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1. Positive selection in the genomes of two Papua New Guinean populations at distinct altitude levels

Author

Mathilde André, Nicolas Brucato, Georgi Hudjasov, Vasili Pankratov, Danat Yermakovich, Francesco Montinaro, Rita Kreevan, Jason Kariwiga, John Muke, Anne Boland, Jean-François Deleuze, Vincent Meyer, Nicholas Evans, Murray P. Cox, Matthew Leavesley, Michael Dannemann, Tõnis Org, Mait Metspalu, Mayukh Mondal, and François-Xavier Ricaut

Subjects
Science
Abstract

Abstract Highlanders and lowlanders of Papua New Guinea have faced distinct environmental stress, such as hypoxia and environment-specific pathogen exposure, respectively. In this study, we explored the top genomics regions and the candidate driver SNPs for selection in these two populations using newly sequenced whole-genomes of 54 highlanders and 74 lowlanders. We identified two candidate SNPs under selection - one in highlanders, associated with red blood cell traits and another in lowlanders, which is associated with white blood cell count – both potentially influencing the heart rate of Papua New Guineans in opposite directions. We also observed four candidate driver SNPs that exhibit linkage disequilibrium with an introgressed haplotype, highlighting the need to explore the possibility of adaptive introgression within these populations. This study reveals that the signatures of positive selection in highlanders and lowlanders of Papua New Guinea align closely with the challenges they face, which are specific to their environments.

Published
2024
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4. Denisovan introgression has shaped the immune system of present-day Papuans.

Author

Davide M Vespasiani, Guy S Jacobs, Laura E Cook, Nicolas Brucato, Matthew Leavesley, Christopher Kinipi, François-Xavier Ricaut, Murray P Cox, and Irene Gallego Romero

Subjects
Genetics, QH426-470
Abstract

Modern humans have admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of both Denisovan and Neanderthal alleles characterised within a set of 56 genomes from Papuan individuals. By comparing the distribution of archaic and non-archaic variants we assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We observe an enrichment of archaic alleles within cis-regulatory elements and transcribed regions of the genome, with Denisovan variants strongly affecting elements active within immune-related cells. We identify 16,048 and 10,032 high-confidence Denisovan and Neanderthal variants that fall within annotated cis-regulatory elements and with the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activity in plasmid reporter assays. Together, these data provide support for a widespread contribution of archaic DNA in shaping the present levels of modern human genetic diversity, with different archaic ancestries potentially affecting multiple phenotypic traits within non-Africans.

Published
2022
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5. Phenotypic differences between highlanders and lowlanders in Papua New Guinea.

Author

Mathilde André, Nicolas Brucato, Sébastien Plutniak, Jason Kariwiga, John Muke, Adeline Morez, Matthew Leavesley, Mayukh Mondal, and François-Xavier Ricaut

Subjects
Medicine, Science
Abstract

ObjectivesAltitude is one of the most demanding environmental pressures for human populations. Highlanders from Asia, America and Africa have been shown to exhibit different biological adaptations, but Oceanian populations remain understudied [Woolcock et al., 1972; Cotes et al., 1974; Senn et al., 2010]. We tested the hypothesis that highlanders phenotypically differ from lowlanders in Papua New Guinea, as a result of inhabiting the highest mountains in Oceania for at least 20,000 years.Materials and methodsWe collected data for 13 different phenotypes related to altitude for 162 Papua New Guineans living at high altitude (Mont Wilhelm, 2,300-2,700 m above sea level (a.s.l.) and low altitude (Daru, ResultsSix phenotypes were significantly different between Papua New Guinean highlanders and lowlanders. Highlanders show shorter height (p-value = 0.001), smaller waist circumference (p-value = 0.002), larger Forced Vital Capacity (FVC) (p-value = 0.008), larger maximal (p-value = 3.20e -4) and minimal chest depth (p-value = 2.37e -5) and higher haemoglobin concentration (p-value = 3.36e -4).DiscussionOur study reports specific phenotypes in Papua New Guinean highlanders potentially related to altitude adaptation. Similar to other human groups adapted to high altitude, the evolutionary history of Papua New Guineans appears to have also followed an adaptive biological strategy for altitude.

Published
2021
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6. Genomic admixture tracks pulses of economic activity over 2,000 years in the Indian Ocean trading network

Author

Nicolas Brucato, Pradiptajati Kusuma, Philippe Beaujard, Herawati Sudoyo, Murray P. Cox, and François-Xavier Ricaut

Subjects
Medicine, Science
Abstract

Abstract The Indian Ocean has long been a hub of interacting human populations. Following land- and sea-based routes, trade drove cultural contacts between far-distant ethnic groups in Asia, India, the Middle East and Africa, creating one of the world’s first proto-globalized environments. However, the extent to which population mixing was mediated by trade is poorly understood. Reconstructing admixture times from genomic data in 3,006 individuals from 187 regional populations reveals a close association between bouts of human migration and trade volumes during the last 2,000 years across the Indian Ocean trading system. Temporal oscillations in trading activity match phases of contraction and expansion in migration, with high water marks following the expansion of the Silk Roads in the 5th century AD, the rise of maritime routes in the 11th century and a drastic restructuring of the trade network following the arrival of Europeans in the 16th century. The economic fluxes of the Indian Ocean trade network therefore directly shaped exchanges of genes, in addition to goods and concepts.

Published
2017
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7. Tracing Arab-Islamic inheritance in Madagascar: study of the Y-chromosome and mitochondrial DNA in the Antemoro.

Author

Mélanie Capredon, Nicolas Brucato, Laure Tonasso, Valérie Choesmel-Cadamuro, François-Xavier Ricaut, Harilanto Razafindrazaka, Andriamihaja Bakomalala Rakotondrabe, Mamisoa Adelta Ratolojanahary, Louis-Paul Randriamarolaza, Bernard Champion, and Jean-Michel Dugoujon

Subjects
Medicine, Science
Abstract

Madagascar is located at the crossroads of the Asian and African worlds and is therefore of particular interest for studies on human population migration. Within the large human diversity of the Great Island, we focused our study on a particular ethnic group, the Antemoro. Their culture presents an important Arab-Islamic influence, but the question of an Arab biological inheritance remains unresolved. We analyzed paternal (n=129) and maternal (n=135) lineages of this ethnic group. Although the majority of Antemoro genetic ancestry comes from sub-Saharan African and Southeast Asian gene pools, we observed in their paternal lineages two specific haplogroups (J1 and T1) linked to Middle Eastern origins. This inheritance was restricted to some Antemoro sub-groups. Statistical analyses tended to confirm significant Middle Eastern genetic contribution. This study gives a new perspective to the large human genetic diversity in Madagascar.

Published
2013
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8. First insight into oral microbiome diversity in Papua New Guineans reveals a specific regional signature

Author

Nicole Pedro, Nicolas Brucato, Bruno Cavadas, Valentine Lisant, Rui Camacho, Christopher Kinipi, Matthew Leavesley, Luisa Pereira, François‐Xavier Ricaut, Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto = University of Porto, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), University of Papua New Guinea (UPNG), and ANR-20-CE12-0003,PapuaEvol,Role évolutif de l'héritage génomique archaique dans la diversité humaine unique de Mélanésie(2020)

Subjects
Papua New Guinea, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Sahul, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Genetics, Environment, Oral microbiome, Ecology, Evolution, Behavior and Systematics, Diet
Abstract

International audience; The oral microbiota is a highly complex and diversified part of the human microbiome. Being located at the interface between the human body and the exterior environment, this microbiota can deepen our understanding of the environmental impacts on the global status of human health. This research topic has been well addressed in Westernized populations, but these populations only represent a fraction of human diversity. Papua New Guinea hosts very diverse environments and one of the most unique human biological diversities worldwide. In this work we performed the first known characterization of the oral microbiome in 85 Papua New Guinean individuals living in different environments, using a qualitative and quantitative approach. We found a significant geographical structure of the Papua New Guineans oral microbiome, especially in the groups most isolated from urban spaces. In comparison to other global populations, two bacterial genera related to iron absorption were significantly more abundant in Papua New Guineans and Aboriginal Australians, which suggests a shared oral microbiome signature. Further studies will be needed to confirm and explore this possible regional-specific oral microbiome profile.

Published
2022
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9. Hand stencils and communal history: A case study from Auwim, East Sepik, Papua New Guinea

Author

Roxanne Tsang, Sebastien Katuk, Sally K. May, Paul S.C. Taçon, François‐Xavier Ricaut, Matthew G. Leavesley, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Archeology, stencils, Papua New Guinea, lieu, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Anthropology, place, ethnographie, ethnography, pochoirs, Papouasie-Nouvelle-Guinée, rock art
Abstract

International audience; Hand stencils directly represent modern humans in landscape settings around the world. Yet their social and cultural contexts are often overlooked due to the lack of ethnography associated with the artwork. This paper explores the hand stencils from Kundumbue and Pundimbung rock art sites, situated in the traditional boundaries of the Auwim people in the East Sepik Province of Papua New Guinea. Combining archaeological rock art analysis with ethnographic knowledge, we demonstrate that the hand stencils are a priority in each clan's place-making practices, around which they construct the community's social narratives. Rock shelters and their rock art also show a form of communal history that is evoked through their production in contemporary settings, in addition to having been a form of esoteric magic in the past. We conclude that hand stencils can have multiple meanings over time and across space as a widespread cultural marker. However, aspects of the identities of individuals, groups and communities who created the now static hand imagery, remain in place.

Published
2023
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11. Denisovan introgression has shaped the immune system of present-day Papuans

Author

Davide M. Vespasiani, Guy S. Jacobs, Laura E. Cook, Nicolas Brucato, Matthew Leavesley, Christopher Kinipi, François-Xavier Ricaut, Murray P. Cox, Irene Gallego Romero, Vespasiani, Davide M [0000-0002-0977-8076], Cook, Laura E [0000-0002-4459-2592], Leavesley, Matthew [0000-0002-4612-8304], Cox, Murray P [0000-0003-1936-0236], Gallego Romero, Irene [0000-0003-1613-8998], and Apollo - University of Cambridge Repository

Subjects
Cancer Research, Biology and life sciences, FOS: Social sciences, Hominidae, Social sciences, Evolution, Molecular, Papua New Guinea, Earth sciences, Immune System, Genetics, Humans, Molecular Biology, Genetics (clinical), Ecology, Evolution, Behavior and Systematics, Neanderthals, Research Article
Abstract

Acknowledgements: We would like to thank all members of the Gallego Romero and McCarthy groups for their helpful discussions and comments on the manuscript. We also wish to acknowledge all of the study participants who generously consented to genome sequencing in the original study, and the leadership of Herawati Sudoyo and Chelzie Crenna Darusalam (Eijkman Institute for Molecular Biology) in generating these datasets., Funder: Leakey Foundation; funder-id: http://dx.doi.org/10.13039/100005966, Funder: University of Melbourne; funder-id: http://dx.doi.org/10.13039/501100001782, Modern humans have admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of both Denisovan and Neanderthal alleles characterised within a set of 56 genomes from Papuan individuals. By comparing the distribution of archaic and non-archaic variants we assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We observe an enrichment of archaic alleles within cis-regulatory elements and transcribed regions of the genome, with Denisovan variants strongly affecting elements active within immune-related cells. We identify 16,048 and 10,032 high-confidence Denisovan and Neanderthal variants that fall within annotated cis-regulatory elements and with the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activity in plasmid reporter assays. Together, these data provide support for a widespread contribution of archaic DNA in shaping the present levels of modern human genetic diversity, with different archaic ancestries potentially affecting multiple phenotypic traits within non-Africans.

Published
2022

12. Rock art and long-distance prehistoric exchange behaviour: a case study from Auwim, East Sepik, Papua New Guinea

Author

Jason Kariwiga, Paul S.C. Taçon, Matthew Leavesley, Hubert Forestier, François-Xavier Ricaut, William Pleiber, Roxanne Tsang, Sébastien Plutniak, Griffith University [Brisbane], University of Papua New Guinea (UPNG), Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT), Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés (TRACES), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Histoire naturelle de l'Homme préhistorique (HNHP), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
010506 paleontology, Archeology, History, stencils, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Rainforest, Oceanography, 01 natural sciences, Prehistory, Papua New Guinea, Cultural continuity, Ethnography, 0601 history and archaeology, Rock art, 0105 earth and related environmental sciences, 060102 archaeology, Ecology, New guinea, prehistoric trade, 06 humanities and the arts, 15. Life on land, Archaeology, Object (philosophy), East Sepik, Torres strait, Geography
Abstract

International audience; Since 1909, patrol officers, anthropologists and archaeologists have identified evidence of a pre-contact trading network linking New Guinea with the Torres Strait. Current research in the Lower Sepik River Basin reported various ethnographic descriptions relating to cultural material objects stenciled on various rock art sites in Auwim, Upper Karawari-Arafundi region, East Sepik, Papua New Guinea (PNG). In addition to the rock art, the broader area has one of the most environmentally intact freshwater basins with lowland rainforests in Melanesia, and is famous for its architectural carvings and spirit houses. This paper reports new research that articulates local ethnographic knowledge about rock art with the art-work itself. The rock art panels contain a wide range of stencils primarily consisting of hands but, importantly, also several objects. One such object is the kina shell. The kina shell stencils are, among other things, indicative of the remarkable distance over which the shells were traded and traditionally used. The Auwim case study is important because it is one of the relatively few sites across PNG for which we still have ethnography of rock art and therefore provides us with important insight into the past-present rock art practices, and concurrently notions of cultural continuity.

Published
2022
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13. Episodes of Diversification and Isolation in Island Southeast Asian and Near Oceanian Male Lineages

Author

Monika Karmin, Rodrigo Flores, Lauri Saag, Georgi Hudjashov, Nicolas Brucato, Chelzie Crenna-Darusallam, Maximilian Larena, Phillip L Endicott, Mattias Jakobsson, J Stephen Lansing, Herawati Sudoyo, Matthew Leavesley, Mait Metspalu, François-Xavier Ricaut, Murray P Cox, Massey University, University of Tartu, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Eijkman Institute for Molecular Biology [Jakarta], Uppsala University, Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Complexity Science Hub Vienna (CSHV), University of Papua New Guinea (UPNG), James Cook University (JCU), and ANR-20-CE12-0003,PapuaEvol,Role évolutif de l'héritage génomique archaique dans la diversité humaine unique de Mélanésie(2020)

Subjects
Male, Evolutionary Biology, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Y chromosome, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, phylogeography, migration, DNA, Mitochondrial, Mitochondria, Evolutionsbiologi, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Asian People, human population genetics, Island Southeast Asia, Genetics, Humans, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Asia, Southeastern, Phylogeny
Abstract

Island Southeast Asia (ISEA) and Oceania host one of the world’s richest assemblages of human phenotypic, linguistic, and cultural diversity. Despite this, the region’s male genetic lineages are globally among the last to remain unresolved. We compiled ∼9.7 Mb of Y chromosome (chrY) sequence from a diverse sample of over 380 men from this region, including 152 first reported here. The granularity of this data set allows us to fully resolve and date the regional chrY phylogeny. This new high-resolution tree confirms two main population bursts: multiple rapid diversifications following the region’s initial settlement ∼50 kya, and extensive expansions

Published
2022
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14. Chronology of natural selection in Oceanian genomes

Author

Nicolas Brucato, Mathilde André, Georgi Hudjashov, Mayukh Mondal, Murray P. Cox, Matthew Leavesley, François-Xavier Ricaut, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Institute of Genomics [Tartu, Estonia], University of Tartu, Massey University, and University of Papua New Guinea (UPNG)

Subjects
Multidisciplinary, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology
Abstract

International audience; As human populations left Asia to first settle in Oceania around 50,000 years ago, they entered a territory ecologically separated from the Old World for millions of years. We analyzed genomic data of 239 modern Oceanian individuals to detect and date signals of selection specific to this region. Combining both relative and absolute dating approaches, we identified a strong selection pattern between 52,000 and 54,000 years ago in the genomes of descendants of the first settlers of Sahul. This strikingly corresponds to the dates of initial settlement as inferred from archaeological evidence. Loci under selection during this period, some showing enrichment in Denisovan ancestry, overlap genes involved in the immune response and diet, especially based on plants. Pathogens and natural resources, especially from endemic plants, therefore appear to have acted as strong selective pressures on the genomes of the first settlers of Sahul

Published
2022
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15. Denisovan introgression has shaped the immune system of present-day Papuans

Author

Murray P. Cox, Irene Gallego Romero, Christopher Kinipi, Guy S. Jacobs, Laura Cook, Matthew Leavesley, Davide Maria Vespasiani, François-Xavier Ricaut, Nicolas Brucato, Melbourne Integrative Genomics, University of Melbourne, Melbourne Integrative Genomics and the School of Mathematics and Statistics, University of Melbourne, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of Papua New Guinea (UPNG), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand, and Massey University

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, Neanderthal, biology, Genetic genealogy, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Introgression, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], biology.organism_classification, Genome, 03 medical and health sciences, 0302 clinical medicine, Sister group, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Evolutionary biology, biology.animal, Allele, Adaptation, Denisovan, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

Modern humans have substantially admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals, whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of archaic alleles of both Denisovan and Neanderthal ancestry characterised within a previously published set of 56 genomes from individuals of Papuan genetic ancestry living in the island of New Guinea. By comparing the distribution of archaic and modern human variants, we are able to assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We detect a consistent signal across Denisovan variants of strong involvement in immune-related processes throughout our analyses. Archaic alleles are often located within cis-regulatory elements and transcribed regions of the genome, suggesting that they are capable of contributing to a wide range of cellular regulatory processes. We identify 3,538 high-confidence Denisovan variants that fall within annotated cis-regulatory elements and have the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes in present-day humans. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating at high frequency within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activities in plasmid reporter assays relative to modern human alleles. Together, these data provide support for the hypothesis that, despite their broadly deleterious nature, archaic alleles actively contribute to modern human phenotypic diversity to this day, and might have facilitated early adaptation to non-African environments.

Published
2021

17. Rock art and (re)production of narratives: A cassowary bone dagger stencil perspective from Auwim, East Sepik, Papua New Guine

Author

Roxanne Tsang, Sebastien Katuk, Sally K. May, Paul S.C. Taçon, François-Xavier Ricaut, Matthew G. Leavesley, School of Humanities, Languages and Social Science and Place, Evolution and Rock Art Heritage Unit, Griffith University Centre for Social and Cultural Research, Gold Coast campus, Griffith University, Queensland 4222, Australia, uwim Village, Upper Karawari-Arafundi Region, East Sepik, Papua New Guinea, Place, Evolution, Rock Art Heritage Unit, Griffith Centre for Social and Cultural Research, Griffith University, Gold Coast Campus, Queensland 4222, Australia, Evolution et Diversité Biologique (EDB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Archaeology, School of Humanities and Social Science, University of Papua New Guinea, Port Moresby, Papua New Guinea, Griffith University [Brisbane], Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and University of Papua New Guinea (UPNG)

Subjects
Cultural Studies, Archeology, New Guinea, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Auwim, Ethnography, Rock art, Casuarius unappendiculatus, [SHS.ANTHRO-SE]Humanities and Social Sciences/Social Anthropology and ethnology, East Sepik
Abstract

Cassowaries (Casuarius) are one of the largest indigenous animal species of New Guinea. Researchers have long been trying to understand their local socio-cultural significance. Here we present new results from interviews recorded in 2018 on ethnography associated with bone daggers, a material culture ornament and tool carved from the cassowary's tibiotarsus. We present a ‘storied notion’—a contemporary narrative from oral history of why cassowary is not simply a bird, and briefly describe cassowary bone ornamentation in Auwim, East Sepik Province of Papua New Guinea. By exploring the material history of Casuarius through a ‘storied notion’ approach, we reveal that cassowary bone daggers in rock art are narrative ideas of the species from its landscape to ornamentation and through to people's cosmological beliefs surrounding Casuarius. We argue that the cassowary bone dagger stencil can be seen as part of the life history of this animal.

Published
2021
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18. Papua New Guinean genomes reveal the complex settlement of north Sahul

Author

Matthew Leavesley, Roxanne Tsang, Jean-François Deleuze, Mayukh Mondal, Jason Kariwiga, Lauri Saag, William Pomat, John Muke, Luca Pagani, Nicolas Brucato, Irene Gallego Romero, Mait Metspalu, Murray P. Cox, Mathilde André, François-Xavier Ricaut, Vincent Meyer, Anne Boland, Teppsy Beni, Herawati Sudoyo, Kylie Sesuki, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), University of Tartu, Griffith University [Brisbane], University of Papua New Guinea (UPNG), University of Queensland [Brisbane], Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Eijkman Institute for Molecular Biology [Jakarta], Dipartimento di Biologia, Università degli Studi di Padova = University of Padua (Unipd), University of Melbourne, Massey University, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Universita degli Studi di Padova

Subjects
Demographic history, Human Migration, Sahul, Population, Oceania, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Biology, AcademicSubjects/SCI01180, Indigenous, Papua New Guinea, 03 medical and health sciences, 0302 clinical medicine, Ethnicity, Genetics, Humans, education, Molecular Biology, Phylogeny, Discoveries, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, geography, education.field_of_study, geography.geographical_feature_category, Human genome, Human migration, business.industry, Australia, AcademicSubjects/SCI01130, Papua New Guinean, Papuan, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Archipelago, Period (geology), Ethnology, business, Settlement (litigation), 030217 neurology & neurosurgery
Abstract

The settlement of Sahul, the lost continent of Oceania, remains one of the most ancient and debated human migrations. Modern New Guineans inherited a unique genetic diversity tracing back 50,000 years, and yet there is currently no model reconstructing their past population dynamics. We generated 58 new whole-genome sequences from Papua New Guinea, filling geographical gaps in previous sampling, specifically to address alternative scenarios of the initial migration to Sahul and the settlement of New Guinea. Here, we present the first genomic models for the settlement of northeast Sahul considering one or two migrations from Wallacea. Both models fit our data set, reinforcing the idea that ancestral groups to New Guinean and Indigenous Australians split early, potentially during their migration in Wallacea where the northern route could have been favored. The earliest period of human presence in Sahul was an era of interactions and gene flow between related but already differentiated groups, from whom all modern New Guineans, Bismarck islanders, and Indigenous Australians descend. The settlement of New Guinea was probably initiated from its southeast region, where the oldest archaeological sites have been found. This was followed by two migrations into the south and north lowlands that ultimately reached the west and east highlands. We also identify ancient gene flows between populations in New Guinea, Australia, East Indonesia, and the Bismarck Archipelago, emphasizing the fact that the anthropological landscape during the early period of Sahul settlement was highly dynamic rather than the traditional view of extensive isolation.

Published
2021
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19. Correction for Frantz et al., Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Ceiridwen J. Edwards, Anders Götherström, Benjamin S. Arbuckle, Linus Girdland-Flink, Domenico Fulgione, Ross Barnett, Michael J Richards, Katerina Trantalidou, Cristina Valdiosera, M. Thomas P. Gilbert, Joris Peters, Louis du Plessis, Jean-Denis Vigne, Joachim Burger, Dian Boric, Richard P. M. A. Crooijmans, Melinda A. Zeder, Erik Meijaard, Wolfram Schier, Panoraia Alexandri, Jörg Schibler, John Chapman, Adrian Balasescu, Greger Larson, Jörg Orschiedt, Anne Tresset, Simon Stoddart, Keith Dobney, Antonio Tagliacozzo, Thomas H. McGovern, Canan Çakirlar, Bea De Cupere, Caroline Malone, Laurent A. F. Frantz, Vesna Dimitrijević, Sepideh Maziar, Andrea Zeeb-Lanz, Cevdet Merih Erek, Adina Boroneant, Ash Erim-Ozdogan, Hendrik-Jan Megens, Azadeh Fatemeh Mohaseb, Hitomi Hongo, Marjan Mashkour, Amelie Scheu, Evan K. Irving-Pease, Michelle Alexander, David Orton, Richard Sabin, László Bartosiewicz, Nenad Tasić, François-Xavier Ricaut, Anastasia Papathanasiou, Darko Radmanovic, Liora Kolska Horwitz, Christina Geoerg, Clive Bonsall, Anna Linderholm, Peter Rowley-Conwy, Audrey T. Lin, Daniel Helmer, Daniel G. Bradley, Roger Matthews, Ron Pinhasi, Ninna Manaseryan, Shiva Sheikhi, Sophie Van Poucke, Lionel Gourichon, Mike J. Church, Kevin G. Daly, Valentin Dumitraşcu, Joséphine Lesur, Mihai Gligor, Martien A. M. Groenen, Alexander Yanevich, Vincent M. Battista, Cleia Detry, Max Price, Rose-Marie Arbogast, Holley Martlew, Allowen Evin, Elisabeth Stephan, Norbert Benecke, John R. Stewart, Ophélie Lebrasseur, Giedre Motuzaite Matuzeviciute, Gennady F. Baryshnikov, Lucia Sarti, Youri van den Hurk, James Haile, Mike Parker Pearson, Arkadiusz Marciniak, Victoria E. Mullin, Jose-Miguel Carreterow, Kurt J. Gron, Alexandros Triantafyllidis, Thomas Cucchi, Rebecca Miller, Jelena Bulatović, and Anton Ervynck

Subjects
Gene Flow, Multidisciplinary, Swine, Library science, Skin Pigmentation, Biological Sciences, Corrections, DNA, Mitochondrial, Domestication, Europe, Middle East, Anthropology, evolution, Animals, Neolithic, DNA, Ancient, History, Ancient, Phylogeny
Abstract

Significance Archaeological evidence indicates that domestic pigs arrived in Europe, alongside farmers from the Near East ∼8,500 y ago, yet mitochondrial genomes of modern European pigs are derived from European wild boars. To address this conundrum, we obtained mitochondrial and nuclear data from modern and ancient Near Eastern and European pigs. Our analyses indicate that, aside from a coat color gene, most Near Eastern ancestry in the genomes of European domestic pigs disappeared over 3,000 y as a result of interbreeding with local wild boars. This implies that pigs were not domesticated independently in Europe, yet the first 2,500 y of human-mediated selection applied by Near Eastern Neolithic farmers played little role in the development of modern European pigs., Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

Published
2020

20. Sahelian pastoralism from the perspective of variants associated with lactase persistence

Author

Frédéric Austerlitz, Viktor Černý, François-Xavier Ricaut, Carina M. Schlebusch, Edita Priehodová, Zuzana Hofmanová, Jana Nováčková, Martina Čížková, Institute of Archaeology of the Czech Academy of Sciences (ARUP / CAS), Czech Academy of Sciences [Prague] (CAS), Éco-Anthropologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Processus d'Activation Sélective par Transfert d'Energie Uni-électronique ou Radiatif (UMR 8640) (PASTEUR), Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden, Éco-Anthropologie (EA), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Uppsala University

Subjects
0106 biological sciences, lactase persistence, subsistence, Arabic, Population, Pastoralism, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Black People, 010603 evolutionary biology, 01 natural sciences, Polymorphism, Single Nucleotide, White People, Anthropology, Physical, Africa, Northern, Ethnicity, Animals, Humans, 0601 history and archaeology, education, Socioeconomics, Lactase, 2. Zero hunger, Transients and Migrants, education.field_of_study, Genetic diversity, 060101 anthropology, Middle East, Haplotype, Subsistence agriculture, 06 humanities and the arts, language.human_language, Arabs, Diet, Lactase persistence, Geography, Milk, Haplotypes, Anthropology, language, Anatomy, African Sahel, pastoralism
Abstract

OBJECTIVES Archeological evidence shows that first nomadic pastoralists came to the African Sahel from northeastern Sahara, where milking is reported by ~7.5 ka. A second wave of pastoralists arrived with the expansion of Arabic tribes in 7th-14th century CE. All Sahelian pastoralists depend on milk production but genetic diversity underlying their lactase persistence (LP) is poorly understood. MATERIALS AND METHODS We investigated SNP variants associated with LP in 1,241 individuals from 29 mostly pastoralist populations in the Sahel. Then, we analyzed six SNPs in the neighboring fragment (419 kb) in the Fulani and Tuareg with the -13910*T mutation, reconstructed haplotypes, and calculated expansion age and growth rate of this variant. RESULTS Our results reveal a geographic localization of two different LP variants in the Sahel: -13910*T west of Lake Chad (Fulani and Tuareg pastoralists) and -13915*G east of there (mostly Arabic-speaking pastoralists). We show that -13910*T has a more diversified haplotype background among the Fulani than among the Tuareg and that the age estimate for expansion of this variant among the Fulani (~8.5 ka) corresponds to introduction of cattle to the area. CONCLUSIONS This is the first study showing that the "Eurasian" LP allele -13910*T is widespread both in northern Europe and in the Sahel; however, it is limited to pastoralists in the Sahel. Since the Fulani haplotype with -13910*T is shared with contemporary Eurasians, its origin could be in a region encompassing the Near East and northeastern Africa in a population ancestral to both Saharan pastoralists and European farmers.

Published
2020
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21. Genome skims analysis of betel palms (Areca spp., Arecaceae) and development of a profiling method to assess their plastome diversity

Author

Pauline Raimondeau, Guillaume Besnard, Nicolas Brucato, François-Xavier Ricaut, Sophie Manzi, Christopher Kinipi, Matthew Leavesley, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of Papua New Guinea (UPNG), James Cook University (JCU), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Genome, Plastid, Arecaceae, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, DNA, Mitochondrial, Herbarium, 010603 evolutionary biology, 01 natural sciences, Genome, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Betel nut domestication, Botany, Genetics, Ribosomal DNA, Areca, Phylogeny, 030304 developmental biology, 0303 health sciences, biology, Phylogenetic tree, Gene Expression Profiling, digestive, oral, and skin physiology, food and beverages, General Medicine, Plastome, Betel, biology.organism_classification, Mitogenome, Phylogeography, Indo-Pacific, Microsatellite, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Genome, Plant, Microsatellite Repeats
Abstract

International audience; The betel nut (Areca catechu L., Arecaceae) is a monoecious cultivated palm tree that is widespread in tropical regions. It is mainly cultivated for producing areca nuts, from which seeds are extracted and chewed by local populations principally in the Indo-Pacific region. Seeds contain alkaloids which are central nervous system stimulants and are highly addictive. Wild relatives of the betel nut are distributed in South Asia and Australasia, with ca. 40-50 Areca species currently recognized. The geographic origin(s) of the betel nut and its subsequent diffusion and diversification remains poorly documented. Here, a genome skimming approach was applied to screen nucleotidic variation in the most abundant genomic regions. Low coverage sequencing data allowed us to assemble full plastomes, mitochondrial regions (either full mitogenomes or the full set of mitochondrial genes) and the nuclear ribosomal DNA cluster for nine representatives of the Areca genus collected in the field and herbarium collections (including a 182-years old specimen collected during the Dumont d'Urville's expedition). These three genomic compartments provided similar phylogenetic signals, and revealed very low genomic diversity in our sample of cultivated betel nut. We finally developed a genotyping method targeting 34 plastid DNA microsatellites. This plastome profiling approach is useful for tracing the spread of matrilineages, and in combination with nuclear genomic data, can resolve the history of the betel nut. Our method also proves to be efficient for analyzing herbarium specimens, even those collected more than 100 years ago.

Published
2021
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22. Testing for Betel Nut Alkaloids in Hair of Papuans Abusers using UPLC–MS/MS and UPLC–Q-Tof-MS

Author

Jean Sébastien Raul, Pascal Kintz, Roxanne Tsang, Laurie Gheddar, François-Xavier Ricaut, Nicolas Brucato, Matthew Leavesley, Alice Ameline, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Institut de Médecine Légale [Strasbourg], and Université Louis Pasteur - Strasbourg I

Subjects
Substance-Related Disorders, [SDV]Life Sciences [q-bio], Health, Toxicology and Mutagenesis, 010402 general chemistry, Toxicology, Tandem mass spectrometry, 01 natural sciences, Analytical Chemistry, chemistry.chemical_compound, Alkaloids, Tandem Mass Spectrometry, medicine, Humans, Environmental Chemistry, Arecoline, Areca, Chromatography, High Pressure Liquid, ComputingMilieux_MISCELLANEOUS, Areca palm, Detection limit, Chemical Health and Safety, Chromatography, biology, 010401 analytical chemistry, Arecaidine, biology.organism_classification, Betel, 0104 chemical sciences, Substance Abuse Detection, Guvacine, chemistry, Chromatography, Liquid, Hair, medicine.drug
Abstract

Betel nut is the fruit of Areca palm, growing in Papua New Guinea. Mixed with limestone and stick mustard, arecoline and guvacoline, which are present in betel nut, are hydrolyzed into arecaidine and guvacine, respectively. As part of the study on dietary habits of Papuans residents, our laboratory was asked to analyze the four alkaloids in hair to document long-term exposure. Hair samples were collected from 19 adult subjects (males = 11; females = 8), by some of the authors, and were sent to the laboratory for analysis. The four alkaloids have very similar chemical structures. In order to accurately identify the drugs, two methods were developed. First, the compounds were identified using an ultra-high-performance liquid chromatography system coupled to time-of-flight mass spectrometry. Then, they were quantified by an ultra-high-performance liquid chromatography system coupled to tandem mass spectrometry. After decontamination with dichloromethane, hair samples were cut into very small segments and 20 mg were incubated in methanol for 2 h 30 min in an ultrasound bath. After cooling, the methanol was evaporated to dryness in presence of 20-μL octanol to prevent volatilization. Nicotine-d4 was used as an internal standard. Linearity was observed for concentrations ranging from the limit of quantification to 20 ng/mg for arecoline, arecaidine, guvacine and guvacoline. Measured concentrations were in the range 60 pg/mg to 18 ng/mg for arecoline (n = 19), 14 pg/mg to 2.5 ng/mg for guvacoline (n = 11), 63 pg/mg to 3.8 ng/mg for arecaidine (n = 11) and 100 pg/mg to 3.2 ng/mg for guvacine (n = 6). There was no correlation between concentrations of arecoline and arecaidine (ratio from 0.01 to 0.18) and guvacoline and guvacine (ratio from 0.06 to 3.50). However, the identification of these substances in hair is a good marker of consumption of betel nut and allows us to document a local practice that remains difficult to evaluate just by questioning.

Published
2019
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23. Multiple Deeply Divergent Denisovan Ancestries in Papuans

Author

Luca Pagani, Mayukh Mondal, Murray P. Cox, Lauri Saag, Daniel Lawson, Mark Stoneking, Guy S. Jacobs, Chelzie Crenna Darusallam, Georgi Hudjashov, François-Xavier Ricaut, J. Stephen Lansing, Pradiptajati Kusuma, Mait Metspalu, Herawati Sudoyo, Jacobs, Guy Sherwin [0000-0002-4698-7758], Apollo - University of Cambridge Repository, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Human Genetics, Evolutionary Genetics, University of Tartu, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
Gene Flow, Neanderthal, Pleistocene, Lineage (evolution), [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Oceania, Introgression, Wallace Line, Genetic Introgression, Genome, archaic ancestry, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, Asian People, biology.animal, Denisovan, Animals, Humans, 030304 developmental biology, Neanderthals, 0303 health sciences, New Guinea, biology, Genome, Human, Haplotype, Genetic Variation, Hominidae, biology.organism_classification, Biological Evolution, Haplotypes, Evolutionary biology, Indonesia, Island Southeast Asia, 030217 neurology & neurosurgery
Abstract

International audience; Genome sequences are known for two archaic hominins-Neanderthals and Denisovans-which interbred with anatomically modern humans as they dispersed out of Africa. We identified high-confidence archaic haplotypes in 161 new genomes spanning 14 island groups in Island Southeast Asia and New Guinea and found large stretches of DNA that are inconsistent with a single introgressing Denisovan origin. Instead, modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages that separated over 350 thousand years ago. Spatial and temporal structure among these lineages suggest that introgression from one of these Denisovan groups predominantly took place east of the Wallace line and continued until near the end of the Pleistocene. A third Denisovan lineage occurs in modern East Asians. This regional mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with multiple Denisovan groups that were geographically isolated from each other over deep evolutionary time.

Published
2019
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24. Evidence of Austronesian Genetic Lineages in East Africa and South Arabia: Complex Dispersal from Madagascar and Southeast Asia

Author

Teresa Rito, Luísa Pereira, Jean-François Deleuze, Mark Stoneking, Verónica Fernandes, Pedro Soares, Anne Boland, Pradiptajati Kusuma, François-Xavier Ricaut, Céline Besse, Nicolas Brucato, Herawati Sudoyo, Connie J. Mulligan, Murray P. Cox, Viktor Černý, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto = University of Porto, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Evolutionary Genetics, Archaeogenetics Laboratory, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Universidade do Porto, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Universidade do Minho, and Instituto de Investigação e Inovação em Saúde

Subjects
0106 biological sciences, Gene Flow, Genetic genealogy, Human Migration, Polynesian motif, Medicina Básica [Ciências Médicas], [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, mitochondrial DNA, Biology, 010603 evolutionary biology, 01 natural sciences, Gene flow, Southeast asia, 03 medical and health sciences, Peninsula, Borneo, Indian Ocean Islands, parasitic diseases, Genetics, East africa, Madagascar, Humans, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, geography, geography.geographical_feature_category, Science & Technology, Human migration, business.industry, Ecology, Arabia, genome-wide data, Africa, Eastern, language.human_language, humanities, Indonesian, Austronesian, Ciências Médicas::Medicina Básica, Genome, Mitochondrial, language, Biological dispersal, business, Research Article
Abstract

The Austronesian dispersal across the Indonesian Ocean to Madagascar and the Comoros has been well documented, but in an unexplained anomaly, few to no traces have been found of the Austronesian expansion in East Africa or the Arabian Peninsula. To revisit this peculiarity, we surveyed the Western Indian Ocean rim populations to identify potential Austronesian genetic ancestry. We generated full mitochondrial DNA genomes and genome-wide genotyping data for these individuals and compared them with the Banjar, the Indonesian source population of the westward Austronesian dispersal. We find strong support for Asian genetic contributions to maternal lineages and autosomal variation in modern day Somalia and Yemen. Surprisingly, this input reveals two apparently different geographic origins and timings of admixture for the Austronesian contact; one at a very early phase (likely associated with the early Austronesian dispersals), and a later movement dating to the end of nineteenth century. These Austronesian gene flows come, respectively, from Madagascar and directly from an unidentified location in Island Southeast Asia. This result reveals a far more complex dynamic of Austronesian dispersals through the Western Indian Ocean than has previously been understood and suggests that Austronesian movements within the Indian Ocean may have been part of a lengthy process, probably continuing well into the modern era., GenoToul bioinformatics facility of Genopole Toulouse Midi-Pyrénées, France. We thank the CNRGH production team for genotyping data generation. This work was supported by French Ministry of Research grant ANR-14-CE31-0013-01 (OCEOADAPTO) to F.-X.R, the French Ministry of Foreign and European Affairs (French Archaeological Mission in Borneo (MAFBO) to F.-X.R.), and the French Embassy in Indonesia through its Cultural and Cooperation Services (Institut Français en Indonésie); a fellowship from the Alexander von Humboldt Foundation to M.P.C.; funding from the Max Planck Society to M.S.; and grants from COMPETE 2020 and a Fundação para a Ciência e a Tecnologia-funded project (POCI-01-0145-FEDER-016609) to V.F

Published
2019
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25. Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Author

Marjan Mashkour, Anastasia Papathanasiou, Joris Peters, John Chapman, Anne Tresset, Simon Stoddart, Antonio Tagliacozzo, Canan Çakirlar, Jörg Schibler, Daniel Helmer, Ceiridwen J. Edwards, Caroline Malone, Vesna Dimitrijević, Andrea Zeeb-Lanz, Christina Geörg, Alexandros Triantafyllidis, Panoraia Alexandri, Ophélie Lebrasseur, Thomas Cucchi, Victoria E. Mullin, Michael P. Richards, James Haile, Laurent A. F. Frantz, Cevdet Merih Erek, John R. Stewart, Joachim Burger, Mihai Gligor, Jörg Orschiedt, Gennady F. Baryshnikov, Lucia Sarti, Rebecca Miller, Youri van den Hurk, Evan K. Irving-Pease, Allowen Evin, Hitomi Hongo, Richard P. M. A. Crooijmans, Jelena Bulatović, Max Price, Keith Dobney, Adina Boroneanţ, Anton Ervynck, Mike Parker Pearson, Joséphine Lesur, Elisabeth Stephan, Holley Martlew, Sepideh Maziar, Kurt J. Gron, Bea De Cupere, Kevin G. Daly, Valentin Dumitraşcu, Anders Götherström, Arkadiusz Marciniak, Azadeh Fatemeh Mohaseb, Richard Sabin, David Orton, Greger Larson, Lionel Gourichon, Cleia Detry, Clive Bonsall, François-Xavier Ricaut, Louis du Plessis, Jean-Denis Vigne, José Miguel Carretero, Benjamin S. Arbuckle, Mike J. Church, Hendrik-Jan Megens, Giedre Motuzaite Matuzeviciute, Linus Girdland-Flink, Domenico Fulgione, Ross Barnett, Ron Pinhasi, Ninna Manaseryan, Liora Kolska Horwitz, Melinda A. Zeder, Peter Rowley-Conwy, Alexander Yanevich, Daniel G. Bradley, Amelie Scheu, László Bartosiewicz, Darko Radmanovic, Shiva Sheikhi, Michelle Alexander, Katerina Trantalidou, Cristina Valdiosera, Adrian Bӑlӑşescu, M. Thomas P. Gilbert, Vincent M. Battista, Anna Linderholm, Norbert Benecke, Aslı Erim-Özdoğan, Rose-Marie Arbogast, Thomas H. McGovern, Audrey T. Lin, Sophie Van Poucke, Roger Matthews, Martien A. M. Groenen, Erik Meijaard, Wolfram Schier, Nenad Tasić, Dusan Boric, Frantz, Laurent A. F., Haile, Jame, Lin, Audrey T., Scheu, Amelie, Geörg, Christina, Benecke, Norbert, Alexander, Michelle, Linderholm, Anna, Mullin, Victoria E., Daly, Kevin G., Battista, Vincent M., Price, Max, Gron, Kurt J., Alexandri, Panoraia, Arbogast, Rose-Marie, Arbuckle, Benjamin, Balaşescu, Adrian, Barnett, Ro, Bartosiewicz, László, Baryshnikov, Gennady, Bonsall, Clive, ̧, Dušan Boric Adina Boroneant, Bulatovic, Jelena, Çakirlar, Canan, Carretero, José-Miguel, Chapman, John, Church, Mike, Crooijmans, Richard, De Cupere, Bea, Detry, Cleia, Dimitrijevic, Vesna, Dumitras ̧cu, Valentin, du Plessis, Loui, Edwards, Ceiridwen J., Merih Erek, Cevdet, ̆an, AslıErim-Özdog, Ervynck, Anton, Fulgione, Domenico, Gligor, Mihai, Götherström, Ander, Gourichon, Lionel, Groenen, Martien A. M., Helmer, Daniel, Hongo, Hitomi, Horwitz, Liora K., Irving-Pease, Evan K., Lebrasseur, Ophélie, Lesur, Joséphine, Malone, Caroline, Manaseryan, Ninna, Marciniak, Arkadiusz, Martlew, Holley, Mashkour, Marjan, Matthews, Roger, Motuzaite Matuzeviciute, Giedre, Maziar, Sepideh, Meijaard, Erik, Mcgovern, Tom, Megens, Hendrik-Jan, Miller, Rebecca, Fatemeh Mohaseb, Azadeh, Orschiedt, Jörg, Orton, David, Papathanasiou, Anastasia, Parker Pearson, Mike, Pinhasi, Ron, Radmanovic, Darko, Ricaut, François-Xavier, Richards, Mike, Sabin, Richard, Sarti, Lucia, Schier, Wolfram, Sheikhi, Shiva, Stephan, Elisabeth, Stewart, John R., Stoddart, Simon, Tagliacozzo, Antonio, Tasic, Nenad, Trantalidou, Katerina, Tresset, Anne, Valdiosera, Cristina, van den Hurk, Youri, Van Poucke, Sophie, Vigne, Jean-Deni, Yanevich, Alexander, Zeeb-Lanz, Andrea, Triantafyllidis, Alexandro, Gilbert, M. Thomas P., Schibler, Jörg, Rowley-Conwy, Peter, Zeder, Melinda, Peters, Jori, Cucchi, Thoma, Bradley, Daniel G., Dobney, Keith, Burger, Joachim, Evin, Allowen, Girdland-Flink, Linu, Larson, Greger, Archaeology of Northwestern Europe, Groningen Institute of Archaeology, Piperno, Dolores R., Repositório da Universidade de Lisboa, Department of Natural Sciences, German Archaeological Institute (DAI), Texas A&M University [College Station], Transplant Research Program [Boston, MA, USA], Boston Children's Hospital, Archéologie et histoire ancienne : Méditerranée - Europe (ARCHIMEDE), Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Department of Anthropology, Baylor University, Baylor University, University of York [York, UK], Stockholm University, Cardiff School of History, Ancient History, Archaeology and Religion, Cardiff University, Romanian Academy of Sciences, Animal Breeding and Genomics Centre, Wageningen University and Research [Wageningen] (WUR), UNIARQ, Universidade de Lisboa = University of Lisbon (ULISBOA), Department of Structural and Functional Biology, University of Naples Federico II = Università degli studi di Napoli Federico II, Stockholm Univ, Dept Biochem & Biophys, S-10691 Stockholm, Sweden, Gestion des ressources naturelles , environnements et sociétés (GReNES), Culture et Environnements, Préhistoire, Antiquité, Moyen-Age (CEPAM), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), ARCHEORIENT - Environnements et sociétés de l'Orient ancien (Archéorient), Université Lumière - Lyon 2 (UL2)-Centre National de la Recherche Scientifique (CNRS), University of Oxford, Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Goethe-Universität Frankfurt am Main, University of Liverpool, HEC Paris - Recherche - Hors Laboratoire, Ecole des Hautes Etudes Commerciales (HEC Paris), School of Archaeology, University College Dublin [Dublin] (UCD), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Department of Human Evolution [Leipzig], Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Connaissance Organisation et Systèmes TECHniques (COSTECH), Université de Technologie de Compiègne (UTC), Department of Archaeology, University of Cambridge [UK] (CAM), Laboratorio di Paleontologia e Archeozoologia, Soprintendenza Speciale al Museo Nazionale Preistorico ed Etnografico 'L. Pigorini', Roma, Museo Nazionale Preistorico Etnografico 'L. Pigorini, Institute of archaeology (UCL), University College of London [London] (UCL), University of Copenhagen = Københavns Universitet (UCPH), University of Basel (Unibas), Institut für Paläoanatomie und Geschichte der Tiermedizin, Ludwig-Maximilians-Universität München (LMU), Department of Archaeology, University of Aberdeen, University of Aberdeen, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Universidade de Lisboa (ULISBOA), Università degli studi di Napoli Federico II, Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), University of Oxford [Oxford], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (KU), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)

Subjects
0301 basic medicine, Swine, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Skin Pigmentation, [SHS]Humanities and Social Sciences, Gene flow, Domestication, ddc:590, BREEDS, DOMESTIC PIGS, HISTORY, 0601 history and archaeology, Neolithic, History, Ancient, Phylogeny, Multidisciplinary, 060102 archaeology, INTROGRESSION, Europe, pigs, domestication, genomes, WILD, 06 humanities and the arts, Archaeological evidence, SPREAD, Coat, Mitochondrial DNA, Evolution, Zoology, Locus (genetics), Biology, Animal Breeding and Genomics, DNA, Mitochondrial, Middle East, 03 medical and health sciences, Animals, Fokkerij en Genomica, DNA, Ancient, General, ddc:930, Haplotype, DNA, 900 Geschichte und Geografie::930 Geschichte des Altertums (bis ca. 499), Archäologie::930 Geschichte des Altertums bis ca. 499, Archäologie, LONG, SIZE, 030104 developmental biology, domestication evolution gene flow Neolithic, WIAS
Abstract

International audience; Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local Euro-pean wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process. domestication | evolution | gene flow | Neolithic

Published
2019
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26. Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

Author

Simona Barlera, Giovanni Birolo, Simon Myers, Viola Grugni, Vincenzo Lorenzo Pascali, Andrea Angius, Mait Metspalu, Francesca Brisighelli, Antonio Torroni, Francesco Montinaro, Hovirag Lancioni, Luísa Pereira, Antonella Mulas, Mohammed Melhaoui, Alessandro Achilli, Serena Aneli, Mohammed Cherkaoui, Peristera Paschou, M. Peyret-Guzzon, Pilar Galan, Giorgio B. Boncoraglio, A. M. Di Blasio, Stéphane Mazières, C. Di Gaetano, Garrett Hellenthal, Giuseppe Matullo, George Stamatoyannopoulos, Joanna Giemza, J. Di Cristofaro, Magdalena Zoledziewska, Irene Cardinali, Georgios Athanasiadis, Cristian Capelli, François-Xavier Ricaut, Jacques Chiaroni, Anna Olivieri, Alessandro Raveane, Luca Pagani, Toomas Kivisild, Abdellatif Baali, Nicolas Brucato, Christian Dina, Jean-Michel Dugoujon, Clare Bycroft, Alberto Piazza, Silvia Parolo, Francesco Cucca, Ornella Semino, Dipartimento di Biologia e Biotecnologie ‘Lazzaro Spallanzani’, University of Pavia, University of Pavia, University of Oxford [Oxford], Aarhus University [Aarhus], Istituto di Ricerche Farmacologiche Mario Negri, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Fondazione 'Istituto Neurologico Nazionale C. Mondino'-Fondazione 'Istituto Neurologico Nazionale C. Mondino', University of Turin, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Dipartimento di Genetica, Biologica e Biochimica, Università degli studi di Torino (UNITO), Laboratoire d'Etude du Rayonnement et de la Matière en Astrophysique (LERMA), École normale supérieure - Paris (ENS Paris)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, PSL Research University (PSL)-PSL Research University (PSL)-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Centre National de la Recherche Scientifique (CNRS), Georgia Tech - CNRS [Metz] (UMI2958), Ecole Nationale Supérieure des Arts et Metiers Metz-SUPELEC-Georgia Institute of Technology [Atlanta]-Georgia Institute of Technology [Lorraine, France]-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Etablissement Français du Sang - Alpes-Méditerranée (EFS - Alpes-Méditerranée), Etablissement Français du Sang, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Génétique des maladies multifactorielles (GMM), Université de Lille, Droit et Santé-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche en Epidémiologie Nutritionnelle (UREN), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Sorbonne Paris Cité (USPC)-Université Paris 13 (UP13)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut National de la Recherche Agronomique (INRA), Equipe 3: EREN- Equipe de Recherche en Epidémiologie Nutritionnelle (CRESS - U1153), Université Paris 13 (UP13)-Institut National de la Recherche Agronomique (INRA)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC), Centre National de la Recherche Scientifique (CNRS), Dipartimento di Genetica e Microbiologica, Università di Pavia, Dipartimento di Genetica e Microbiologia, Instituto de Investigação e Inovação em Saúde, Raveane, A, Aneli, S, Montinaro, F, Athanasiadis, G, Barlera, S, Birolo, G, Boncoraglio, G, Di Blasio, A, Di Gaetano, C, Pagani, L, Parolo, S, Paschou, P, Piazza, A, Stamatoyannopoulos, G, Angius, A, Brucato, N, Cucca, F, Hellenthal, G, Mulas, A, Peyret-Guzzon, M, Zoledziewska, M, Baali, A, Bycroft, C, Cherkaoui, M, Chiaroni, J, Di Cristofaro, J, Dina, C, Dugoujon, J, Galan, P, Giemza, J, Kivisild, T, Mazieres, S, Melhaoui, M, Metspalu, M, Myers, S, Pereira, L, Ricaut, F, Brisighelli, F, Cardinali, I, Grugni, V, Lancioni, H, Pascali, V, Torroni, A, Semino, O, Matullo, G, Achilli, A, Olivieri, A, Capelli, C, Mazières, Stéphane, Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani' = Department of Biology and Biotechnology [Univ di Pavia] (DBB UNIPV), Università degli Studi di Pavia = University of Pavia (UNIPV), University of Oxford, Università degli studi di Torino = University of Turin (UNITO), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire de Paris, Université Paris sciences et lettres (PSL)-Université de Cergy Pontoise (UCP), Georgia Tech Lorraine [Metz], Ecole Nationale Supérieure des Arts et Metiers Metz-Georgia Institute of Technology [Atlanta]-Ecole Supérieure d'Electricité - SUPELEC (FRANCE)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Université Paris 13 (UP13)-Institut National de la Recherche Agronomique (INRA)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), École normale supérieure - Paris (ENS Paris), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Sorbonne Paris Cité (USPC)-Université Paris 13 (UP13)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université (HESAM)-HESAM Université (HESAM)-Institut National de la Recherche Agronomique (INRA), HESAM Université (HESAM)-HESAM Université (HESAM)-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA), Università degli Studi di Pavia, Institut National de la Recherche Agronomique (INRA)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Paris 13 (UP13)-Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), and Université Paris 13 (UP13)-Institut National de la Recherche Agronomique (INRA)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
SELECTION, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Distribution (economics), Population genetics, Neanderthal genome project, 0302 clinical medicine, Peninsula, HISTORY, Databases, Genetic, ADAPTATION, Research Articles, History, Ancient, media_common, Neanderthals, MODERN HUMANS, 0303 health sciences, Multidisciplinary, geography.geographical_feature_category, POPULATION GENETICS, GENOMICS, EUROPE, Population Genetic, SciAdv r-articles, ASSOCIATION, [SHS.ANTHRO-BIO] Humanities and Social Sciences/Biological anthropology, Multidisciplinary Sciences, ADMIXTURE, Geography, Italy, Ethnology, Science & Technology - Other Topics, Neanderthals / genetics, Research Article, EUROPE, MIGRATION, media_common.quotation_subject, Pastoralism, Human Genetic, Settore BIO/08 - ANTROPOLOGIA, GENETIC-STRUCTURE, SEQUENCE, White People, 03 medical and health sciences, Bronze Age, POPULATION GENETICS, Genetic variation, Animals, Humans, DNA, Ancient, European Continental Ancestry Group / genetics, 030304 developmental biology, Science & Technology, business.industry, Genome, Human, Genetic Drift, Human Genetics, Anthropology, GENOME-WIDE PATTERNS, business, GENOMICS, 030217 neurology & neurosurgery, Diversity (politics), Genome-Wide Association Study
Abstract

A population in a natural crossroad within Europe reveals multiple ancient contributions and substantial population structure., European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non–steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.

Published
2019
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27. Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe

Author

Vincenzo Lorenzo Pascali, Francesca Brisighelli, Simona Barlera, Luca Pagani, Nicolas Brucato, Joanna Giemza, Hovirag Lancioni, Clare Bycroft, Alberto Piazza, Jean-Michel Dugoujon, Antonella Mulas, Mohammed Cherkaoui, Francesco Cucca, Giovanni Birolo, Alessandro Achilli, Serena Aneli, C. Di Gaetano, M. Peyret-Guzzon, Garrett Hellenthal, Pilar Galan, A. M. Di Blasio, Giuseppe Matullo, Christian Dina, Antonio Torroni, George Stamatoyannopoulos, Irene Cardinali, Viola Grugni, Luísa Pereira, Mait Metspalu, Georgios Athanasiadis, Peristera Paschou, Abdellatif Baali, Cristian Capelli, Mohammed Melhaoui, François-Xavier Ricaut, Simon Myers, Andrea Angius, Francesco Montinaro, Ornella Semino, Anna Olivieri, Toomas Kivisild, Magdalena Zoledziewska, Giorgio B. Boncoraglio, Silvia Parolo, and Alessandro Raveane

Subjects
0303 health sciences, Genetic diversity, Neanderthal, geography.geographical_feature_category, biology, Pastoralism, Neanderthal genome project, 03 medical and health sciences, 0302 clinical medicine, Geography, Bronze Age, Peninsula, biology.animal, Genetic variation, Genetic structure, Ethnology, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

European populations display low genetic diversity as the result of long term blending of the small number of ancient founding ancestries. However it is still unclear how the combination of ancient ancestries related to early European foragers, Neolithic farmers and Bronze Age nomadic pastoralists can fully explain genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the overall continental diversity, but to date have been systematically understudied. Here we characterised the ancestry profiles of modern-day Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe and the rest of the world. Italian genomes captured several ancient signatures, including a non-steppe related substantial ancestry contribution ultimately from the Caucasus. Differences in ancestry composition as the result of migration and admixture generated in Italy the largest degree of population structure detected so far in the continent and shaped the amount of Neanderthal DNA present in modern-day populations. One sentence summary Ancient and historical admixture events shaped the genetic structure of modern-day Italians, the ancestry profile of Southern European populations and the continental distribution of Neanderthal legacy.

Published
2018
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28. The Comoros Show the Earliest Austronesian Gene Flow into the Swahili Corridor

Author

Jacques Chiaroni, Mohammed Omar, Murray P. Cox, Bertrand Fin, Stéphane Mazières, Farida Alshamali, Anne Boland, Pradiptajati Kusuma, Nicole Boivin, Marie-Claude Simeone-Senelle, Joseph Wainaina Ng’ang’a, Pascal Bailly, Alison Crowther, Alexander Adelaar, François-Xavier Ricaut, Mark Stoneking, Luísa Pereira, Nicolas Brucato, Jean-François Deleuze, Verónica Fernandes, Coralie Frassati, Instituto de Investigação e Inovação em Saúde, Human Genetics, Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Anthropologie bio-culturelle, Droit, Ethique et Santé (ADES), Aix Marseille Université (AMU)-EFS ALPES MEDITERRANEE-Centre National de la Recherche Scientifique (CNRS), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Langage, LAngues et Cultures d'Afrique Noire (LLACAN), Institut National des Langues et Civilisations Orientales (Inalco)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Etablissement Français du Sang - Alpes-Méditerranée (EFS - Alpes-Méditerranée), Etablissement Français du Sang, Dubai Police General Headquarters, Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Evolutionary Genetics, University of Oxford [Oxford], Archaeogenetics Laboratory, Sorenson Molecular Genealogy Foundation, Universidade do Porto = University of Porto, Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and University of Oxford

Subjects
0301 basic medicine, Gene Flow, Asia, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Population genetics, Bantu languages, Admixture, 030105 genetics & heredity, migration, Polymorphism, Single Nucleotide, Article, Comoros, Gene flow, 03 medical and health sciences, Genetics, Madagascar, Humans, education, Genetics (clinical), Migration, Swahili, education.field_of_study, geography.geographical_feature_category, Middle East, Australia, population genetics, Genetic Variation, Kenya, East Africa, language.human_language, 030104 developmental biology, Geography, Genetics, Population, Archipelago, language, Ethnology, Biological dispersal, admixture, Population Genetics
Abstract

At the dawn of the second millennium, the expansion of the Indian Ocean trading network aligned with the emergence of an outward-oriented community along the East African coast to create a cosmopolitan cultural and trading zone known as the Swahili Corridor. On the basis of analyses of new genome-wide genotyping data and uniparental data in 276 individuals from coastal Kenya and the Comoros islands, along with large-scale genetic datasets from the Indian Ocean rim, we reconstruct historical population dynamics to show that the Swahili Corridor is largely an eastern Bantu genetic continuum. Limited gene flows from the Middle East can be seen in Swahili and Comorian populations at dates corresponding to historically documented contacts. However, the main admixture event in southern insular populations, particularly Comorian and Malagasy groups, occurred with individuals from Island Southeast Asia as early as the 8th century, reflecting an earlier dispersal from this region. Remarkably, our results support recent archaeological and linguistic evidence-based suggestions that the Comoros archipelago was the earliest location of contact between Austronesian and African populations in the Swahili Corridor. We acknowledge support from the GenoToul bioinformatics facility of Genopole Toulouse Midi-Pyre´ne´es, France. This research was supported by French Ministry of Research grant ANR-14-CE31-0013-01 (OCEOADAPTO) to F.-X.R, a Rutherford Fellowship from the Royal Society of New Zealand (RDF-10- MAU-001), a fellowship from the Alexander von Humboldt Foundation to M.P.C., and grants from COMPETE 2020 and a Fundac¸a˜o para a Cieˆncia e a Tecnologia-funded project (POCI-01-0145-FEDER-016609) to V.F. We thank Kamil Merito for his help collecting East African samples. We thank all the local Swahili and Comorian communities who participated in this study.

Published
2018
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29. Genomic admixture tracks pulses of economic activity over 2,000 years in the Indian Ocean trading network

Author

Pradiptajati Kusuma, Philippe Beaujard, Nicolas Brucato, François-Xavier Ricaut, Murray P. Cox, Herawati Sudoyo, Human Genetics, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre d'Etudes des Mondes Africains (CEMAf), Université Paris 1 Panthéon-Sorbonne (UP1)-Université de Provence - Aix-Marseille 1-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Paris 1 Panthéon-Sorbonne (UP1)-Université de Provence - Aix-Marseille 1-École pratique des hautes études (EPHE), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Economics, Restructuring, Human Migration, Science, Genomic data, Population Dynamics, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Article, 03 medical and health sciences, Humans, 14. Life underwater, Economic geography, Indian Ocean, Multidisciplinary, Middle East, Human migration, business.industry, Population mixing, Genetic Variation, Genomics, Models, Theoretical, Trade network, Indian ocean, Genetics, Population, 030104 developmental biology, Geography, Medicine, business
Abstract

The Indian Ocean has long been a hub of interacting human populations. Following land- and sea-based routes, trade drove cultural contacts between far-distant ethnic groups in Asia, India, the Middle East and Africa, creating one of the world’s first proto-globalized environments. However, the extent to which population mixing was mediated by trade is poorly understood. Reconstructing admixture times from genomic data in 3,006 individuals from 187 regional populations reveals a close association between bouts of human migration and trade volumes during the last 2,000 years across the Indian Ocean trading system. Temporal oscillations in trading activity match phases of contraction and expansion in migration, with high water marks following the expansion of the Silk Roads in the 5th century AD, the rise of maritime routes in the 11th century and a drastic restructuring of the trade network following the arrival of Europeans in the 16th century. The economic fluxes of the Indian Ocean trade network therefore directly shaped exchanges of genes, in addition to goods and concepts.

Published
2017
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30. Genomic landscape of human diversity across Madagascar

Author

Amal Arachiche, Mireille Mialy Rakotomalala, Veronica Pereda-Loth, Anne Boland, Mark Stoneking, Nelly Ranaivo Rabetokotany, Sander Adelaar, Sendra Lejamble, Laure Tonaso, Fulgence Fanony, Miakabola Andriamampianina Raharijesy, Olivier Thomas, Jean-François Deleuze, Herawati Sudoyo, François-Xavier Ricaut, Thierry Letellier, Lolona Razafindralambo, Philippe Grange, Bodo Ravololomanga, Chantal Radimilahy, Margit Heiske, Bako Rasoarifetra, Ramilisonina, Ahmed Mohamed Abdallah, Shengyu Ni, Jean-Aimé Rakotoarisoa, Lucien M.A. Rakotozafy, Stéphanie Schiavinato, Harilanto Razafindrazaka, Pradiptajati Kusuma, Ignace Rakoto, Denis Pierron, Nicolas Brucato, Philippe Beaujard, Michel Razafiarivony, Christophe Rocher, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Université d'Antananarivo, Physiopathologie mitochondriale, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Eijkman Institute for Molecular Biology [Jakarta], Department of Pharmacy, Faculty of Science & Mathematics, Islamic University of Indonesia, Islamic University of Indonesia, Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft, Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut des Mondes Africains (IMAF), Université Paris 1 Panthéon-Sorbonne (UP1)-Institut de Recherche pour le Développement (IRD)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), La Rochelle Université (ULR), University of Melbourne, ANR-12-PDOC-0037,GENO-MIX,Admixture fonctionnelle : étude génomique des adaptations métaboliques lors d'un mélange de population.(2012), ANR-14-CE31-0013,OCEOADAPTO,Histoire des populations dans l'Océan Indien : Adaptation biologique des populations issu de la traite des esclaves et de la dispersion indonésienne vers Madagascar(2014), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, RICAUT, FRANCOIS-XAVIER, Retour Post-Doctorant - Admixture fonctionnelle : étude génomique des adaptations métaboliques lors d'un mélange de population. - - GENO-MIX2012 - ANR-12-PDOC-0037 - PDOC - VALID, Appel à projets générique - Histoire des populations dans l'Océan Indien : Adaptation biologique des populations issu de la traite des esclaves et de la dispersion indonésienne vers Madagascar - - OCEOADAPTO2014 - ANR-14-CE31-0013 - Appel à projets générique - VALID, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Institut de Recherche pour le Développement (IRD)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), and Université de La Rochelle (ULR)

Subjects
Male, 0301 basic medicine, media_common.quotation_subject, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Population, Ethnic group, Black People, Distribution (economics), Bantu languages, 030105 genetics & heredity, 03 medical and health sciences, Asian People, parasitic diseases, Ethnicity, Madagascar, Humans, genetics, Colonization, proto-globalization, education, Indian Ocean, Malagasy origins, Aged, media_common, education.field_of_study, Multidisciplinary, Middle East, Genome, Human, Ecology, business.industry, Genetic Variation, genome-wide data, Middle Aged, Genealogy, [SHS.ANTHRO-BIO] Humanities and Social Sciences/Biological anthropology, 030104 developmental biology, Geography, PNAS Plus, Genetic structure, Female, business, Genome-Wide Association Study, Diversity (politics)
Abstract

International audience; Although situated ∼400 km from the east coast of Africa, Madagascar exhibits cultural, linguistic, and genetic traits from both Southeast Asia and Eastern Africa. The settlement history remains contentious; we therefore used a grid-based approach to sample at high resolution the genomic diversity (including maternal lineages, paternal lineages, and genome-wide data) across 257 villages and 2,704 Malagasy individuals. We find a common Bantu and Austronesian descent for all Malagasy individuals with a limited paternal contribution from Europe and the Middle East. Admixture and demographic growth happened recently, suggesting a rapid settlement of Madagascar during the last millennium. However, the distribution of African and Asian ancestry across the island reveals that the admixture was sex biased and happened heterogeneously across Madagascar, suggesting independent colonization of Madagascar from Africa and Asia rather than settlement by an already admixed population. In addition, there are geographic influences on the present genomic diversity, independent of the admixture, showing that a few centuries is sufficient to produce detectable genetic structure in human populations.

Published
2017
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31. Testing for betel nut alkaloids in hair using UHPLC-MS/MS and UHPLC-Q-ToF-MS

Author

François-Xavier Ricaut, Matthew Leavesley, Emilie Feisthauer, Pascal Kintz, Nicolas Brucato, Roxanne Tsang, Laurie Gheddar, Alice Ameline, and Jean-Sébastien Raul

Subjects
Nut, Chromatography, biology, Health, Toxicology and Mutagenesis, Catechu, Arecaidine, Toxicology, biology.organism_classification, Betel, Uhplc ms ms, chemistry.chemical_compound, Guvacine, chemistry, medicine, Arecoline, Areca, medicine.drug
Abstract

Objective Simultaneous identification and quantification of 4 betel nut alkaloids (arecoline, arecaidine, guvacoline and guvacine), in the hair of papuans abusers. Background Betel nut or areca nut, also known as “buai” in Papua New Guinea is the fruit of Areca catechu palm. This nut is highly consumed by the local population and represents a large part of the internal commercial activity of the island. The betel nut is mixed with lime powder made of shell or coral and stick mustard, which is a kind of bean also called “daka”. This mixture, of a typical red color, is chewed all along the day and finally spat in the street by the residents. Two major compounds are presents in betel nut: arecoline and guvacoline. In presence of lime (alkaline conditions), these alkaloids are hydrolyzed into arecaidine and guvacine respectively. These 4 substances have stimulating, anorectic and mildly euphoric effects. Some side effects are associated with this addiction, and the use of betel nut is the principal cause of mouth and esophagus cancer in Papua New Guinea. As part of the study on dietary habits, phenotypic and genetic diversity of papuans residents, our laboratory was asked to analyze the active substances in hair to document exposure. Hair samples were collected from 19 adult subjects (males = 11; females = 8) by some of the authors and sent to the laboratory for analysis. Method The 4 alkaloids of betel nut have very similar chemical structures. In order to identify accurately the drugs, two methods were developed. First, the compounds were identified using an ultra-high-performance liquid chromatography system coupled to time-of-flight mass spectrometry (Waters XEVO® G2-XS qTof). Then, they were quantified by an ultra-high-performance liquid chromatography system coupled to tandem mass spectrometry (Waters XEVO® TQD). Hair samples were twice decontaminated with dichloromethane and cut into very small segments using scissors. Given the curvy nature of all the specimens, there was no attempt to do segmentation. Then, 20 mg were incubated in methanol during 2 h 30 in an ultrasound bath. After cooling, the methanol was evaporated to dryness in presence of 20 μL octanol to prevent volatilization. Results Linearity was observed for concentration ranging from LOQ to 20 ng/mg with a correlation coefficient R2 of 0.9994, 0.9999, 0.9999 and 0.9981 for arecoline, arecaidine, guvacine and guvacoline respectively. Measured concentrations were in the range: 60 pg/mg to 18 ng/mg for arecoline (n = 19), 14 pg/mg to 2.5 ng/mg for guvacoline (n = 11), 63 pg/mg to 3.8 ng/mg for arecaidine (n = 11) and 100 pg/mg to 3.2 ng/mg for guvacine (n = 6). Conclusion There was no correlation between concentrations of arecoline and arecaidine (ratio arecaidine/arecoline from 0.01 to 0.18) and guvacoline and guvacine (ratio guvacine/guvacoline from 0.06 to 3.50). However, the identification of these substances in hair is a good marker of consumption of betel nut, and allows to document a local practice which remains difficult to evaluate just by questioning.

Published
2019
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32. Selective sweep on human amylase genes postdates the split with Neanderthals

Author

Lauri Saag, Martin K. Jones, S M Abdullah, Mario Mitt, Joseph Wee, Guy S. Jacobs, Toomas Kivisild, Miroslava Derenko, Charlotte E. Inchley, Reedik Mägi, Mait Metspalu, François-Xavier Ricaut, Nzar A. A. Shwan, Maru Mormina, Richard Villems, Boris Malyarchuk, John A.L. Armour, Tiago Antao, Cynthia D. A. Larbey, Christina A. Eichstaedt, Ene Metspalu, Georgi Hudjashov, Luca Pagani, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), University of Tartu, Human Genetics, Leverhulme Centre for Human Evolutionary Studies University of Cambridge, University of Cambridge [UK] (CAM), UMR 6578 : Anthropologie Bio-Culturelle (UAABC), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Larbey, Cynthia [0000-0002-9632-2746], Jacobs, Guy [0000-0002-4698-7758], Jones, Martin [0000-0003-0930-8012], Kivisild, Toomas [0000-0002-6297-7808], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, Male, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Gene Dosage, Locus (genetics), Biology, Article, Evolution, Molecular, 03 medical and health sciences, Genetic variation, Animals, Humans, 0601 history and archaeology, Amylase, Gene, Neanderthals, Genetics, Genetic diversity, 060101 anthropology, Multidisciplinary, Genome, Human, Genetic Variation, 06 humanities and the arts, Fixation (population genetics), 030104 developmental biology, Amylases, biology.protein, Female, Selective sweep, Low copy number
Abstract

Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.

Published
2016
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33. Multi-layered population structure in Island Southeast Asians

Author

Joseph Wee, Toomas Kivisild, Bryndis Yngvadottir, Pradiptajati Kusuma, S M Abdullah, Tiago Antao, Denis Pierron, Eadaoin Harney, Nicolas Brucato, Thierry Letellier, Cristina Castillo, Luca Pagani, François-Xavier Ricaut, Alexander Mörseburg, Mait Metspalu, Alexia Cardona, Tom Hoogervorst, Human Genetics, Centre National de la Recherche Scientifique (CNRS), Department of Genetics [Boston], Harvard Medical School [Boston] (HMS), University College of London [London] (UCL), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Physiopathologie mitochondriale, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Tartu, Leverhulme Centre for Human Evolutionary Studies University of Cambridge, University of Cambridge [UK] (CAM), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Genetics, Genetics (clinical), Vietnamese, Human Migration, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, 030105 genetics & heredity, Southeast asian, Article, Burmese, 03 medical and health sciences, Asian People, parasitic diseases, Humans, education, Asia, Southeastern, Malay, Islands, education.field_of_study, Human migration, business.industry, language.human_language, 030104 developmental biology, Geography, language, Biological dispersal, Ethnology, Mainland, business
Abstract

International audience; The history of human settlement in Southeast Asia has been complex and involved several distinct dispersal events. Here, we report the analyses of 1825 individuals from Southeast Asia including new genome-wide genotype data for 146 individuals from three Mainland Southeast Asian (Burmese, Malay and Vietnamese) and four Island Southeast Asian (Dusun, Filipino, Kankanaey and Murut) populations. While confirming the presence of previously recognised major ancestry components in the Southeast Asian population structure, we highlight the Kankanaey Igorots from the highlands of the Philippine Mountain Province as likely the closest living representatives of the source population that may have given rise to the Austronesian expansion. This conclusion rests on independent evidence from various analyses of autosomal data and uniparental markers. Given the extensive presence of trade goods, cultural and linguistic evidence of Indian influence in Southeast Asia starting from 2.5 kya, we also detect traces of a South Asian signature in different populations in the region dating to the last couple of thousand years.

Published
2016
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34. Genomic analyses inform on migration events during the peopling of Eurasia

Author

N. V. Ekomasova, Elza Khusnutdinova, Andrea Bamberg Migliano, Vedrana Škaro, Georgi Hudjashov, L. A. Atramentova, Murray P. Cox, Evelin Mihailov, Marta Mirazón Lahr, Mait Metspalu, Herawati Sudoyo, Monika Karmin, Alexia Cardona, Florin Mircea Iliescu, Melissa A. Wilson Sayres, Bayazit Yunusbayev, Dilbar Dalimova, Boris Malyarchuk, Michael D. Petraglia, Rita Khusainova, Grigor Zoraqi, Mark G. Thomas, Gazi Nurun Nahar Sultana, Irina Evseeva, Kuvat T. Momynaliev, François-Xavier Ricaut, Jainagul Isakova, A. S. Karunas, Reedik Mägi, Joseph Lachance, Kristiina Tambets, Lejla Mulahasanovic, Elena Balanovska, S M Abdullah, Levon Yepiskoposyan, Oleg Balanovsky, Nicolas Brucato, Yali Xue, Lauri Saag, Andrea Manica, Christina A. Eichstaedt, Mario Mitt, Florian Clemente, Ene Metspalu, Sardana A. Fedorova, Chris Tyler-Smith, Andres Metspalu, Charlotte E. Inchley, Pagbajabyn Nymadawa, Matthew Leavesley, Marina Gubina, Guy S. Jacobs, David M. Lambert, Craig Muller, Thierry Letellier, Elvira Pocheshkhova, Qasim Ayub, Joseph Wee, Pascale Gerbault, Zhaxylyk Sabitov, Doron M. Behar, Nikolay A. Barashkov, Dragan Primorac, Christiana L. Scheib, Tiago Antao, Evelyn Jagoda, Olga Utevska, Jeffrey D. Wall, Sarah A. Tishkoff, Toomas Kivisild, Gyaneshwer Chaubey, Shahlo Turdikulova, Eske Willerslev, Alena Kushniarevich, Lehti Saag, Chandana Basu Mallick, I. M. Khidiyatova, Ludmila P. Osipova, Alexander Mörseburg, Hovhannes Sahakyan, Damir Marjanović, Larisa Damba, Richard Villems, Anders Eriksson, Miroslava Derenko, Sergei Litvinov, Daniel Lawson, Rasmus Nielsen, V. L. Akhmetova, Maru Mormina, Mari Järve, Luca Pagani, George Andriadze, Michael DeGiorgio, Mikhail Voevoda, Daria V. Lichman, Michael C. Westaway, Sarah Kaewert, Wellcome Trust Genome Campus, The Wellcome Trust Sanger Institute [Cambridge], Human Evolution, University of Pennsylvania [Philadelphia], Institute of Molecular Biology and Medicine, International Network for the Sequencing of resPIRratory vIrusEs (INSPIRE), Department of Oncology, Human Genetics, Physiopathologie mitochondriale, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Leverhulme Centre for Human Evolutionary Studies University of Cambridge, University of Cambridge [UK] (CAM), The Estonian Genome Center, University of Tartu, Institute of Cytology and Genetics, Russian Academy of Sciences [Moscow] (RAS), School of Archaeology, University of Oxford [Oxford], Russian Academy of Medical Sciences, Institute of Biochemistry and Genetics [Bashkortostan Republic, Russia], Russian Academy of Sciences / Ufa Scientific Centre [Bashkortostan Republic, Russia]], Dept Integrat Biol, UMR 6578 : Anthropologie Bio-Culturelle (UAABC), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Swedish Institute of Space Physics [Uppsala] (IRF), University of Pennsylvania, University of Oxford, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Eriksson, Anders [0000-0003-3436-3726], Cardona, Alexia [0000-0002-7877-5565], Scheib, Christiana [0000-0003-4158-8296], Jacobs, Guy [0000-0002-4698-7758], Mirazon Lahr, Marta [0000-0001-5752-5770], Manica, Andrea [0000-0003-1895-450X], Willerslev, Eske [0000-0002-7081-6748], Kivisild, Toomas [0000-0002-6297-7808], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, History, Native Hawaiian or Other Pacific Islander, Biological anthropology, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Population Dynamics, Datasets as Topic, Evolutionary biology, Balancing selection, Genome, genome, peopling, Eurasia, 0302 clinical medicine, Effective population size, History, Ancient, Neanderthals, Genetics, education.field_of_study, Multidisciplinary, Continental Population Groups, Human migration, Fossils, Medicine (all), Genomics, 3. Good health, Europe, Oceanic Ancestry Group, Human, Biotechnology, Estonia, Gene Flow, Genome evolution, Heterozygote, Asia, General Science & Technology, 1.1 Normal biological development and functioning, Human Migration, Population, Biology, Evolutionary genetics, Article, Ancient, Africa, Animals, Genetics, Population, Genome, Human, Humans, New Guinea, 03 medical and health sciences, education, business.industry, Human evolutionary genetics, Racial Groups, Human Genome, 030104 developmental biology, Generic health relevance, business, 030217 neurology & neurosurgery
Abstract

High-coverage whole-genome sequence studies have so far focused on a limited number1 of geographically restricted populations2, 3, 4, 5, or been targeted at specific diseases, such as cancer6. Nevertheless, the availability of high- resolution genomic data has led to the development of new methodologies for inferring population history7, 8, 9 and refuelled the debate on the mutation rate in humans10. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record11, and admixture between AMHs and Neanderthals predating the main Eurasian expansion12, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75, 000 years ago.

Published
2016
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35. Borneo as a half empty pot: Pottery assemblage from Liang Abu, East Kalimantan

Author

Jean-Georges Ferrie, Adhi Agus Oktaviana, Jean-Michel Chazine, Astolfo Gomes de Mello Araujo, François-Xavier Ricaut, Bambang Sugiyanto, Simon Puaud, Sébastien Plutniak, Laboratoire Interdisciplinaire Solidarités, Sociétés, Territoires (LISST), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-École Nationale Supérieure de Formation de l'Enseignement Agricole de Toulouse-Auzeville (ENSFEA)-Centre National de la Recherche Scientifique (CNRS), De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), Pusat Penelitian Arkeologi Nasional, Centre de Recherche et de Documentation sur l'Océanie (CREDO), École des hautes études en sciences sociales (EHESS)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-École des hautes études en sciences sociales (EHESS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-École Nationale Supérieure de Formation de l'Enseignement Agricole de Toulouse-Auzeville (ENSFEA)-Centre National de la Recherche Scientifique (CNRS), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
010506 paleontology, Pottery, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Petrography, Context (language use), 01 natural sciences, law.invention, law, Assemblage (archaeology), Refitting analysis, 0601 history and archaeology, Radiocarbon dating, Stratigraphy (archaeology), 0105 earth and related environmental sciences, Earth-Surface Processes, 060102 archaeology, Kalimantan, Excavation, 06 humanities and the arts, Archaeology, Austronesian, Indonesia, Geology, Rock shelter
Abstract

http://www.elsevier.com/locate/quaint; International audience; This study is the first in-depth archaeological examination of a pottery assemblage found in the Indonesian part of Borneo Island. It aims to balance the regional knowledge of this large island, since the majority of information comes from sites located in the Malaysian northern part. Excavations in the Liang Abu rock shelter (East Kalimantan) led to the discovery and analysis of 1104 potsherds. The discussion on the upper part of the stratigraphy is based on the refitting relations between sherds. We propose some methodological improvements on the refitting analysis, based on the use of graph theory. The main ceramic layer is radiocarbon dated to 1672 ± 21 BP and 1524 ± 22 BP. Results from the petrographic analyses carried out on six sherds are presented and give a reference for future comparative investigations. Vessel morphology and stylistic features are presented, including those of red-slipped, cord-marked and incised pottery sherds. These results are discussed within the context of the settlement history in the Eastern part of Borneo and issues specific to archaeological investigations in tropical regions.; Cette étude constitue la première analyse archéologique approfondie d'un assemblage céramique découvert dans la partie indonésienne de l'île de Bornéo. Elle vise à ré-équilibrer notre connaissance de cette vaste île, dans la mesure où l'essentiel de nos connaissances proviennent de sites localisés dans sa partie nord, malaisienne. Les fouilles de l'abri sous roche de Liang Abu (Kalimantan Est) ont permis la découverte et l'analyse de 1104 fragments céramiques. La partie supérieure de la stratigraphie est discutée à partir des relations de remontages entre ces fragments. Nous proposons quelques perfectionnements méthodologiques pour l'analyse de ces relations, en recourant à la théorie des graphes. La principale couche à céramique a été daté par radiocarbone à 1672±21 BP et 1524±22 BP. Les résultats des analyses pétrographiques réalisées sur six fragments sont présentés et fournissent une référence pour de futures analyses comparatives. Les caractéristiques morphologiques et stylistiques des vases sont présentés, notamment ceux présentant des engobes rouges, des impressions cordées et des décors incisés. Ces résultats sont discutés en les rapportant aux débats sur l'histoire du peuplement dans la partie est de Bornéo, ainsi qu'aux problèmes spécifiquement posés en archéologie des régions tropicales.

Published
2016
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36. Western Eurasian genetic influences in the Indonesian archipelago

Author

Pradiptajati Kusuma, Murray P. Cox, Nicolas Brucato, Thierry Letellier, François-Xavier Ricaut, Herawati Sudoyo, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Human Genetics, Physiopathologie mitochondriale, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Genetic diversity, South asia, Middle East, Indonesian archipelago, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, virus diseases, Islam, respiratory system, 030105 genetics & heredity, language.human_language, Indonesian, 03 medical and health sciences, Indian ocean, 030104 developmental biology, Geography, parasitic diseases, Islamization, language, Ethnology, geographic locations, ComputingMilieux_MISCELLANEOUS, Earth-Surface Processes
Abstract

Western Eurasia, notably the Near East and South Asia (Indian sub-continent), has interacted with Indonesia through Indian Ocean trade (the Maritime Silk Route) for more than 2000 years. The Indianization, and later Islamization, of Indonesia was enacted largely through trading activities, but also spread with help from the many Indianized and Islamic kingdoms that reigned over parts of the Indonesian archipelago during this time. Western Eurasian interaction left behind not only imported trade goods and cultural features, but also genetic traces. To locate the primary areas of Western Eurasian genetic influence in Indonesia, we have assembled published uniparental genetic data from ∼2900 Indonesian individuals. Frequency distributions show that Western Eurasian paternal lineages are found more commonly than Western Eurasian maternal lineages. Furthermore, the origins of these paternal lineages are more diverse than the corresponding maternal lineages, predominantly tracing back to South West and South Asia, and the Indian sub-continent, respectively. Indianized kingdoms in the Indonesian archipelago likely played a major role in dispersing Western Eurasian lineages, as these kingdoms overlap geographically with the current distribution of individuals carrying Western Eurasian genetic markers. Our data highlight the important role of these Western Eurasian migrants in contributing to the complexity of genetic diversity across the Indonesian archipelago today.

Published
2016
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37. Towards a Chronology of Borneo's Pottery: New Data from East Kalimantan

Author

Plutniak, Sébastien, Adhi Agus Oktaviana, Bambang Sugiyanto, Jean-Georges Ferrié, Grenet, Michel, François-Xavier Ricaut, Laboratoire Interdisciplinaire Solidarités, Sociétés, Territoires (LISST), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-École Nationale Supérieure de Formation de l'Enseignement Agricole de Toulouse-Auzeville (ENSFEA)-Centre National de la Recherche Scientifique (CNRS), Pusat Penelitian dan Pengembangan Arkeologi Nasional (Arkenas), Balai Arkeologi, Banjarmasin, De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Economies, sociétés et environnements préhistoriques (ESEP), Centre National de la Recherche Scientifique (CNRS)-Université de Provence - Aix-Marseille 1-Université Joseph Fourier - Grenoble 1 (UJF), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-École Nationale Supérieure de Formation de l'Enseignement Agricole de Toulouse-Auzeville (ENSFEA)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Université de Provence - Aix-Marseille 1-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Archaeology, Pottery, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Indonesia, Kalimantan, pottery vessels, earthenwares, ComputingMilieux_MISCELLANEOUS, Austronesian studies
Abstract

Poster presented to the “Movement of goods and people around the South China Sea in East Indonesia from the Late Neolithic to the Metal Age” session of the 8th World Archaeological Congress, 28-08-2016/02-09-2016,Kyoto, Japan.

Published
2016
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38. Contrasting Linguistic and Genetic Origins of the Asian Source Populations of Malagasy

Author

Murray P. Cox, Pradiptajati Kusuma, Denis Pierron, Nicolas Brucato, Harilanto Razafindrazaka, François-Xavier Ricaut, Herawati Sudoyo, Thierry Letellier, Alexander Adelaar, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Human Genetics, Aix Marseille Université (AMU), Physiopathologie mitochondriale, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Genotyping Techniques, Range (biology), Human Migration, Remote Oceania, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Ethnic group, 030105 genetics & heredity, Southeast asian, Article, 03 medical and health sciences, Asian People, parasitic diseases, Ethnicity, Madagascar, Humans, East coast, Multidisciplinary, Human migration, business.industry, Ecology, Genetic data, Linguistics, 030104 developmental biology, Geography, business, Tropical Asia
Abstract

The Austronesian expansion, one of the last major human migrations, influenced regions as distant as tropical Asia, Remote Oceania and Madagascar, off the east coast of Africa. The identity of the Asian groups that settled Madagascar is particularly mysterious. While language connects Madagascar to the Ma’anyan of southern Borneo, haploid genetic data are more ambiguous. Here, we screened genome-wide diversity in 211 individuals from the Ma’anyan and surrounding groups in southern Borneo. Surprisingly, the Ma’anyan are characterized by a distinct, high frequency genomic component that is not found in Malagasy. This novel genetic layer occurs at low levels across Island Southeast Asia and hints at a more complex model for the Austronesian expansion in this region. In contrast, Malagasy show genomic links to a range of Island Southeast Asian groups, particularly from southern Borneo, but do not have a clear genetic connection with the Ma’anyan despite the obvious linguistic association.

Published
2016
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39. New insights on the late Pleistocene-Holocene lithic industry in East Kalimantan (Borneo) ; contribution of three rock shelter sites in the karstic area of the Mangkalihat Peninsula

Author

Ruly Fauzy, Jean-Michel Chazine, Josette Sarel, Bambang Sugiyanto, François-Xavier Ricaut, Michel Grenet, Adhi Agus Oktaviana, Travaux et recherches archéologiques sur les cultures, les espaces et les sociétés (TRACES), Ministère de la Culture et de la Communication (MCC)-École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche et de Documentation sur l'Océanie (CREDO), École des hautes études en sciences sociales (EHESS)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut national de recherches archéologiques préventives (Inrap), Pusat Penelitian Arkeologi Nasional, Balai Arkeologi, Banjarmasin, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Economies, sociétés et environnements préhistoriques (ESEP), Université Joseph Fourier - Grenoble 1 (UJF)-Université de Provence - Aix-Marseille 1-Centre National de la Recherche Scientifique (CNRS), Human Genetics, Centre National de la Recherche Scientifique (CNRS), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Pusat Penelitian dan Pengembangan Arkeologi Nasional (Arkenas), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS)

Subjects
010506 paleontology, Knapping technics, Pleistocene, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, 01 natural sciences, Lithic technology, Peninsula, Borneo, 0601 history and archaeology, Sequence stratigraphy, Holocene, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Earth-Surface Processes, geography, Island SEA, 060101 anthropology, geography.geographical_feature_category, Kalimantan, Excavation, 06 humanities and the arts, 15. Life on land, Karst, Archaeology, Indonesia, Geology, Rock shelter
Abstract

This paper aims to present some aspects of the Late Pleistocene–Holocene lithic industry in the inland East Kalimantan region by studying the assemblages found in three rock shelter sites in the karstic area of the Mangkalihat peninsula. This study analyzes these assemblages in their regional techno-complex taking into consideration the environmental components. It focuses on certain aspects of stone flaking technology and the trends in the reduction sequences of the assemblages. Our results shows that the reduction sequences, flaking technology and the typology of the blanks and tools, persisted across the Pleistocene/Holocene boundary, as revealed in Liang Abu where the lithic artifacts were found throughout the stratigraphic sequence (over at least 20,000 years). Other excavations in Liang Jon and Liang Pemalawan have confirmed this continuity until the historical eras. In addition, this research emphasizes the potential influence of the environmental and climatic stability (persistence of the rain forest) during at least the last 40,000 years in this region, as well as the inland geographical location, on the continuity of the local stone flaking technology.

Published
2016
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40. Ancient Solomon Islands mtDNA: assessing Holocene settlement and the impact of European contact

Author

Murray P. Cox, Marta Mirazon-Lahr, Tim Thomas, Maggie Bellatti, François-Xavier Ricaut, Robert Foley, Maru Mormina, Human Genetics, Centre National de la Recherche Scientifique (CNRS), Leverhulme Centre for Human Evolutionary Studies University of Cambridge, and University of Cambridge [UK] (CAM)

Subjects
Archeology, education.field_of_study, geography, geography.geographical_feature_category, Remote Oceania, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Population, Biology, Southeast asian, Haplogroup, Genealogy, Ancient DNA, Archipelago, Ethnology, education, Near Oceania, ComputingMilieux_MISCELLANEOUS, Solomon Islander
Abstract

Archaeologists, linguists and geneticists generally agree that Near Oceania was subject to two major pulses of human dispersal: a Pleistocene occupation around 40,000 BP and a Late-Holocene migration at 3500 BP commonly associated with the Austronesian expansion out of Taiwan. The latter led to the development of the Lapita cultural complex in the Bismarck Archipelago which resulted in the settlement of Remote Oceania and there are a variety of competing models (express train, slow boat, entangled bank, etc.) used to explain this. Recent genetic studies have focused on this issue, but none of them have taken into consideration the bias possibly introduced by 19th-century historically reported population decline caused by European contact. In this paper we present a case study to test the effect of 19th–20th century colonial impact on the mitochondrial DNA diversity of Solomon Islanders and to investigate the complex stratigraphy of settlement in this archipelago during and after the Lapita period. We extracted DNA from hairs and teeth belonging to 21 individuals collected by the Somerville expedition during the late 19th-century, and typed them for mitochondrial DNA (mtDNA) hypervariable region I (HVS-I) and the intergenic COII/tRNALys 9-base pair deletion (9 bp-del). Comparison of these genetic data with those available from the modern Solomon Islanders and Southeast Asian and Oceanic populations conflicts with the hypothesis of drastic changes in Solomon maternal genepool diversity, indicating that the last century putative bottleneck is not detectable through our genetic data. In addition, the ancient and modern Solomon haplogroup distribution (e.g. M27 haplogroup) suggests, in agreement with some archaeological and linguistic models, that Early Lapita populations expanding out of the Bismarck Archipelago had little or no contact with indigenous non-Austronesian populations in Bougainville and the Solomon Islands. This finding indicates smaller scale analyses reveal a more complex reality of genetic admixture in some parts of Oceania than is often assumed in current debates.

Published
2010
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41. A recent bottleneck of Y chromosome diversity coincides with a global change in culture

Author

Sardana A. Fedorova, Ene Metspalu, Anne-Mai Ilumäe, Siiri Rootsi, Lisenka E.L.M. Vissers, François-Xavier Ricaut, Tatiana M. Karafet, David M. Lambert, Richard Villems, Elza Khusnutdinova, Denis Pierron, Daria V. Lichman, Pradiptajati Kusuma, Shahlo Turdikulova, Alena Kushniarevich, Boris Malyarchuk, Anders Eriksson, Bayazit Yunusbayev, Olga Utevska, Ludmila P. Osipova, Christina A. Eichstaedt, Monika Karmin, S. S. Litvinov, Knut Johnsen, Joseph Wee Tien Seng, Reedik Mägi, Alexia Cardona, Oleg Balanovsky, Dragan Primorac, Dilbar Dalimova, Pagbajabyn Nymadawa, Krishna R. Veeramah, Andrea Manica, Rita Khusainova, I. M. Khidiyatova, Michael F. Hammer, Kuvat T. Momynaliev, Sarah A. Tishkoff, Toomas Kivisild, Michael C. Westaway, Zhaxylyk Sabitov, Tarmo Puurand, S M Abdullah, Lejla Kovacevic, Levon Yepiskoposyan, Chris Tyler-Smith, Mario Mitt, Rane Willerslev, Mark G. Thomas, Qasim Ayub, Gazi Nurun Nahar Sultana, Jainagul Isakova, Christian Gilissen, Kristiina Tambets, Craig Muller, Gyaneshwer Chaubey, Thorfinn Sand Korneliussen, Miroslava Derenko, Farida Akhatova, V. L. Akhmetova, Joris A. Veltman, Ulvi Gerst Talas, Hovhannes Sahakyan, Maru Mormina, L. A. Atramentova, Andrea Bamberg Migliano, Vedrana Škaro, Georgi Hudjashov, N. N. Trofimova, Rasmus Nielsen, Mari Järve, Luca Pagani, George Andriadze, Evelin Mihailov, Lauri Saag, Michael DeGiorgio, Mikk Eelmets, Harilanto Razafindrazaka, Irina Evseeva, Murray P. Cox, Elvira Pocheshkhova, Nikolay A. Barashkov, Eva Liis Loogväli, Neil Bradman, Joseph Lachance, Grigor Zoraqi, Eske Willerslev, Melissa A. Wilson Sayres, Elena Balanovska, Fernando L. Mendez, Peter A. Underhill, Doron M. Behar, Mário Vicente, Maido Remm, Mait Metspalu, Yali Xue, Florian Clemente, Andres Metspalu, Zuzana Faltyskova, Damir Marjanović, Dept Evolutionary Biol, University of Tartu, Leverhulme Centre for Human Evolutionary Studies University of Cambridge, University of Cambridge [UK] (CAM), Human Evolution, The Wellcome Trust Sanger Institute [Cambridge], University of Pennsylvania, Human Genetics, Centre National de la Recherche Scientifique (CNRS), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Environmental Futures Research Institute, Griffith University [Brisbane], Institute of Molecular Biology and Medicine, International Network for the Sequencing of resPIRratory vIrusEs (INSPIRE), Department of Oncology, Radboud University Medical Center [Nijmegen], The Estonian Genome Center, Swedish Institute of Space Physics [Uppsala] (IRF), Marketing Department, Institute of Cytology and Genetics, Russian Academy of Sciences [Moscow] (RAS), Russian Academy of Medical Sciences, Institute of Biochemistry and Genetics [Bashkortostan Republic, Russia], Russian Academy of Sciences / Ufa Scientific Centre [Bashkortostan Republic, Russia]], Wellcome Trust Genome Campus, Department of Psychiatry and Behavioral Sciences [Stanford], Stanford Medicine, Stanford University-Stanford University, Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Dept Integrat Biol, UMR 6578 : Anthropologie Bio-Culturelle (UAABC), Université de la Méditerranée - Aix-Marseille 2-Centre National de la Recherche Scientifique (CNRS), Université Tartu, University of Pennsylvania [Philadelphia], Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, and University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)

Subjects
Male, Most recent common ancestor, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, bottleneck, Y chromosome diversity, global change in culture, Human genetic variation, Biology, DNA, Mitochondrial, Haplogroup, Bottleneck, Evolution, Molecular, 03 medical and health sciences, Genetics, Humans, education, Phylogeny, Genetics (clinical), 030304 developmental biology, 0303 health sciences, education.field_of_study, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Chromosomes, Human, Y, Base Sequence, Models, Genetic, Research, Racial Groups, 030305 genetics & heredity, Haplotype, Genetic Variation, Sequence Analysis, DNA, Genetics, Population, Ancient DNA, Haplotypes, Evolutionary biology, Biological dispersal
Abstract

It is commonly thought that human genetic diversity in non-African populations was primarily shaped by a recent out-of-Africa dispersal. Here we present a large geographical Y chromosome study using 459 high coverage sequences, including 302 newly reported here. We date the Y chromosomal Most Recent Common Ancestor (MRCA) in Africa at 254 (95% CI 192- 307) kya and differentiation of African and non-African lineages 52-121 kya. The age estimates for major non-African founder haplogroups cluster closely in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. We find that the highest basal Y chromosome diversity outside Africa has been preserved in South and Southeast Asians while extant Y chromosome diversity in Europe and the Near East stems from a small number of mid-Holocene founders. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck, followed by a fast recovery in Old World populations dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

Published
2015
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42. Ancient DNA analysis of human neolithic remains found in northeastern Siberia

Author

Bertrand Ludes, François-Xavier Ricaut, Eric Crubézy, Christine Keyser-Tracqui, and A. Fedoseeva

Subjects
0303 health sciences, education.field_of_study, Mitochondrial DNA, Sequence analysis, Population, Haplotype, Biology, Archaeology, humanities, Haplogroup, Hypervariable region, 03 medical and health sciences, 0302 clinical medicine, Ancient DNA, Evolutionary biology, Anthropology, Microsatellite, 030216 legal & forensic medicine, Anatomy, education, geographic locations, 030304 developmental biology
Abstract

We successfully extracted DNA from a bone sample of a Neolithic skeleton (dated 3,600 +/- 60 years BP) excavated in northeastern Yakutia (east Siberia). Ancient DNA was analyzed by autosomal STRs (short tandem repeats) and by sequencing of the hypervariable region I (HV1) of the mitochondrial DNA (mtDNA) control region. The STR profile, the mitochondrial haplotype, and the haplogroup determined were compared with those of modern Eurasian and Native American populations. The results showed the affinity of this ancient skeleton with both east Siberian/Asian and Native American populations.

Published
2005
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43. Genetic analysis and ethnic affinities from two Scytho-Siberian skeletons

Author

Eric Crubézy, Bertrand Ludes, François-Xavier Ricaut, Christine Keyser-Tracqui, and Laurence Cammaert

Subjects
Genetics, 0303 health sciences, education.field_of_study, Mitochondrial DNA, 060101 anthropology, Human Y-chromosome DNA haplogroup, Population, 06 humanities and the arts, Biology, Genetic analysis, humanities, Haplogroup, Hypervariable region, 03 medical and health sciences, Ancient DNA, Anthropology, Microsatellite, 0601 history and archaeology, Anatomy, education, 030304 developmental biology
Abstract

We extracted DNA from two skeletons belonging to the Sytho-Siberian population, which were excavated from the Sebystei site (dating back 2,500 years) in the Altai Republic (Central Asia). Ancient DNA was analyzed by autosomal short tandem repeats (STRs) and by the sequencing of the hypervariable region 1 (HV1) of the mitochondrial DNA (mtDNA) control region. The results showed that these two skeletons were not close relatives. Moreover, their haplogroups were characteristic of Asian populations. Comparison with the haplogroup of 3,523 Asian and American individuals linked one skeleton with a putative ancestral paleo-Asiatic population and the other with Chinese populations. It appears that the genetic study of ancient populations of Central Asia brings important elements to the understanding of human population movements in Asia.

Published
2003
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44. Genome-wide evidence of Austronesian-Bantu admixture and cultural reversion in a hunter-gatherer group of Madagascar

Author

Roger M. Blench, Tiago Antao, Harilanto Razafindrazaka, Luca Pagani, Chantal Radimilahy, Toomas Kivisild, Thierry Letellier, François-Xavier Ricaut, Clement Sambo, Jean-Aimé Rakotoarisoa, Denis Pierron, Mélanie Capredon, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Human Genetics, Centre National de la Recherche Scientifique (CNRS), Centre de Recherches Littéraires et Historiques de l'Océan Indien (CRLHOI), Contacts de Cultures, de Littératures et de Civilisations (CCLC), Université de La Réunion (UR)-Université de La Réunion (UR), Université d'Antananarivo, Mallam Dendo Consultancy, Physiopathologie mitochondriale, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Santé et de la Recherche Médicale (INSERM), Leverhulme Centre for Human Evolutionary Studies University of Cambridge, University of Cambridge [UK] (CAM), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, Genetic genealogy, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Culture, Ethnic group, Black People, Social Sciences, Context (language use), Bantu languages, Biology, Southeast asian, migration, Polymorphism, Single Nucleotide, settlement, 03 medical and health sciences, 0302 clinical medicine, Asian People, Population Groups, Ethnicity, Madagascar, Humans, education, Hunter-gatherer, 030304 developmental biology, Oligonucleotide Array Sequence Analysis, 0303 health sciences, education.field_of_study, Multidisciplinary, Geography, Homozygote, Linguistics, Austronesian languages, DNA, 15. Life on land, Genealogy, Genetics, Population, Haplotypes, 030217 neurology & neurosurgery, Migration, Settlement, Algorithms
Abstract

International audience; Linguistic and cultural evidence suggest that Madagascar was the final point of two major dispersals of Austronesian- and Bantu-speaking populations. Today, the Mikea are described as the last-known Malagasy population reported to be still practicing a hunter-gatherer lifestyle. It is unclear, however, whether the Mikea descend from a remnant population that existed before the arrival of Austronesian and Bantu agriculturalists or whether it is only their lifestyle that separates them from the other contemporary populations of South Madagascar. To address these questions we have performed a genome-wide analysis of >700,000 SNP markers on 21 Mikea, 24 Vezo, and 24 Temoro individuals, together with 50 individuals from Bajo and Lebbo populations from Indonesia. Our analyses of these data in the context of data available from other Southeast Asian and African populations reveal that all three Malagasy populations are derived from the same admixture event involving Austronesian and Bantu sources. In contrast to the fact that most of the vocabulary of the Malagasy speakers is derived from the Barito group of the Austronesian language family, we observe that only one-third of their genetic ancestry is related to the populations of the Java-Kalimantan-Sulawesi area. Because no additional ancestry components distinctive for the Mikea were found, it is likely that they have adopted their hunter-gatherer way of life through cultural reversion, and selection signals suggest a genetic adaptation to their new lifestyle.

Published
2014
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45. Tracing Arab-Islamic inheritance in Madagascar: study of the Y-chromosome and mitochondrial DNA in the Antemoro

Author

Harilanto Razafindrazaka, Laure Tonasso, Mamisoa Adelta Ratolojanahary, Louis-Paul Randriamarolaza, Mélanie Capredon, Nicolas Brucato, Jean-Michel Dugoujon, Bernard Champion, François-Xavier Ricaut, Valérie Choesmel-Cadamuro, Andriamihaja Bakomalala Rakotondrabe, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre de Recherches Littéraires et Historiques de l'Océan Indien (CRLHOI), Contacts de Cultures, de Littératures et de Civilisations (CCLC), Université de La Réunion (UR)-Université de La Réunion (UR), Human Genetics, Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Université d'Antananarivo, Déplacements, Identités, Regards, Écritures (DIRE), Université de La Réunion (UR), Laboratoire d'Anthropobiologie (LA), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3)

Subjects
Male, Asia, Population genetics, Genetic genealogy, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Inheritance Patterns, Ethnic group, lcsh:Medicine, Human genetic variation, Biology, Southeast asian, DNA, Mitochondrial, Islam, Haplogroup, Comoros, 03 medical and health sciences, Databases, Genetic, Ethnicity, Madagascar, Humans, lcsh:Science, 030304 developmental biology, Recombination, Genetic, Genetics, Principal Component Analysis, 0303 health sciences, Chromosomes, Human, Y, Multidisciplinary, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Geography, lcsh:R, 030305 genetics & heredity, Haplotype, Arabs, Phylogeography, Haplotypes, Evolutionary biology, Africa, Haplogroups, Female, lcsh:Q, Gene pool, Microsatellite Repeats, Research Article
Abstract

International audience; Madagascar is located at the crossroads of the Asian and African worlds and is therefore of particular interest for studies on human population migration. Within the large human diversity of the Great Island, we focused our study on a particular ethnic group, the Antemoro. Their culture presents an important Arab-Islamic influence, but the question of an Arab biological inheritance remains unresolved. We analyzed paternal (n=129) and maternal (n=135) lineages of this ethnic group. Although the majority of Antemoro genetic ancestry comes from sub-Saharan African and Southeast Asian gene pools, we observed in their paternal lineages two specific haplogroups (J1 and T1) linked to Middle Eastern origins. This inheritance was restricted to some Antemoro sub-groups. Statistical analyses tended to confirm significant Middle Eastern genetic contribution. This study gives a new perspective to the large human genetic diversity in Madagascar.

Published
2013
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46. Does the Tat polymorphism originate in northern Mongolia?

Author

B. Ludes, Christine Keyser-Tracqui, E. Petkovski, François-Xavier Ricaut, Eric Crubézy, and Prisca Blandin

Subjects
Genetics, Ancient DNA, General Medicine, Biology
Abstract

It has been suggested that the Y-chromosomal T→C transition arose in Mongolia ~2400–4000 years ago. To test this hypothesis, we screened 2300-year-old Mongolian male specimens and ancient Yakut male specimens for this Y-chromosomal marker. Our results demonstrate that the mutation was present in Asia 2300 years ago.

Published
2004
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47. A Time Series of Prehistoric Mitochondrial DNA Reveals Western European Genetic Diversity Was Largely Established by the Bronze Age

Author

Eric Crubézy, Jean Guilaine, Bertrand Ludes, Marie Lacan, Murray P. Cox, Christine Keyser, Francis Duranthon, François-Xavier Ricaut, Human Genetics, Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Anthropobiologie (LA), École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Muséum d'Histoire Naturelle de Toulouse, Institut de Médecine Légale - IML (Paris, France), Collège de France (CdF (institution)), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
010506 paleontology, Genetic diversity, 060101 anthropology, Haplogroup H, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, 06 humanities and the arts, General Medicine, Human genetic variation, Chalcolithic, 01 natural sciences, Archaeology, Haplogroup, Prehistory, Geography, Evolutionary biology, Bronze Age, 0601 history and archaeology, Mesolithic, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences
Abstract

A major unanswered question concerns the roles of continuity versus change in prehistoric Europe. For the first time, genetic samples of reasonable size taken at multiple time points are revealing piecemeal snapshots of European prehistory at different dates and places across the continent. Here, we pull these disparate datasets together to illustrate how human genetic variation has changed spatially and temporally in Europe from the Mesolithic through to the present day. Mitochondrial DNA (mtDNA) haplogroups were determined for 532 European individuals from four major eras: the Mesolithic, Neolithic, Chalcolithic (late Neolithic/early Bronze Age transition) and Modern periods. The Mesolithic was characterized by low mtDNA diversity. These initial European settler haplogroups declined rapidly in the Neolithic, as farmers from the east introduced a new suite of mtDNA lineages into Western Europe. For the first time, we show that the Chalcolithic was also a time of substantial genetic change in Europe. However, rather than the arrival of new mtDNA lineages, this period was characterized by major fluctuations in the frequencies of existing haplogroups. Besides the expansion of haplogroup H, there were few major changes in mtDNA diversity from the Chalcolithic to modern times, thus suggesting that the basic profile of mod- ern western European mtDNA diversity was largely established by the Bronze Age.

Published
2012
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48. Mitochondrial analysis of a Byzantine population reveals the differential impact of multiple historical events in South Anatolia

Author

Nicolas Brucato, Ronny Decorte, François-Xavier Ricaut, Claudio Ottoni, Nancy Vanderheyden, Marc Waelkens, Human Genetics, Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
History, Turkey, Molecular Sequence Data, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, population, MESH: Genetics, Population, Ancient history, Settore BIO/08, MESH: Genes, Mitochondrial, DNA, Mitochondrial, Article, 03 medical and health sciences, Peninsula, Genetics, MESH: Turkey, Humans, Anatolia, Byzantine, genes, education, ancient DNA, Genetics (clinical), 030304 developmental biology, Differential impact, 0303 health sciences, geography, education.field_of_study, geography.geographical_feature_category, MESH: Humans, MESH: Molecular Sequence Data, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], mtDNA, Human evolutionary genetics, 030305 genetics & heredity, MESH: DNA, Mitochondrial, DNA, mitochondrial, Genes, Mitochondrial, Genetics, Population, Ancient DNA, Period (geology), byzantine, MtDNA, DNA, mitochondrial, humans, molecular sequence data, genes, mitochondrial, genetics, population, Byzantine architecture, Mountain range
Abstract

International audience; The archaeological site of Sagalassos is located in Southwest Turkey, in the western part of the Taurus mountain range. Human occupation of its territory is attested from the late 12th millennium BP up to the 13th century AD. By analysing the mtDNA variation in 85 skeletons from Sagalassos dated to the 11th-13th century AD, this study attempts to reconstruct the genetic signature potentially left in this region of Anatolia by the many civilizations, which succeeded one another over the centuries until the mid-Byzantine period (13th century BC). Authentic ancient DNA data were determined from the control region and some SNPs in the coding region of the mtDNA in 53 individuals. Comparative analyses with up to 157 modern populations allowed us to reconstruct the origin of the mid-Byzantine people still dwelling in dispersed hamlets in Sagalassos, and to detect the maternal contribution of their potential ancestors. By integrating the genetic data with historical and archaeological information, we were able to attest in Sagalassos a significant maternal genetic signature of Balkan/Greek populations, as well as ancient Persians and populations from the Italian peninsula. Some contribution from the Levant has been also detected, whereas no contribution from Central Asian population could be ascertained.

Published
2011
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49. Cranial Discrete Traits in a Byzantine Population and Eastern Mediterranean Population Movements

Author

François-Xavier Ricaut, Marc Waelkens, and Centre National de la Recherche Scientifique (CNRS)

Subjects
Gene Flow, Male, Turkey, Cephalometry, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Context (language use), Gene flow, 03 medical and health sciences, Bronze Age, Genetics, Cluster Analysis, Humans, 0601 history and archaeology, Multidimensional scaling, education, Molecular Biology, Africa South of the Sahara, Genetics (clinical), Ecology, Evolution, Behavior and Systematics, Holocene, 030304 developmental biology, 0303 health sciences, education.field_of_study, 060101 anthropology, Middle East, Mediterranean Region, Data Collection, Genetic Variation, 06 humanities and the arts, Emigration and Immigration, 15. Life on land, Archaeology, Genetics, Population, Geography, Female, Byzantium, Cartography, Byzantine architecture
Abstract

International audience; Since the beginning of the Holocene, the Anatolian region has been a crossroads for populations and civilizations from Europe, Asia, and the Near to Middle East, with increasing interactions since the Bronze Age. In this context, we examine cranial discrete traits from a Byzantine population from southwest Turkey, excavated at the archeological site of Sagalassos; the site displays human occupation since the 12th millennium B.P. To investigate the biological history of this population, we analyzed the frequency distribution of 17 cranial discrete traits from Sagalassos and 27 Eurasian and African populations. Ward's clustering procedure and multidimensional scaling analyses of the standardized mean measure of divergence (MMD(st)), based on trait frequencies, were used to represent the biological affinity between populations. Our results, considered within a large interpretive framework that takes into account the idea that populations are dynamic entities affected by various influences through time and space, revealed different strata of the Sagalassos biological history. Indeed, beyond an expected biological affinity of the Sagalassos population with eastern Mediterranean populations, we also detected affinities with sub-Saharan and northern and central European populations. We hypothesize that these affinity patterns in the Sagalassos biological package are the traces of the major migratory events that affected southwest Anatolia over the last millennia, as suggested from biological, archeological, and historical data.

Published
2008
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50. Mitochondrial DNA Variation in Karkar Islanders

Author

Matthew Leavesley, J. Staughton, Marta Mirazón Lahr, François-Xavier Ricaut, Robert Foley, C. Arganini, Maggie Bellatti, Tim Thomas, Department of Anthropology [University of Cambridge], University of Cambridge [UK] (CAM), Department of Archaeology and Anthropology, and Centre National de la Recherche Scientifique (CNRS)

Subjects
Mitochondrial DNA, education.field_of_study, Base Sequence, Geography, Population, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Genetic Variation, Population genetics, Biology, DNA, Mitochondrial, Haplogroup, Papua New Guinea, Phylogeography, Haplotypes, Evolutionary biology, Genetic structure, Genetics, Humans, Papuan languages, education, Phylogeny, Genetics (clinical), Human mitochondrial DNA haplogroup
Abstract

International audience; We analyzed 375 base pairs (bp) of the first hypervariable region (HVS-I) of the mitochondrial DNA (mtDNA) control region and intergenic COII/tRNALys 9-bp deletion from 47 Karkar Islanders (north coast of Papua New Guinea) belonging to the Waskia Papuan language group. To address questions concerning the origin and evolution of this population we compared the Karkar mtDNA haplotypes and haplogroups to those of neighbouring East Asians and Oceanic populations. The results of the phylogeographic analysis show grouping in three different clusters of the Karkar Islander mtDNA lineages: one group of lineages derives from the first Pleistocene settlers of New Guinea-Island Melanesia, a second set derives from more recent arrivals of Austronesian speaking populations, and the third contains lineages specific to the Karkar Islanders, but still rooted to Austronesian and New Guinea-Island Melanesia populations. Our results suggest (i) the absence of a strong association between language and mtDNA variation and, (ii) reveal that the mtDNA haplogroups F1a1, M7b1 and E1a, which probably originated in Island Southeast Asia and may be considered signatures of Austronesian population movements, are preserved in the Karkar Islanders but absent in other New Guinea-Island Melanesian populations. These findings indicate that the Karkar Papuan speakers retained a certain degree of their own genetic uniqueness and a high genetic diversity. We present a hypothesis based on archaeological, linguistic and environmental datasets to argue for a succession of (partial) depopulation and repopulation and expansion events, under conditions of structured interaction, which may explain the variability expressed in the Karkar mtDNA.

Published
2008
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