28 research outputs found

    Natural selection and demography in ancient human introgression

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    The ability to recover ancient DNA from skeletal material has completely transformed the field of evolutionary anthropology, making it possible to sequence the genomes of individuals who lived thousands of years ago. In addition to solving the long-standing question of admixture between neanderthals and modern humans and uncovering evidence of dramatic migration events throughout human history, ancient DNA has become an important resource for understanding many facets of natural selection, which is often challenging using today's genetic variation alone. Chapter 1 examines the dynamics of negative selection acting against Neanderthal ancestry in modern humans and establishes its limits over long evolutionary timescales. It shows that the previously reported monotonic decline in Neanderthal ancestry over the last fifty-thousand years, thought to be a result of negative selection, is a statistical artifact caused by incorrect assumptions about modern human demographic history, in particular the gene flow between Africa and West Eurasia. Re-estimation of the Neanderthal ancestry proportions over time using a more robust statistic no longer infers a significant decline in Neanderthal ancestry, which is proven to be consistent with simulations of negative selection across a wide range of selection parameters. Chapter 2 describes the first comprehensive analysis of the Y chromosomes of neanderthals and Denisovans. Although Neanderthals and Denisovans form a sister group to modern humans at the autosomal level, Neanderthal Y chromosomes are more similar to modern humans than Denisovan Y chromosomes. In fact, the Y chromosomes of late neanderthals represent a lineage introgressed from an early modern human population. This introgression, which occurred hundreds of thousands of years, completely replaced the Y chromosomes of early neanderthals, reflecting the observations made from mitochondrial DNA. Population genetic simulations of selection and introgression show that although a complete replacement of both mitochondrial DNA and Y chromosomes is unlikely under neutrality, higher deleterious burden of neanderthals predicts a rapid replacement of both loci by their modern human counterparts. Finally, Chapter 3 presents an R package admixer, designed to facilitate the programming of automated, fully reproducible population genetic analyses using ADMIXTOOLS, a suite of programs widely used in ancient DNA research

    Natural selection and demography in ancient human introgression

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    Ancient Admixture into Africa from the ancestors of non-Africans

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    Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe

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

    Extensive ethnolinguistic diversity in Vietnam reflects multiple sources of genetic diversity

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    Vietnam features extensive ethnolinguistic diversity and occupies a key position in Mainland Southeast Asia (MSEA). Yet, the genetic diversity of Vietnam remains relatively unexplored, especially with genome-wide data, because previous studies have focused mainly on the majority Kinh group. Here we analyze newly-generated genome-wide SNP data for the Kinh and 21 additional ethnic groups in Vietnam, encompassing all five major language families in MSEA. In addition to analyzing the allele and haplotype sharing within the Vietnamese groups, we incorporate published data from both nearby modern populations and ancient samples for comparison. In contrast to previous studies that suggested a largely indigenous origin for Vietnamese genetic diversity, we find that Vietnamese ethnolinguistic groups harbor multiple sources of genetic diversity that likely reflect different sources for the ancestry associated with each language family. However, linguistic diversity does not completely match genetic diversity: there have been extensive interactions between the Hmong-Mien and Tai-Kadai groups; different Austro-Asiatic groups show different affinities with other ethnolinguistic groups; and we identified a likely case of cultural diffusion in which some Austro-Asiatic groups shifted to Austronesian languages during the past 2,500 years. Overall, our results highlight the importance of genome-wide data from dense sampling of ethnolinguistic groups in providing new insights into the genetic diversity and history of an ethnolinguistically-diverse region, such as Vietnam

    Dual ancestries and ecologies of the Late Glacial Palaeolithic in Britain

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    Genetic investigations of Upper Palaeolithic Europe have revealed a complex and transformative history of human population movements and ancestries, with evidence of several instances of genetic change across the European continent in the period following the Last Glacial Maximum (LGM). Concurrent with these genetic shifts, the post-LGM period is characterized by a series of significant climatic changes, population expansions and cultural diversification. Britain lies at the extreme northwest corner of post-LGM expansion and its earliest Late Glacial human occupation remains unclear. Here we present genetic data from Palaeolithic human individuals in the United Kingdom and the oldest human DNA thus far obtained from Britain or Ireland. We determine that a Late Upper Palaeolithic individual from Gough's Cave probably traced all its ancestry to Magdalenian-associated individuals closely related to those from sites such as El Mirón Cave, Spain, and Troisiùme Caverne in Goyet, Belgium. However, an individual from Kendrick's Cave shows no evidence of having ancestry related to the Gough’s Cave individual. Instead, the Kendrick’s Cave individual traces its ancestry to groups who expanded across Europe during the Late Glacial and are represented at sites such as Villabruna, Italy. Furthermore, the individuals differ not only in their genetic ancestry profiles but also in their mortuary practices and their diets and ecologies, as evidenced through stable isotope analyses. This finding mirrors patterns of dual genetic ancestry and admixture previously detected in Iberia but may suggest a more drastic genetic turnover in northwestern Europe than in the southwest

    Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy

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    AbstractSouthern Italy was characterised by a complex prehistory that started with different Palaeolithic cultures, later followed by the Neolithic transition and the demic dispersal from the Pontic-Caspian Steppe during the Bronze Age. Archaeological and historical evidence points to demic and cultural influences between Southern Italians and the Balkans, starting with the initial Palaeolithic occupation until historical and modern times. To shed light on the dynamics of these contacts, we analysed a genome-wide SNP dataset of more than 700 individuals from the South Mediterranean area (102 from Southern Italy), combined with ancient DNA from neighbouring areas. Our findings revealed high affinities of South-Eastern Italians with modern Eastern Peloponnesians, and a closer affinity of ancient Greek genomes with those from specific regions of South Italy than modern Greek genomes. The higher similarity could be associated with the presence of a Bronze Age component ultimately originating from the Caucasus and characterised by high frequencies of Iranian and Anatolian Neolithic ancestries. Furthermore, to reveal possible signals of natural selection, we looked for extremely differentiated allele frequencies among Northern and Southern Italy, uncovering putatively adapted SNPs in genes involved in alcohol metabolism, nevi features and immunological traits, such as ALDH2, NID1 and CBLB

    Interpreting mismatches between linguistic and genetic patterns among speakers of Tanimuka (Eastern Tukanoan) and Yukuna (Arawakan)

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    Northwestern Amazonia is home to a great degree of linguistic diversity, and the human societies in that region are part of complex networks of interaction that predate the arrival of Europeans. This study investigates the population and language contact dynamics between two languages found within this region, Yukuna and Tanimuka, which belong to the Arawakan and Tukanoan language families, respectively. We use evidence from linguistics, ethnohistory, ethnography and population genetics to provide new insights into the contact dynamics between these and other human groups in NWA. Our results show that the interaction between these groups intensified in the last 500 years, to the point that it is difficult to differentiate between them genetically. However, this close interaction has led to more substantial contact-induced language changes in Tanimuka than in Yukuna, consistent with a scenario of language shift and asymmetrical power relations

    Ancient DNA from Guam and the peopling of the Pacific

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    We know more about the settlement of Polynesia than we do about the settlement of the Mariana Islands in the western Pacific. There is debate over where people came from to get to the Marianas, with various lines of evidence pointing to the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago, and over how the ancestors of the present Mariana Islanders, the Chamorro, might be related to Polynesians. We analyzed ancient DNA from Guam from two skeletons dating to ˜2,200 y ago and found that their ancestry is linked to the Philippines. Moreover, they are closely related to early Lapita skeletons from Vanuatu and Tonga, suggesting that the early Mariana Islanders may have been involved in the colonization of Polynesia.Humans reached the Mariana Islands in the western Pacific by ˜3,500 y ago, contemporaneous with or even earlier than the initial peopling of Polynesia. They crossed more than 2,000 km of open ocean to get there, whereas voyages of similar length did not occur anywhere else until more than 2,000 y later. Yet, the settlement of Polynesia has received far more attention than the settlement of the Marianas. There is uncertainty over both the origin of the first colonizers of the Marianas (with different lines of evidence suggesting variously the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago) as well as what, if any, relationship they might have had with the first colonizers of Polynesia. To address these questions, we obtained ancient DNA data from two skeletons from the Ritidian Beach Cave Site in northern Guam, dating to ˜2,200 y ago. Analyses of complete mitochondrial DNA genome sequences and genome-wide SNP data strongly support ancestry from the Philippines, in agreement with some interpretations of the linguistic and archaeological evidence, but in contradiction to results based on computer simulations of sea voyaging. We also find a close link between the ancient Guam skeletons and early Lapita individuals from Vanuatu and Tonga, suggesting that the Marianas and Polynesia were colonized from the same source population, and raising the possibility that the Marianas played a role in the eventual settlement of Polynesia.All data used in this paper are in the main text or in the SI Appendix. The new data reported in this paper have been deposited in the European Nucleotide Archive, https://www.ebi.ac.uk/ena/browser/home (accession no. PRJEB40707)

    Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry

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    Modern humans appeared in Europe by at least 45,000 years ago1–5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania7 and Siberia8 who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common
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