baltic Corded Ware culture, and the Yamnaya horizon, in contrast to larger genetic differentiation between populations associated with western Corded Ware culture and the Yamnaya horizon. This indicates that females with steppe ancestry contributed to the formation of populations associated with the eastern Corded Ware culture while more local people, likely of Neolithic farmer ancestry, contributed to the formation of populations associated with western Corded Ware culture.

  • 34.
    Kilinc, Gulsah Merve
    et al.
    Stockholm Univ, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden.
    Kashuba, Natalija
    Stockholm Univ, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden;Univ Oslo, Museum Cultural Hist, N-0164 Oslo, Norway.
    Yaka, Reyhan
    Middle East Tech Univ, Dept Biol Sci, TR-06800 Ankara, Turkey.
    Sumer, Arev Pelin
    Middle East Tech Univ, Dept Biol Sci, TR-06800 Ankara, Turkey.
    Yuncu, Eren
    Middle East Tech Univ, Dept Biol Sci, TR-06800 Ankara, Turkey.
    Shergin, Dmitrij
    Ivanov, Grigorij Leonidovich
    Irkutsk Museum Reg Studies, Irkutsk 664003, Irkutsk Oblast, Russia.
    Kichigin, Dmitrii
    Irkutsk State Univ, Lab Archaeol & Ethnog, Fac Hist & Methods, Dept Humanitarian & Aesthet Educ,Pedag Inst, Irkutsk 664011, Irkutsk Oblast, Russia;Irkutsk State Tech Univ, Irkutsk Natl Res Tech Univ, Lab Archaeol Paleoecol & Subsistence Strategies P, Irkutsk 664074, Irkutsk Oblast, Russia.
    Pestereva, Kjunnej
    MK Ammosov North Eastern Fed Univ NEFU, Fed State Autonomous Educ Inst Higher Educ, Yakutsk 677000, Sakha Republic, Russia.
    Volkov, Denis
    Ctr Preservat Hist & Cultural Heritage Amur Reg, Blagoveshchensk 675000, Amur Oblast, Russia.
    Mandryka, Pavel
    Siberian Fed Univ, Krasnoyarsk 660041, Krasnoyarskiy K, Russia.
    Kharinskii, Artur
    Irkutsk State Tech Univ, Irkutsk Natl Res Tech Univ, Lab Archaeol Paleoecol & Subsistence Strategies P, Irkutsk 664074, Irkutsk Oblast, Russia.
    Tishkin, Alexey
    Altai State Univ, Dept Archaeol Ethnog & Museol, Lab Interdisciplinary Studies Archaeol Western Si, Barnaul, Altaiskiy Kray, Russia.
    Ineshin, Evgenij
    Irkutsk State Univ, Lab Archaeol & Ethnog, Fac Hist & Methods, Dept Humanitarian & Aesthet Educ,Pedag Inst, Irkutsk 664011, Irkutsk Oblast, Russia.
    Kovychev, Evgeniy
    Transbaikal State Univ, Fac Hist, Chita 672039, Zabaykalsky Kra, Russia.
    Stepanov, Aleksandr
    MK Ammosov North Eastern Fed Univ NEFU, Fed State Autonomous Educ Inst Higher Educ, Yakutsk 677000, Sakha Republic, Russia.
    Alekseev, Aanatolij
    Acad Sci Sakha Republ, Inst Humanities Res & Indigenous Studies IHRISN, Yakutsk 677000, Sakha Republic, Russia.
    Fedoseeva, Svetlana Aleksandrovna
    Russian Acad Sci, Inst Arctic Archaeol & Paleoecol, Yakutsk 677000, Sakha Republic, Russia.
    Somel, Mehmet
    Middle East Tech Univ, Dept Biol Sci, TR-06800 Ankara, Turkey.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Krzewinska, Maja
    Stockholm Univ, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden.
    Stora, Jan
    Stockholm Univ, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden.
    Gotherstrom, Anders
    Stockholm Univ, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden.
    Investigating Holocene human population history in North Asia using ancient mitogenomes2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 8969Article in journal (Refereed)
    Abstract [en]

    Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c. 13,790 BP and c. 1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (Ne) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene.

  • 35. Kopelman, Naama M.
    et al.
    Mayzel, Jonathan
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Rosenberg, Noah A.
    Mayrose, Itay
    Clumpak: a program for identifying clustering modes and packaging population structure inferences across K2015In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 15, no 5, p. 1179-1191Article in journal (Refereed)
    Abstract [en]

    The identification of the genetic structure of populations from multilocus genotype data has become a central component of modern population-genetic data analysis. Application of model-based clustering programs often entails a number of steps, in which the user considers different modelling assumptions, compares results across different predetermined values of the number of assumed clusters (a parameter typically denoted K), examines multiple independent runs for each fixed value of K, and distinguishes among runs belonging to substantially distinct clustering solutions. Here, we present Clumpak (Cluster Markov Packager Across K), a method that automates the postprocessing of results of model-based population structure analyses. For analysing multiple independent runs at a single K value, Clumpak identifies sets of highly similar runs, separating distinct groups of runs that represent distinct modes in the space of possible solutions. This procedure, which generates a consensus solution for each distinct mode, is performed by the use of a Markov clustering algorithm that relies on a similarity matrix between replicate runs, as computed by the software Clumpp. Next, Clumpak identifies an optimal alignment of inferred clusters across different values of K, extending a similar approach implemented for a fixed K in Clumpp and simplifying the comparison of clustering results across different K values. Clumpak incorporates additional features, such as implementations of methods for choosing K and comparing solutions obtained by different programs, models, or data subsets. Clumpak, available at , simplifies the use of model-based analyses of population structure in population genetics and molecular ecology.

  • 36.
    Krzewinska, Maja
    et al.
    Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, SE-10691 Stockholm, Sweden.
    Kilinc, Gulsah Merve
    Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, SE-10691 Stockholm, Sweden.
    Juras, Anna
    Adam Mickiewicz Univ, Fac Biol, Inst Anthropol, Dept Human Evolutionary Biol, Umultowska 89, PL-61614 Poznan, Poland.
    Koptekin, Dilek
    Middle East Tech Univ, Dept Hlth Informat, TR-06800 Ankara, Turkey.
    Chylenski, Maciej
    Adam Mickiewicz Univ, Fac Hist, Inst Archaeol, Umultowska 89D, PL-61614 Poznan, Poland.
    Nikitin, Alexey G.
    Grand Valley State Univ, Biol Dept, 1 Campus Dr, Allendale, MI 49401 USA.
    Shcherbakov, Nikolai
    Bashkir State Pedag Univ, Lab Methodol & Methods Humanitarian Res, Octyabrskoy Revolutsii 3A, Ufa 450007, Russia.
    Shuteleva, Iia
    Bashkir State Pedag Univ, Lab Methodol & Methods Humanitarian Res, Octyabrskoy Revolutsii 3A, Ufa 450007, Russia;Bashkir State Univ, Inst Hist & State Management, Zaki Validy St 32, Ufa 450076, Russia.
    Leonova, Tatiana
    Bashkir State Pedag Univ, Lab Methodol & Methods Humanitarian Res, Octyabrskoy Revolutsii 3A, Ufa 450007, Russia.
    Kraeva, Liudmila
    Orenburg State Pedag Univ, Archaeol Lab, Orenburg, Russia.
    Sungatov, Flarit A.
    Bashkir State Univ, Archaeol Lab, Str Validi Z 32, Ufa, Russia.
    Sultanova, Alfija N.
    Bashkir State Univ, Archaeol Lab, Str Validi Z 32, Ufa, Russia.
    Potekhina, Inna
    Natl Acad Sci Ukraine, Inst Archaeol, Kiev, Ukraine.
    Lukasik, Sylwia
    Adam Mickiewicz Univ, Fac Biol, Inst Anthropol, Dept Human Evolutionary Biol, Umultowska 89, PL-61614 Poznan, Poland.
    Krenz-Niedbala, Marta
    Adam Mickiewicz Univ, Fac Biol, Inst Anthropol, Dept Human Evolutionary Biol, Umultowska 89, PL-61614 Poznan, Poland.
    Dalen, Love
    Swedish Museum Nat Hist, Dept Bioinformat & Genet, POB 50007, S-10405 Stockholm, Sweden.
    Sinika, Vitaly
    Taras Shevchenko Univ Tiraspol, October St 25, Tiraspol 3300, Moldova;Nizhnevartovsk State Univ, Lenin St 56, Khanty Mansi Autonomous 628605, Yugra, Russia.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Johannesburg, Ctr Anthropol Res, POB 524, ZA-2006 Auckland Pk, South Africa;Univ Johannesburg, Dept Anthropol & Dev Studies, POB 524, ZA-2006 Auckland Pk, South Africa.
    Stora, Jan
    Stockholm Univ, Dept Archaeol & Classical Studies, Osteoarchaeol Res Lab, Lilla Frescativagen 7, SE-10691 Stockholm, Sweden.
    Gotherstrom, Anders
    Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, SE-10691 Stockholm, Sweden.
    Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads2018In: Science Advances, E-ISSN 2375-2548, Vol. 4, no 10, article id eaat4457Article in journal (Refereed)
    Abstract [en]

    For millennia, the Pontic-Caspian steppe was a connector between the Eurasian steppe and Europe. In this scene, multidirectional and sequential movements of different populations may have occurred, including those of the Eurasian steppe nomads. We sequenced 35 genomes (low to medium coverage) of Bronze Age individuals (Srubnaya-Alakulskaya) and Iron Age nomads (Cimmerians, Scythians, and Sarmatians) that represent four distinct cultural entities corresponding to the chronological sequence of cultural complexes in the region. Our results suggest that, despite genetic links among these peoples, no group can be considered a direct ancestor of the subsequent group. The nomadic populations were heterogeneous and carried genetic affinities with populations from several other regions including the Far East and the southern Urals. We found evidence of a stable shared genetic signature, making the eastern Pontic-Caspian steppe a likely source of western nomadic groups.

  • 37.
    Krzewinska, Maja
    et al.
    Univ Stockholm, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden.
    Kjellstrom, Anna
    Univ Stockholm, Dept Archaeol & Class Studies, Osteoarchaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Hedenstierna-Jonson, Charlotte
    Univ Stockholm, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden.
    Zachrisson, Torun
    Univ Stockholm, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden.
    Omrak, Ayca
    Univ Stockholm, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden.
    Yaka, Reyhan
    Middle East Tech Univ, Dept Biol Sci, TR-06800 Ankara, Turkey.
    Kilinc, Gulsah Merve
    Univ Stockholm, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden.
    Somel, Mehmet
    Middle East Tech Univ, Dept Biol Sci, TR-06800 Ankara, Turkey.
    Sobrado, Veronica
    Univ Stockholm, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden.
    Evans, Jane
    British Geol Survey, NERC Isotope Geosci Lab, Nottingham NG12 5GG, England.
    Knipper, Conine
    Curt Engelhorn Zentrum Archaometrie, D6,3, D-68159 Mannheim, Germany.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Sci Life Lab, Tomtebodavagen 23A, S-17165 Solna, Sweden.
    Stora, Jan
    Univ Stockholm, Dept Archaeol & Class Studies, Osteoarchaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden.
    Gotherstrom, Anders
    Univ Stockholm, Dept Archaeol & Class Studies, Archaeol Res Lab, Lilla Frescativagen 7, S-10691 Stockholm, Sweden;Sci Life Lab, Tomtebodavagen 23A, S-17165 Solna, Sweden.
    Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town2018In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 28, no 17, p. 2730-2738.e10Article in journal (Refereed)
    Abstract [en]

    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 10th to 12th century Swedish town of Sigtuna. The data revealed high genetic diversity among the early urban residents. The observed variation exceeds the genetic diversity in distinct modern-day and Iron Age groups of central and northern Europe. Strontium isotope data suggest mixed local and non-local origin of the townspeople. Our results uncover the social system underlying the urbanization process of the Viking World of which mobility was an intricate part and was comparable between males and females. The inhabitants of Sigtuna were heterogeneous in their genetic affinities, probably reflecting both close and distant connections through an established network, confirming that early urbanization processes in northern Europe were driven by migration.

  • 38.
    Kuhn, Jose Manuel Monroy
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Estimating genetic kin relationships in prehistoric populations2018In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 13, no 4, article id e0195491Article in journal (Refereed)
    Abstract [en]

    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.

  • 39. Li, Junrui
    et al.
    Li, Haipeng
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Li, Sen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sjödin, Per
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Joint analysis of demography and selection in population genetics: where do we stand and where could we go?2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 1, p. 28-44Article, review/survey (Refereed)
    Abstract [en]

    Teasing apart the effects of selection and demography on genetic polymorphism remains one of the major challenges in the analysis of population genomic data. The traditional approach has been to assume that demography would leave a genome-wide signature, whereas the effect of selection would be local. In the light of recent genomic surveys of sequence polymorphism, several authors have argued that this approach is questionable based on the evidence of the pervasive role of positive selection and that new approaches are needed. In the first part of this review, we give a few empirical and theoretical examples illustrating the difficulty in teasing apart the effects of selection and demography on genomic polymorphism patterns. In the second part, we review recent efforts to detect recent positive selection. Most available methods still rely on an a priori classification of sites in the genome but there are many promising new approaches. These new methods make use of the latest developments in statistics, explore aspects of the data that had been neglected hitherto or take advantage of the emerging population genomic data. A current and promising approach is based on first estimating demographic and genetic parameters, using, e.g., a likelihood or approximate Bayesian computation framework, focusing on extreme outlier regions, and then using an independent method to confirm these. Finally, especially for species where evidence of natural selection has been limited, more experimental and versatile approaches that contrast populations under varied environmental constraints might be more successful compared with species-wide genome scans in search of specific signatures.

  • 40.
    Li, Sen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Estimating demographic parameters from large-scale population genomic data using Approximate Bayesian Computation2012In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 13, p. 22-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The Approximate Bayesian Computation (ABC) approach has been used to infer demographic parameters for numerous species, including humans. However, most applications of ABC still use limited amounts of data, from a small number of loci, compared to the large amount of genome-wide population-genetic data which have become available in the last few years.

    RESULTS: We evaluated the performance of the ABC approach for three 'population divergence' models - similar to the 'isolation with migration' model - when the data consists of several hundred thousand SNPs typed for multiple individuals by simulating data from known demographic models. The ABC approach was used to infer demographic parameters of interest and we compared the inferred values to the true parameter values that was used to generate hypothetical "observed" data. For all three case models, the ABC approach inferred most demographic parameters quite well with narrow credible intervals, for example, population divergence times and past population sizes, but some parameters were more difficult to infer, such as population sizes at present and migration rates. We compared the ability of different summary statistics to infer demographic parameters, including haplotype and LD based statistics, and found that the accuracy of the parameter estimates can be improved by combining summary statistics that capture different parts of information in the data. Furthermore, our results suggest that poor choices of prior distributions can in some circumstances be detected using ABC. Finally, increasing the amount of data beyond some hundred loci will substantially improve the accuracy of many parameter estimates using ABC.

    CONCLUSIONS: We conclude that the ABC approach can accommodate realistic genome-wide population genetic data, which may be difficult to analyze with full likelihood approaches, and that the ABC can provide accurate and precise inference of demographic parameters from these data, suggesting that the ABC approach will be a useful tool for analyzing large genome-wide datasets.

  • 41.
    Li, Sen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Genetic variation reveals large-scale population expansion and migration during the expansion of Bantu-speaking peoples2014In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 281, no 1793, article id 20141448Article in journal (Refereed)
    Abstract [en]

    The majority of sub-Saharan Africans today speak a number of closely related languages collectively referred to as 'Bantu' languages. The current distribution of Bantu-speaking populations has been found to largely be a consequence of the movement of people rather than a diffusion of language alone. Linguistic and single marker genetic studies have generated various hypotheses regarding the timing and the routes of the Bantu expansion, but these hypotheses have not been thoroughly investigated. In this study, we re-analysed microsatellite markers typed for large number of African populations that-owing to their fast mutation rates-capture signatures of recent population history. We confirm the spread of west African people across most of sub-Saharan Africa and estimated the expansion of Bantu-speaking groups, using a Bayesian approach, to around 5600 years ago. We tested four different divergence models for Bantu-speaking populations with a distribution comprising three geographical regions in Africa. We found that the most likely model for the movement of the eastern branch of Bantu-speakers involves migration of Bantu-speaking groups to the east followed by migration to the south. This model, however, is only marginally more likely than other models, which might indicate direct movement from the west and/or significant gene flow with the western Branch of Bantu-speakers. Our study use multi-loci genetic data to explicitly investigate the timing and mode of the Bantu expansion and it demonstrates that west African groups rapidly expanded both in numbers and over a large geographical area, affirming the fact that the Bantu expansion was one of the most dramatic demographic events in human history.

  • 42.
    Lombard, Marlize
    et al.
    University of Johannesburg, Centre for Anthropological Research, Johannesburg, South Africa; University of Johannesburg, Department of Anthropology and Development Studies, Johannesburg, South Africa.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. University of Johannesburg, Centre for Anthropological Research, Johannesburg, South Africa; University of Johannesburg, Department of Anthropology and Development Studies, Johannesburg, South Africa; .
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. University of Johannesburg, Centre for Anthropological Research, Johannesburg, South Africa; University of Johannesburg, Department of Anthropology and Development Studies, Johannesburg, South Africa.
    Ancient human DNA: How sequencing the genome of a boy from Ballito Bay changed human history2018In: South African Journal of Science, ISSN 0038-2353, E-ISSN 1996-7489, Vol. 114, no 1-2, article id a0253Article in journal (Other academic)
  • 43.
    Lombard, Marlize
    et al.
    Univ Johannesburg, Palaeo Res Inst, POB 524, ZA-2006 Auckland Pk, South Africa.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Johannesburg, Palaeo Res Inst, POB 524, ZA-2006 Auckland Pk, South Africa.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Johannesburg, Palaeo Res Inst, POB 524, ZA-2006 Auckland Pk, South Africa.
    Svensson, Emma
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Munters, Arielle R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Coutinho, Alexandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Edlund, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Zipfel, Bernhard
    Univ Witwatersrand, Evolutionary Studies Inst, Johannesburg, South Africa;Univ Witwatersrand, Sch Geosci, Johannesburg, South Africa.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Johannesburg, Palaeo Res Inst, POB 524, ZA-2006 Auckland Pk, South Africa.
    Genetic data and radiocarbon dating question Plovers Lake as a Middle Stone Age hominin-bearing site2019In: Journal of Human Evolution, ISSN 0047-2484, E-ISSN 1095-8606, Vol. 131, p. 203-209Article in journal (Refereed)
    Abstract [en]

    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.

  • 44.
    Malmström, Helena
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Johannesburg, Ctr Anthropol Res, Dept Anthropol & Dev Studies, ZA-2006 Auckland Pk, South Africa.
    Günther, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Svensson, Emma M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Juras, Anna
    Adam Mickiewia Univ Poznan, Dept Human Evolutionary Biol, Inst Anthropol, Fac Biol, Ul Uniwersytetu Poznanskiego 6, PL-61614 Poznan, Poland.
    Fraser, Magdalena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History.
    Munters, Arielle R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Pospieszny, Lukasz
    Univ Bristol, Dept Anthropol & Archaeol, Bristol BS8 1UU, Avon, England;Polish Acad Sci, Inst Archaeol & Ethnol, Ctr Studies Late Antiqu & Early Medieval Times, PL-61612 Poznan, Poland.
    Tõrv, Mari
    Univ Tartu, Dept Archaeol, Inst Hist & Archaeol, EE-50090 Tartu, Estonia.
    Lindström, Jonathan
    Linneaus Univ, Grad Sch Contract Archaeol, Dept Archaeol, S-39182 Kalmar, Sweden.
    Götherström, Anders
    Stockholm Univ, Archaeol Res Lab, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden.
    Storå, Jan
    Stockholm Univ, Osteoarchaeol Res Lab, Dept Archaeol & Class Studies, S-10691 Stockholm, Sweden.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Univ Johannesburg, Ctr Anthropol Res, Dept Anthropol & Dev Studies, ZA-2006 Auckland Pk, South Africa.
    The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon2019In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 286, no 1912, article id 20191528Article in journal (Refereed)
    Abstract [en]

    The Neolithic period is characterized by major cultural transformations and human migrations, with lasting effects across Europe. To understand the population dynamics in Neolithic Scandinavia and the Baltic Sea area, we investigate the genomes of individuals associated with the Battle Axe Culture (BAC), a Middle Neolithic complex in Scandinavia resembling the continental Corded Ware Culture (CWC). We sequenced 11 individuals (dated to 3330-1665 calibrated before common era (cal BCE)) from modern-day Sweden, Estonia, and Poland to 0.26-3.24x coverage. Three of the individuals were from CWC contexts and two from the central-Swedish BAC burial 'Bergsgraven'. By analysing these genomes together with the previously published data, we show that the BAC represents a group different from other Neolithic populations in Scandinavia, revealing stratification among cultural groups. Similar to continental CWC, the BAC-associated individuals display ancestry from the Pontic-Caspian steppe herders, as well as smaller components originating from hunter-gatherers and Early Neolithic farmers. Thus, the steppe ancestry seen in these Scandinavian BAC individuals can be explained only by migration into Scandinavia. Furthermore, we highlight the reuse of megalithic tombs of the earlier Funnel Beaker Culture (FBC) by people related to BAC. The BAC groups likely mixed with resident middle Neolithic farmers (e.g. FBC) without substantial contributions from Neolithic foragers.

  • 45.
    Malmström, Helena Jankovic
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Linderholm, Anna
    Skoglund, Pontus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Stora, Jan
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gilbert, M. Thomas P.
    Holmlund, Gunilla
    Willerslev, Eske
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Liden, Kerstin
    Gotherstrom, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process2015In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 370, no 1660, p. 20130373-Article in journal (Refereed)
    Abstract [en]

    The European Neolithization process started around 12 000 years ago in the Near East. The introduction of agriculture spread north and west throughout Europe and a key question has been if this was brought about by migrating individuals, by an exchange of ideas or a by a mixture of these. The earliest farming evidence in Scandinavia is found within the Funnel Beaker Culture complex (Trichterbecherkultur, TRB) which represents the northernmost extension of Neolithic farmers in Europe. The TRB coexisted for almost a millennium with hunter-gatherers of the Pitted Ware Cultural complex (PWC). If migration was a substantial part of the Neolithization, even the northerly TRB community would display a closer genetic affinity to other farmer populations than to hunter-gatherer populations. We deep-sequenced the mitochondrial hypervariable region 1 from seven farmers (six TRB and one Battle Axe complex, BAC) and 13 hunter-gatherers (PWC) and authenticated the sequences using postmortem DNA damage patterns. A comparison with 124 previously published sequences from prehistoric Europe shows that the TRB individuals share a close affinity to Central European farmer populations, and that they are distinct from hunter-gatherer groups, including the geographically close and partially contemporary PWC that show a close affinity to the European Mesolithic hunter-gatherers.

  • 46.
    Malmström, Helena
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Linderholm, Anna
    Liden, Kerstin
    Stora, Jan
    Molnar, Petra
    Holmlund, Gunilla
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    High frequency of lactose intolerance in a prehistoric hunter-gatherer population in northern Europe2010In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 10, p. 89-Article in journal (Refereed)
    Abstract [en]

    Background: Genes and culture are believed to interact, but it has been difficult to find direct evidence for the process. One candidate example that has been put forward is lactase persistence in adulthood, i.e. the ability to continue digesting the milk sugar lactose after childhood, facilitating the consumption of raw milk. This genetic trait is believed to have evolved within a short time period and to be related with the emergence of sedentary agriculture. Results: Here we investigate the frequency of an allele (-13910*T) associated with lactase persistence in a Neolithic Scandinavian population. From the 14 individuals originally examined, 10 yielded reliable results. We find that the T allele frequency was very low (5%) in this Middle Neolithic hunter-gatherer population, and that the frequency is dramatically different from the extant Swedish population (74%). Conclusions: We conclude that this difference in frequency could not have arisen by genetic drift and is either due to selection or, more likely, replacement of hunter-gatherer populations by sedentary agriculturalists.

  • 47.
    Naidoo, Thijessen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Centre for Anthropological Research, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Soodyall, Himla
    Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa..
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Centre for Anthropological Research, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    Loss-of-function variants among Khoe and San individualsManuscript (preprint) (Other academic)
  • 48.
    Naidoo, Thijessen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Patterns of variation in cis-regulatory regions: examining evidence of purifying selection2018In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 19, article id 95Article in journal (Refereed)
    Abstract [en]

    Background: With only 2 % of the human genome consisting of protein coding genes, functionality across the rest of the genome has been the subject of much debate. This has gained further impetus in recent years due to a rapidly growing catalogue of genomic elements, based primarily on biochemical signatures (e.g. the ENCODE project). While the assessment of functionality is a complex task, the presence of selection acting on a genomic region is a strong indicator of importance. In this study, we apply population genetic methods to investigate signals overlaying several classes of regulatory elements.

    Results: We disentangle signals of purifying selection acting directly on regulatory elements from the confounding factors of demography and purifying selection linked to e.g. nearby protein coding regions. We confirm the importance of regulatory regions proximal to coding sequence, while also finding differential levels of selection at distal regions. We note differences in purifying selection among transcription factor families. Signals of constraint at some genomic classes were also strongly dependent on their physical location relative to coding sequence. In addition, levels of selection efficacy across genomic classes differed between African and non-African populations.

    Conclusions: In order to assign a valid signal of selection to a particular class of genomic sequence, we show that it is crucial to isolate the signal by accounting for the effects of demography and linked-purifying selection. Our study highlights the intricate interplay of factors affecting signals of selection on functional elements.

  • 49.
    Naidoo, Thijessen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Sjödin, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Centre for Anthropological Research, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Centre for Anthropological Research, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    Selective sweeps among transcribed pseudogenes underline their utility in the human genomeManuscript (preprint) (Other academic)
  • 50.
    Naidoo, Thijessen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Xu, Jingzi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Vicente, Mário
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Soodyall, Himla
    Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Centre for Anthropological Research, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    Schlebusch, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Centre for Anthropological Research, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa.
    Full genomic Y chromosomal variation in southern African Khoe-San populationsManuscript (preprint) (Other academic)
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