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Bozlak E, Radovic L, Remer V, Rigler D, Allen L, Brem G, Stalder G, Castaneda C, Cothran G, Raudsepp T, Okuda Y, Moe KK, Moe HH, Kounnavongsa B, Keonouchanh S, Van NH, Vu VH, Shah MK, Nishibori M, Kazymbet P, Bakhtin M, Zhunushov A, Paul RC, Dashnyam B, Nozawa K, Almarzook S, Brockmann GA, Reissmann M, Antczak DF, Miller DC, Sadeghi R, von Butler-Wemken I, Kostaras N, Han H, Manglai D, Abdurasulov A, Sukhbaatar B, Ropka-Molik K, Stefaniuk-Szmukier M, Lopes MS, da Câmara Machado A, Kalashnikov VV, Kalinkova L, Zaitev AM, Novoa-Bravo M, Lindgren G, Brooks S, Rosa LP, Orlando L, Juras R, Kunieda T, Wallner B. Refining the evolutionary tree of the horse Y chromosome. Sci Rep 2023; 13:8954. [PMID: 37268661 DOI: 10.1038/s41598-023-35539-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/19/2023] [Indexed: 06/04/2023] Open
Abstract
The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the world. We analyze target enriched sequencing data of 5 Mb of the Y chromosome from 76 domestic males, together with 89 whole genome sequenced domestic males and five Przewalski's horses from previous studies. The resulting phylogeny comprises 153 HTs defined by 2966 variants and offers unprecedented resolution into the history of horse paternal lineages. It reveals the presence of a remarkable number of previously unknown haplogroups in Mongolian horses and insular populations. Phylogenetic placement of HTs retrieved from 163 archaeological specimens further indicates that most of the present-day Y-chromosomal variation evolved after the domestication process that started around 4200 years ago in the Western Eurasian steppes. Our comprehensive phylogeny significantly reduces ascertainment bias and constitutes a robust evolutionary framework for analyzing horse population dynamics and diversity.
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Affiliation(s)
- Elif Bozlak
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
- Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Lara Radovic
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
- Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Viktoria Remer
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Doris Rigler
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Lucy Allen
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Gabrielle Stalder
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, 1210, Vienna, Austria
| | - Caitlin Castaneda
- School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Gus Cothran
- School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Terje Raudsepp
- School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Yu Okuda
- Museum of Dinosaur Research, Okayama University of Science, Okayama, Japan
| | - Kyaw Kyaw Moe
- Department of Pathology and Microbiology, University of Veterinary Science, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Hla Hla Moe
- Department of Genetics and Animal Breeding, University of Veterinary Science, Yezin, Nay Pyi Taw, 05282, Myanmar
| | - Bounthavone Kounnavongsa
- National Agriculture and Forestry Research Institute (Lao) Resources, Livestock Research Center, Xaythany District, Vientiane, Laos
| | - Soukanh Keonouchanh
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Nguyen Huu Van
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Van Hai Vu
- Faculty of Animal Science and Veterinary Medicine, University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Manoj Kumar Shah
- Faculty of Animal Science, Veterinary Science and Fisheries, Agriculture and Forestry University, Rampur, 44209, Nepal
| | - Masahide Nishibori
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, 739-8528, Japan
| | - Polat Kazymbet
- Radiobiological Research Institute, JSC Astana Medical University, Astana, 010000, Republic of Kazakhstan
| | - Meirat Bakhtin
- Institute of Biotechnology, National Academy of Sciences of the Kyrgyz Republic, Bishkek, 720071, Kyrgyz Republic
| | - Asankadyr Zhunushov
- Institute of Biotechnology, National Academy of Sciences of the Kyrgyz Republic, Bishkek, 720071, Kyrgyz Republic
| | - Ripon Chandra Paul
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
- Faculty of Animal Science and Veterinary Medicine, Patuakhali Science and Technology University, Barishal, Bangladesh
| | - Bumbein Dashnyam
- Institute of Biological Sciences, Mongolian Academy of Sciences, Ulaan Baator, Mongolia
| | - Ken Nozawa
- Primate Research Institute, Kyoto University, Aichi, Japan
| | - Saria Almarzook
- Albrecht Daniel Thaer-Institut, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Gudrun A Brockmann
- Albrecht Daniel Thaer-Institut, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Monika Reissmann
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Donald C Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Raheleh Sadeghi
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Ines von Butler-Wemken
- Barb Horse Breeding Organisation VFZB E. V., Verein der Freunde und Züchter Des Berberpferdes E.V., Kirchgasse 11, 67718, Schmalenberg, Germany
| | | | - Haige Han
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Dugarjaviin Manglai
- Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Abdugani Abdurasulov
- Department of Agriculture, Faculty of Natural Sciences and Geography, Osh State University, 723500, Osh, Kyrgyzstan
| | - Boldbaatar Sukhbaatar
- Sector of Surveillance and Diagnosis of Infectious Diseases, State Central Veterinary Laboratory, Ulaanbaatar, 17024, Mongolia
| | - Katarzyna Ropka-Molik
- National Research Institute of Animal Production, Animal Molecular Biology, 31-047, Cracow, Poland
| | | | - Maria Susana Lopes
- Biotechnology Centre of Azores, University of Azores, 9700-042, Angra do Heroísmo, Portugal
| | | | | | - Liliya Kalinkova
- All-Russian Research Institute for Horse Breeding, Ryazan, 391105, Russia
| | - Alexander M Zaitev
- All-Russian Research Institute for Horse Breeding, Ryazan, 391105, Russia
| | - Miguel Novoa-Bravo
- Genética Animal de Colombia SAS., Av. Calle 26 #69-76, 111071, Bogotá, Colombia
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, 3001, Leuven, Belgium
| | - Samantha Brooks
- Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Laura Patterson Rosa
- Department of Agriculture and Industry, Sul Ross State University, Alpine, TX, 79832, USA
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Rytis Juras
- School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA.
| | - Tetsuo Kunieda
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
- Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Japan.
| | - Barbara Wallner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210, Vienna, Austria.
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Swart Y, van Eeden G, Uren C, van der Spuy G, Tromp G, Möller M. GWAS in the southern African context. PLoS One 2022; 17:e0264657. [PMID: 36170230 PMCID: PMC9518849 DOI: 10.1371/journal.pone.0264657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 08/06/2022] [Indexed: 11/18/2022] Open
Abstract
Researchers would generally adjust for the possible confounding effect of population structure by considering global ancestry proportions or top principle components. Alternatively, researchers would conduct admixture mapping to increase the power to detect variants with an ancestry effect. This is sufficient in simple admixture scenarios, however, populations from southern Africa can be complex multi-way admixed populations. Duan et al. (2018) first described local ancestry adjusted allelic (LAAA) analysis as a robust method for discovering association signals, while producing minimal false positive hits. Their simulation study, however, was limited to a two-way admixed population. Realizing that their findings might not translate to other admixture scenarios, we simulated a three- and five-way admixed population to compare the LAAA model to other models commonly used in genome-wide association studies (GWAS). We found that, given our admixture scenarios, the LAAA model identifies the most causal variants in most of the phenotypes we tested across both the three-way and five-way admixed populations. The LAAA model also produced a high number of false positive hits which was potentially caused by the ancestry effect size that we assumed. Considering the extent to which the various models tested differed in their results and considering that the source of a given association is unknown, we recommend that researchers use multiple GWAS models when analysing populations with complex ancestry.
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Affiliation(s)
- Yolandi Swart
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerald van Eeden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
| | - Gian van der Spuy
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- SAMRC-SHIP South African Tuberculosis Bioinformatics Initiative (SATBBI), Center for Bioinformatics and Computational Biology, Cape Town, South Africa
| | - Gerard Tromp
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
- SAMRC-SHIP South African Tuberculosis Bioinformatics Initiative (SATBBI), Center for Bioinformatics and Computational Biology, Cape Town, South Africa
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
- * E-mail:
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van Eeden G, Uren C, Pless E, Mastoras M, van der Spuy GD, Tromp G, Henn BM, Möller M. The recombination landscape of the Khoe-San likely represents the upper limits of recombination divergence in humans. Genome Biol 2022; 23:172. [PMID: 35945619 PMCID: PMC9361568 DOI: 10.1186/s13059-022-02744-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 08/01/2022] [Indexed: 11/10/2022] Open
Abstract
Background Recombination maps are important resources for epidemiological and evolutionary analyses; however, there are currently no recombination maps representing any African population outside of those with West African ancestry. We infer the demographic history for the Nama, an indigenous Khoe-San population of southern Africa, and derive a novel, population-specific recombination map from the whole genome sequencing of 54 Nama individuals. We hypothesise that there are no publicly available recombination maps representative of the Nama, considering the deep population divergence and subsequent isolation of the Khoe-San from other African groups. Results We show that the recombination landscape of the Nama does not cluster with any continental groups with publicly available representative recombination maps. Finally, we use selection scans as an example of how fine-scale differences between the Nama recombination map and the combined Phase II HapMap recombination map can impact the outcome of selection scans. Conclusions Fine-scale differences in recombination can meaningfully alter the results of a selection scan. The recombination map we infer likely represents an upper bound on the extent of divergence we expect to see for a recombination map in humans and would be of interest to any researcher that wants to test the sensitivity of population genetic or GWAS analysis to recombination map input. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02744-5.
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Affiliation(s)
- Gerald van Eeden
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Caitlin Uren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, 7602, South Africa
| | - Evlyn Pless
- Department of Anthropology, Center for Population Biology and the Genome Center, University of California (UC) Davis, Davis, CA, USA
| | - Mira Mastoras
- Department of Anthropology, Center for Population Biology and the Genome Center, University of California (UC) Davis, Davis, CA, USA
| | - Gian D van der Spuy
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, 7602, South Africa.,SAMRC-SHIP South African Tuberculosis Bioinformatics Initiative (SATBBI), Center for Bioinformatics and Computational Biology, Cape Town, South Africa
| | - Gerard Tromp
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, 7602, South Africa.,SAMRC-SHIP South African Tuberculosis Bioinformatics Initiative (SATBBI), Center for Bioinformatics and Computational Biology, Cape Town, South Africa
| | - Brenna M Henn
- Department of Anthropology, Center for Population Biology and the Genome Center, University of California (UC) Davis, Davis, CA, USA
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa. .,Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, 7602, South Africa.
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4
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Choudhury A, Sengupta D, Ramsay M, Schlebusch C. Bantu-speaker migration and admixture in southern Africa. Hum Mol Genet 2021; 30:R56-R63. [PMID: 33367711 PMCID: PMC8117461 DOI: 10.1093/hmg/ddaa274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 01/16/2023] Open
Abstract
The presence of Early and Middle Stone Age human remains and associated archeological artifacts from various sites scattered across southern Africa, suggests this geographic region to be one of the first abodes of anatomically modern humans. Although the presence of hunter-gatherer cultures in this region dates back to deep times, the peopling of southern Africa has largely been reshaped by three major sets of migrations over the last 2000 years. These migrations have led to a confluence of four distinct ancestries (San hunter-gatherer, East-African pastoralist, Bantu-speaker farmer and Eurasian) in populations from this region. In this review, we have summarized the recent insights into the refinement of timelines and routes of the migration of Bantu-speaking populations to southern Africa and their admixture with resident southern African Khoe-San populations. We highlight two recent studies providing evidence for the emergence of fine-scale population structure within some South-Eastern Bantu-speaker groups. We also accentuate whole genome sequencing studies (current and ancient) that have both enhanced our understanding of the peopling of southern Africa and demonstrated a huge potential for novel variant discovery in populations from this region. Finally, we identify some of the major gaps and inconsistencies in our understanding and emphasize the importance of more systematic studies of southern African populations from diverse ethnolinguistic groups and geographic locations.
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Affiliation(s)
- Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Michele Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Carina Schlebusch
- Palaeo-Research Institute, University of Johannesburg, Auckland Park 2006, South Africa
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala 75326, Sweden
- SciLifeLab, Uppsala 75237, Sweden
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5
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Petr M, Hajdinjak M, Fu Q, Essel E, Rougier H, Crevecoeur I, Semal P, Golovanova LV, Doronichev VB, Lalueza-Fox C, de la Rasilla M, Rosas A, Shunkov MV, Kozlikin MB, Derevianko AP, Vernot B, Meyer M, Kelso J. The evolutionary history of Neanderthal and Denisovan Y chromosomes. Science 2020; 369:1653-1656. [PMID: 32973032 DOI: 10.1126/science.abb6460] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/06/2020] [Indexed: 12/31/2022]
Abstract
Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.
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Affiliation(s)
- Martin Petr
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.,The Francis Crick Institute, NW1 1AT London, UK
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Elena Essel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Hélène Rougier
- Department of Anthropology, California State University, Northridge, Northridge, CA 91330-8244, USA
| | | | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | | | | | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Marco de la Rasilla
- Área de Prehistoria, Departamento de Historia, Universidad de Oviedo, 33011 Oviedo, Spain
| | - Antonio Rosas
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoli P Derevianko
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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6
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Searching for the roots of the first free African American community. Sci Rep 2020; 10:20634. [PMID: 33244039 PMCID: PMC7691995 DOI: 10.1038/s41598-020-77608-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/13/2020] [Indexed: 11/30/2022] Open
Abstract
San Basilio de Palenque is an Afro-descendant community near Cartagena, Colombia, founded in the sixteenth century. The recognition of the historical and cultural importance of Palenque has promoted several studies, namely concerning the African roots of its first inhabitants. To deepen the knowledge of the origin and diversity of the Palenque parental lineages, we analysed a sample of 81 individuals for the entire mtDNA Control Region as well as 92 individuals for 27 Y-STRs and 95 for 51 Y-SNPs. The results confirmed the strong isolation of the Palenque, with some degree of influx of Native American maternal lineages, and a European admixture exclusively mediated by men. Due to the high genetic drift observed, a pairwise FST analysis with available data on African populations proved to be inadequate for determining population affinities. In contrast, when a phylogenetic approach was used, it was possible to infer the phylogeographic origin of some lineages in Palenque. Contradicting previous studies indicating a single African origin, our results evidence parental genetic contributions from widely different African regions.
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7
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Villaescusa P, Seidel M, Nothnagel M, Pinotti T, González-Andrade F, Alvarez-Gila O, M de Pancorbo M, Roewer L. A Y-chromosomal survey of Ecuador's multi-ethnic population reveals new insights into the tri-partite population structure and supports an early Holocene age of the rare Native American founder lineage C3-MPB373. Forensic Sci Int Genet 2020; 51:102427. [PMID: 33254102 DOI: 10.1016/j.fsigen.2020.102427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/03/2020] [Accepted: 11/10/2020] [Indexed: 10/23/2022]
Abstract
Ecuador is a multiethnic and pluricultural country with a complex history defined by migration and admixture processes. The present study aims to increase our knowledge on the Ecuadorian Native Amerindian groups and the unique South American Y-chromosome haplogroup C3-MPB373 through the analysis of up to 23 Y-chromosome STRs (Y-STRs) and several Y-SNPs in a sample of 527 Ecuadorians from 7 distinct populations and geographic areas, including Kichwa and non-Kichwa Native Amerindians, Mestizos and Afro-Ecuadorians. Our results reveal the presence of C3-MPB373 both in the Amazonian lowland Kichwa with frequencies up to 28 % and, for the first time, in notable proportions in Kichwa populations from the Ecuadorian highlands. The substantially higher frequencies of C3-MPB373 in the Amazonian lowlands found in Kichwa and Waorani individuals suggest a founder effect in that area. Notably, estimates for the time to the most recent common ancestor (TMRCA) in the range of 7.2-9.0 kya point to an ancient origin of the haplogroup and suggest an early Holocene expansion of C3-MPB373 into South America. Finally, the pairwise genetic distances (RST) separate the Kichwa Salasaka from all the other Native Amerindian and Ecuadorian groups, indicating a so far hidden diversity among the Kichwa-speaking populations and suggesting a more southern origin of this population. In sum, our study provides a more in-depth knowledge of the male genetic structure of the multiethnic Ecuadorian population, as well as a valuable reference dataset for forensic use.
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Affiliation(s)
- Patricia Villaescusa
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain.
| | - Maria Seidel
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Nothnagel
- Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Cologne, Germany; University Hospital Cologne, Cologne, Germany
| | - Thomaz Pinotti
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Oscar Alvarez-Gila
- Department of Medieval, Early Modern and American History, Faculty of Letters, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Lutz Roewer
- Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany
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8
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Wu R, Peng D, Ren H, Li R, Li H, Wang N, Shen X, Huang E, Zhang Y, Sun H. Characterization of genetic polymorphisms in Nigerians residing in Guangzhou using massively parallel sequencing. Forensic Sci Int Genet 2020; 48:102323. [PMID: 32574994 DOI: 10.1016/j.fsigen.2020.102323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 05/21/2020] [Accepted: 06/03/2020] [Indexed: 01/13/2023]
Abstract
African populations exhibit extensive linguistic and cultural diversity but are less studied from a population genetic standpoint. Although much genetic data on admixed African individuals, such as African Americans, have been published, genetic polymorphism data, especially that based on sequence-based typing, are still insufficient in indigenous Africans. In this study, we examined the genetic diversity of 85 Nigerians residing in Guangzhou, China. Forensically relevant genetic markers, including autosomal short tandem repeats (A-STRs), X-chromosomal STRs (X-STRs), Y-chromosomal STRs (Y-STRs), and identity-informative single nucleotide polymorphisms (iiSNPs) were genotyped to uncover the genetic polymorphisms of this population. Sequence-based allelic variations were observed in 22 A-STRs, ten Y-STRs, and four X-STRs. Using massively parallel sequencing (MPS), the allele number increased from 475 length-based alleles to 683 sequence-based alleles. Compared to other populations, the overall observed heterozygosity of the 27 A-STRs was the highest in Nigerians, which reflected the higher genetic diversity of this population. The combined match probability of the 27 A-STRs was low at 9.06 × 10-38. When both A-STRs and iiSNPs were considered, the cumulative discrimination power, and combined power of exclusion for duo and trio paternity testing was 1-2.97 × 10-57, 1-2.20 × 10-10 and 1-4.61 × 10-17, respectively, which demonstrated that the STRs and SNPs analyzed here can be applied to forensic investigations. In summary, this study uncovers the genetic features of the Nigerian population and provides valuable frequency data for forensic applications.
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Affiliation(s)
- Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Han Ren
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Haixia Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Xuefeng Shen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China
| | - Erwen Huang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China.
| | - Yinming Zhang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China.
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, PR China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, PR China.
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9
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Naidoo T, Xu J, Vicente M, Malmström H, Soodyall H, Jakobsson M, Schlebusch CM. Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences. Genome Biol Evol 2020; 12:1031-1039. [PMID: 32697300 PMCID: PMC7375190 DOI: 10.1093/gbe/evaa098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2020] [Indexed: 12/30/2022] Open
Abstract
Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, however, has removed this bias and allowed for the discovery of thousands of new variants for use in improving the Y-chromosome phylogeny and computing estimates that are more accurate. Here, we describe the high-coverage sequencing of the whole Y chromosome in a data set of 19 male Khoe-San individuals in comparison with existing whole Y-chromosome sequence data. Due to the increased resolution, we potentially resolve the source of haplogroup B-P70 in the Khoe-San, and reconcile recently published haplogroup A-M51 data with the most recent version of the ISOGG Y-chromosome phylogeny. Our results also improve the positioning of tentatively placed new branches of the ISOGG Y-chromosome phylogeny. The distribution of major Y-chromosome haplogroups in the Khoe-San and other African groups coincide with the emerging picture of African demographic history; with E-M2 linked to the agriculturalist Bantu expansion, E-M35 linked to pastoralist eastern African migrations, B-M112 linked to earlier east-south gene flow, A-M14 linked to shared ancestry with central African rainforest hunter-gatherers, and A-M51 potentially unique to the Khoe-San.
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Affiliation(s)
- Thijessen Naidoo
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Sweden
- Science for Life Laboratory, Uppsala, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Jingzi Xu
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Mário Vicente
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Sweden
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
| | - Himla Soodyall
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Service, Johannesburg, South Africa
- Academy of Science of South Africa
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Sweden
- Science for Life Laboratory, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
| | - Carina M Schlebusch
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Sweden
- Science for Life Laboratory, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
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10
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Joint Genetic Analyses of Mitochondrial and Y-Chromosome Molecular Markers for a Population from Northwest China. Genes (Basel) 2020; 11:genes11050564. [PMID: 32443545 PMCID: PMC7290686 DOI: 10.3390/genes11050564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/09/2020] [Accepted: 05/11/2020] [Indexed: 12/27/2022] Open
Abstract
The genetic markers on mitochondria DNA (mtDNA) and Y-chromosome can be applied as a powerful tool in population genetics. We present a study to reveal the genetic background of Kyrgyz group, a Chinese ethnic group living in northwest China, and genetic polymorphisms of 60 loci on maternal inherited mtDNA and 24 loci on paternal inherited Y-chromosome short tandem repeats (Y-STRs) were investigated. The relationship between the two systems was tested, and the result indicated that they were statistically independent from each other. The genetic distances between Kyrgyz group and 11 reference populations for mtDNA, and 13 reference populations for Y-STRs were also calculated, respectively. The present results demonstrated that the Kyrgyz group was genetically closer to East Asian populations than European populations based on the mtDNA loci but the other way around for the Y-STRs. The genetic analyses could largely strengthen the understanding for the genetic background of the Kyrgyz group.
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11
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Kutanan W, Kampuansai J, Srikummool M, Brunelli A, Ghirotto S, Arias L, Macholdt E, Hübner A, Schröder R, Stoneking M. Contrasting Paternal and Maternal Genetic Histories of Thai and Lao Populations. Mol Biol Evol 2020; 36:1490-1506. [PMID: 30980085 PMCID: PMC6573475 DOI: 10.1093/molbev/msz083] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The human demographic history of Mainland Southeast Asia (MSEA) has not been well studied; in particular, there have been very few sequence-based studies of variation in the male-specific portions of the Y chromosome (MSY). Here, we report new MSY sequences of ∼2.3 mB from 914 males and combine these with previous data for a total of 928 MSY sequences belonging to 59 populations from Thailand and Laos who speak languages belonging to three major Mainland Southeast Asia families: Austroasiatic, Tai-Kadai, and Sino-Tibetan. Among the 92 MSY haplogroups, two main MSY lineages (O1b1a1a* [O-M95*] and O2a* [O-M324*]) contribute substantially to the paternal genetic makeup of Thailand and Laos. We also analyze complete mitochondrial DNA genome sequences published previously from the same groups and find contrasting pattern of male and female genetic variation and demographic expansions, especially for the hill tribes, Mon, and some major Thai groups. In particular, we detect an effect of postmarital residence pattern on genetic diversity in patrilocal versus matrilocal groups. Additionally, both male and female demographic expansions were observed during the early Mesolithic (∼10 ka), with two later major male-specific expansions during the Neolithic period (∼4–5 ka) and the Bronze/Iron Age (∼2.0–2.5 ka). These two later expansions are characteristic of the modern Austroasiatic and Tai-Kadai groups, respectively, consistent with recent ancient DNA studies. We simulate MSY data based on three demographic models (continuous migration, demic diffusion, and cultural diffusion) of major Thai groups and find different results from mitochondrial DNA simulations, supporting contrasting male and female genetic histories.
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Affiliation(s)
- Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Metawee Srikummool
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Andrea Brunelli
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Silvia Ghirotto
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Leonardo Arias
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Enrico Macholdt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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12
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Haber M, Jones AL, Connell BA, Asan, Arciero E, Yang H, Thomas MG, Xue Y, Tyler-Smith C. A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans Out of Africa. Genetics 2019; 212:1421-1428. [PMID: 31196864 PMCID: PMC6707464 DOI: 10.1534/genetics.119.302368] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/10/2019] [Indexed: 12/31/2022] Open
Abstract
Present-day humans outside Africa descend mainly from a single expansion out ∼50,000-70,000 years ago, but many details of this expansion remain unclear, including the history of the male-specific Y chromosome at this time. Here, we reinvestigate a rare deep-rooting African Y-chromosomal lineage by sequencing the whole genomes of three Nigerian men described in 2003 as carrying haplogroup DE* Y chromosomes, and analyzing them in the context of a calibrated worldwide Y-chromosomal phylogeny. We confirm that these three chromosomes do represent a deep-rooting DE lineage, branching close to the DE bifurcation, but place them on the D branch as an outgroup to all other known D chromosomes, and designate the new lineage D0. We consider three models for the expansion of Y lineages out of Africa ∼50,000-100,000 years ago, incorporating migration back to Africa where necessary to explain present-day Y-lineage distributions. Considering both the Y-chromosomal phylogenetic structure incorporating the D0 lineage, and published evidence for modern humans outside Africa, the most favored model involves an origin of the DE lineage within Africa with D0 and E remaining there, and migration out of the three lineages (C, D, and FT) that now form the vast majority of non-African Y chromosomes. The exit took place 50,300-81,000 years ago (latest date for FT lineage expansion outside Africa - earliest date for the D/D0 lineage split inside Africa), and most likely 50,300-59,400 years ago (considering Neanderthal admixture). This work resolves a long-running debate about Y-chromosomal out-of-Africa/back-to-Africa migrations, and provides insights into the out-of-Africa expansion more generally.
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Affiliation(s)
- Marc Haber
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | | | - Bruce A Connell
- Glendon College, York University, Toronto, Ontario M4N 3N6, Canada
| | - Asan
- BGI-Shenzhen, Shenzhen 518083, China
| | - Elena Arciero
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China
- James D. Watson Institute of Genome Science, 310008 Hangzhou, China
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, WC1E 6BT, UK, and University College London (UCL) Genetics Institute, University College London, WC1E 6BT, UK
| | - Yali Xue
- The Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
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13
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Fan S, Kelly DE, Beltrame MH, Hansen MEB, Mallick S, Ranciaro A, Hirbo J, Thompson S, Beggs W, Nyambo T, Omar SA, Meskel DW, Belay G, Froment A, Patterson N, Reich D, Tishkoff SA. African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. Genome Biol 2019; 20:82. [PMID: 31023338 PMCID: PMC6485071 DOI: 10.1186/s13059-019-1679-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 03/22/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Africa is the origin of modern humans within the past 300 thousand years. To infer the complex demographic history of African populations and adaptation to diverse environments, we sequenced the genomes of 92 individuals from 44 indigenous African populations. RESULTS Genetic structure analyses indicate that among Africans, genetic ancestry is largely partitioned by geography and language, though we observe mixed ancestry in many individuals, consistent with both short- and long-range migration events followed by admixture. Phylogenetic analysis indicates that the San genetic lineage is basal to all modern human lineages. The San and Niger-Congo, Afroasiatic, and Nilo-Saharan lineages were substantially diverged by 160 kya (thousand years ago). In contrast, the San and Central African rainforest hunter-gatherer (CRHG), Hadza hunter-gatherer, and Sandawe hunter-gatherer lineages were diverged by ~ 120-100 kya. Niger-Congo, Nilo-Saharan, and Afroasiatic lineages diverged more recently by ~ 54-16 kya. Eastern and western CRHG lineages diverged by ~ 50-31 kya, and the western CRHG lineages diverged by ~ 18-12 kya. The San and CRHG populations maintained the largest effective population size compared to other populations prior to 60 kya. Further, we observed signatures of positive selection at genes involved in muscle development, bone synthesis, reproduction, immune function, energy metabolism, and cell signaling, which may contribute to local adaptation of African populations. CONCLUSIONS We observe high levels of genomic variation between ethnically diverse Africans which is largely correlated with geography and language. Our study indicates ancient population substructure and local adaptation of Africans.
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Affiliation(s)
- Shaohua Fan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Present Address: State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai, China
| | - Derek E Kelly
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Marcia H Beltrame
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Matthew E B Hansen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Alessia Ranciaro
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jibril Hirbo
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Present Address: Division of Genetic Medicine, Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN, 37232, USA
| | - Simon Thompson
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - William Beggs
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Thomas Nyambo
- Department of Biochemistry, Muhimbili University of Health and Allied Sciences, Dares Salaam, Tanzania
| | - Sabah A Omar
- Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Gurja Belay
- Department of Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah A Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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14
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Smeds L, Kojola I, Ellegren H. The evolutionary history of grey wolf Y chromosomes. Mol Ecol 2019; 28:2173-2191. [PMID: 30788868 PMCID: PMC6850511 DOI: 10.1111/mec.15054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 12/30/2022]
Abstract
Analyses of Y chromosome haplotypes uniquely provide a paternal picture of evolutionary histories and offer a very useful contrast to studies based on maternally inherited mitochondrial DNA (mtDNA). Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf (Canis lupis) Y chromosome, probably representing most of the male-specific, nonampliconic sequence from the euchromatic part of the chromosome. We characterized this sequence and then identified ≈1,500 Y-linked single nucleotide polymorphisms in a sample of 145 resequenced male wolves, including 75 Finnish wolf genomes newly sequenced in this study, and in 24 dogs and eight other canids. We found 53 Y chromosome haplotypes, of which 26 were seen in grey wolves, that clustered in four major haplogroups. All four haplogroups were represented in samples of Finnish wolves, showing that haplogroup lineages were not partitioned on a continental scale. However, regional population structure was indicated because individual haplotypes were never shared between geographically distant areas, and genetically similar haplotypes were only found within the same geographical region. The deepest split between grey wolf haplogroups was estimated to have occurred 125,000 years ago, which is considerably older than recent estimates of the time of divergence of wolf populations. The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, or wolf paternal introgression, starting 29,000 years ago. We also addressed the disputed origin of a recently founded population of Scandinavian wolves and observed that founding as well as most recent immigrant haplotypes were present in the neighbouring Finnish population, but not in sequenced wolves from elsewhere in the world, or in dogs.
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Affiliation(s)
- Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Ilpo Kojola
- Natural Resources Institute Finland (Luke), Rovaniemi, Finland
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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15
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Enamel pearls: Their occurrence in recent human populations and earliest manifestation in the modern human lineage. Arch Oral Biol 2019; 101:147-155. [PMID: 30939297 DOI: 10.1016/j.archoralbio.2019.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/22/2019] [Accepted: 03/04/2019] [Indexed: 12/28/2022]
Abstract
OBJECTIVE To document and describe the occurrence of an enamel pearl on the distal root surface of the maxillary M3 of the fossil hominin specimen from Florisbad, South Africa that is dated to ca. 259,000 years B.P., and is an early representative of Homo sapiens or as a member of the evolutionary line that was directly ancestral to modern humans. DESIGN The molar was examined macroscopically and by micro-computed tomography (μCT) to enable accurate measurement and visualization of the structure of the enamel pearl. RESULTS The single pearl has a diameter of 0.97 mm; it is a Type 2 "composite" pearl comprising an enamel cap and dentine core without pulp chamber involvement. The size of the Florisbad pearl falls within or just below the size ranges of this anomaly in modern human samples. Type 2 pearls are most commonly encountered in recent human populations, and the location of the pearl on the distal root surface of the Florisbad M3 is consistent with its most frequent location in recent humans. Pearls in recent human populations affect between 0.2-4.8% of individuals, and 1.7-6.8% of permanent molars. Pearls have been documented in several prehistoric human dentitions, and all examples are less than 4000 years old. CONCLUSIONS Enamel pearls have been associated with periodontal disease, but it is not possible to relate its presence to the advanced periodontal inflammation and alveolar bone loss in the Florisbad fossil. Florisbad presents the earliest evidence of this anomaly in the fossil record pertaining to modern humans.
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16
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Oliveira S, Hübner A, Fehn AM, Aço T, Lages F, Pakendorf B, Stoneking M, Rocha J. The role of matrilineality in shaping patterns of Y chromosome and mtDNA sequence variation in southwestern Angola. Eur J Hum Genet 2018; 27:475-483. [PMID: 30467412 DOI: 10.1038/s41431-018-0304-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/25/2018] [Accepted: 11/01/2018] [Indexed: 11/09/2022] Open
Abstract
Southwestern Angola is a region characterized by contact between indigenous foragers and incoming food-producers, involving genetic and cultural exchanges between peoples speaking Kx'a, Khoe-Kwadi, and Bantu languages. Although present-day Bantu speakers share a patrilocal residence pattern and matrilineal principle of clan and group membership, a highly stratified social setting divides dominant pastoralists from marginalized groups that subsist on alternative strategies and have previously been thought to have pre-Bantu origins. Here, we compare new high-resolution sequence data from 2.3 Mb of the male-specific region of the Y chromosome (MSY) from 170 individuals with previously reported mitochondrial DNA (mtDNA) genomes, to investigate the population history of seven representative southwestern Angolan groups (Himba, Kuvale, Kwisi, Kwepe, Twa, Tjimba, !Xun), and to study the causes and consequences of sex-biased processes in their genetic variation. We found no clear link between the formerly Kwadi-speaking Kwepe and pre-Bantu eastern African migrants, and no pre-Bantu MSY lineages among Bantu-speaking groups, except for small amounts of "Khoisan" introgression. We therefore propose that irrespective of their subsistence strategies, all Bantu-speaking groups of the area share a male Bantu origin. Additionally, we show that in Bantu-speaking groups, the levels of among-group and between-group variation are higher for mtDNA than for MSY. These results, together with our previous demonstration that the matriclanic systems of southwestern Angolan Bantu groups are genealogically consistent, suggest that matrilineality strongly enhances both female population sizes and interpopulation mtDNA variation.
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Affiliation(s)
- Sandra Oliveira
- CIBIO/InBIO: Research Center in Biodiversity and Genetic Resources, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Anne-Maria Fehn
- CIBIO/InBIO: Research Center in Biodiversity and Genetic Resources, 4485-661, Vairão, Portugal.,Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, 00745, Jena, Germany.,Institute for African Studies, Goethe University, 60323, Frankfurt, Germany
| | - Teresa Aço
- Centro de Estudos do Deserto (CEDO), Namibe, Angola
| | - Fernanda Lages
- ISCED/Huíla-Instituto Superior de Ciências da Educação, Lubango, Angola
| | - Brigitte Pakendorf
- Laboratoire Dynamique du Langage, UMR5596, CNRS & Univ Lyon, 69007, Lyon, France
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Jorge Rocha
- CIBIO/InBIO: Research Center in Biodiversity and Genetic Resources, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.,ISCED/Huíla-Instituto Superior de Ciências da Educação, Lubango, Angola
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17
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Arias L, Schröder R, Hübner A, Barreto G, Stoneking M, Pakendorf B. Cultural Innovations Influence Patterns of Genetic Diversity in Northwestern Amazonia. Mol Biol Evol 2018; 35:2719-2735. [PMID: 30169717 PMCID: PMC6231495 DOI: 10.1093/molbev/msy169] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the nonrecombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic exogamy, a marital practice in which men are required to marry women speaking a different language. We identified 2,969 SNPs in the NRY sequences, only 925 of which were previously described. The NRY and mtDNA data showed different sex-specific demographic histories: female effective population size has been larger than that of males through time, which might reflect larger variance in male reproductive success. Both markers show an increase in lineage diversification beginning ∼5,000 years ago, which may reflect the intensification of agriculture, technological innovations, and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, we find similar excesses of NRY versus mtDNA between-population divergence at both the local and continental scale, suggesting long-term stability of female versus male migration. We also find evidence of the impact of sociocultural practices on diversity patterns. Finally, our study highlights the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between sexes.
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Affiliation(s)
- Leonardo Arias
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Laboratorio de Genética Molecular Humana, Departamento de Biología, Universidad del Valle, Cali, Colombia
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Guillermo Barreto
- Laboratorio de Genética Molecular Humana, Departamento de Biología, Universidad del Valle, Cali, Colombia
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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Abstract
Levels and patterns of genetic diversity can provide insights into a population’s history. In species with sex chromosomes, differences between genomic regions with unique inheritance patterns can be used to distinguish between different sets of possible demographic and selective events. This review introduces the differences in population history for sex chromosomes and autosomes, provides the expectations for genetic diversity across the genome under different evolutionary scenarios, and gives an introductory description for how deviations in these expectations are calculated and can be interpreted. Predominantly, diversity on the sex chromosomes has been used to explore and address three research areas: 1) Mating patterns and sex-biased variance in reproductive success, 2) signatures of selection, and 3) evidence for modes of speciation and introgression. After introducing the theory, this review catalogs recent studies of genetic diversity on the sex chromosomes across species within the major research areas that sex chromosomes are typically applied to, arguing that there are broad similarities not only between male-heterogametic (XX/XY) and female-heterogametic (ZZ/ZW) sex determination systems but also any mating system with reduced recombination in a sex-determining region. Further, general patterns of reduced diversity in nonrecombining regions are shared across plants and animals. There are unique patterns across populations with vastly different patterns of mating and speciation, but these do not tend to cluster by taxa or sex determination system.
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Affiliation(s)
- Melissa A Wilson Sayres
- School of Life Sciences, Center for Evolution and Medicine, The Biodesign Institute, Arizona State University
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19
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Bajić V, Barbieri C, Hübner A, Güldemann T, Naumann C, Gerlach L, Berthold F, Nakagawa H, Mpoloka SW, Roewer L, Purps J, Stoneking M, Pakendorf B. Genetic structure and sex-biased gene flow in the history of southern African populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:656-671. [PMID: 30192370 PMCID: PMC6667921 DOI: 10.1002/ajpa.23694] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 07/13/2018] [Accepted: 07/15/2018] [Indexed: 12/31/2022]
Abstract
Objectives We investigated the genetic history of southern African populations with a special focus on their paternal history. We reexamined previous claims that the Y‐chromosome haplogroup E1b1b (E‐M293) was brought to southern Africa by pastoralists from eastern Africa, and investigated patterns of sex‐biased gene flow in southern Africa. Materials and methods We analyzed previously published complete mtDNA genome sequences and ∼900 kb of NRY sequences from 23 populations from Namibia, Botswana, and Zambia, as well as haplogroup frequencies from a large sample of southern African populations and 23 newly genotyped Y‐linked STR loci for samples assigned to haplogroup E1b1b. Results Our results support an eastern African origin for Y‐chromosome haplogroup E1b1b (E‐M293); however, its current distribution in southern Africa is not strongly associated with pastoralism, suggesting more complex demographic events and/or changes in subsistence practices in this region. The Bantu expansion in southern Africa had a notable genetic impact and was probably a rapid, male‐dominated expansion. Our finding of a significant increase in the intensity of the sex‐biased gene flow from north to south may reflect changes in the social dynamics between Khoisan and Bantu groups over time. Conclusions Our study shows that the population history of southern Africa has been complex, with different immigrating groups mixing to different degrees with the autochthonous populations. The Bantu expansion led to heavily sex‐biased admixture as a result of interactions between Khoisan females and Bantu males, with a geographic gradient which may reflect changes in the social dynamics between Khoisan and Bantu groups over time.
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Affiliation(s)
- Vladimir Bajić
- Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Chiara Barbieri
- Department of Linguistic and Cultural Evolution, MPI for the Science of Human History, Jena, Germany.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Alexander Hübner
- Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Tom Güldemann
- Department of Linguistic and Cultural Evolution, MPI for the Science of Human History, Jena, Germany.,Institute of Asian and African Studies, Humboldt University, Berlin, Germany
| | - Christfried Naumann
- Institute of Asian and African Studies, Humboldt University, Berlin, Germany
| | - Linda Gerlach
- Department of Human Behavior, Ecology and Culture, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Falko Berthold
- Max Planck Research Group on Comparative Population Linguistics, MPI for Evolutionary Anthropology, Leipzig, Germary
| | - Hirosi Nakagawa
- Institute of Global Studies, Tokyo University of Foreign Studies, Tokyo, Japan
| | - Sununguko W Mpoloka
- Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Lutz Roewer
- Charité - Universitätsmedizin Berlin, Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Berlin, Germany
| | - Josephine Purps
- Charité - Universitätsmedizin Berlin, Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Berlin, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, MPI for Evolutionary Anthropology, Leipzig, Germany
| | - Brigitte Pakendorf
- Laboratoire «Dynamique du Langage», CNRS & Université de Lyon, Lyon, France
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20
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D’Atanasio E, Trombetta B, Bonito M, Finocchio A, Di Vito G, Seghizzi M, Romano R, Russo G, Paganotti GM, Watson E, Coppa A, Anagnostou P, Dugoujon JM, Moral P, Sellitto D, Novelletto A, Cruciani F. The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages. Genome Biol 2018; 19:20. [PMID: 29433568 PMCID: PMC5809971 DOI: 10.1186/s13059-018-1393-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/19/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Little is known about the peopling of the Sahara during the Holocene climatic optimum, when the desert was replaced by a fertile environment. RESULTS In order to investigate the role of the last Green Sahara in the peopling of Africa, we deep-sequence the whole non-repetitive portion of the Y chromosome in 104 males selected as representative of haplogroups which are currently found to the north and to the south of the Sahara. We identify 5,966 mutations, from which we extract 142 informative markers then genotyped in about 8,000 subjects from 145 African, Eurasian and African American populations. We find that the coalescence age of the trans-Saharan haplogroups dates back to the last Green Sahara, while most northern African or sub-Saharan clades expanded locally in the subsequent arid phase. CONCLUSIONS Our findings suggest that the Green Sahara promoted human movements and demographic expansions, possibly linked to the adoption of pastoralism. Comparing our results with previously reported genome-wide data, we also find evidence for a sex-biased sub-Saharan contribution to northern Africans, suggesting that historical events such as the trans-Saharan slave trade mainly contributed to the mtDNA and autosomal gene pool, whereas the northern African paternal gene pool was mainly shaped by more ancient events.
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Affiliation(s)
- Eugenia D’Atanasio
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Università di Roma, Rome, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Maria Bonito
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Andrea Finocchio
- Dipartimento di Biologia, Università di Roma “Tor Vergata”, Rome, Italy
| | - Genny Di Vito
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Mara Seghizzi
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Rita Romano
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Rome, Italy
| | - Gianluca Russo
- Dipartimento di Sanità Pubblica e Malattie Infettive, Sapienza Università di Roma, Rome, Italy
| | - Giacomo Maria Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | | | - Alfredo Coppa
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Paolo Anagnostou
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
- Istituto Italiano di Antropologia, Rome, Italy
| | - Jean-Michel Dugoujon
- Centre National de la Recherche Scientifique (CNRS), Université Toulouse-3–Paul-Sabatier, Toulouse, France
| | - Pedro Moral
- Department of Animal Biology-Anthropology, Biodiversity Research Institute, University of Barcelona, Barcelona, Spain
| | | | - Andrea Novelletto
- Dipartimento di Biologia, Università di Roma “Tor Vergata”, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto di Biologia e Patologia Molecolari, CNR, Rome, Italy
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21
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Contrasting maternal and paternal genetic variation of hunter-gatherer groups in Thailand. Sci Rep 2018; 8:1536. [PMID: 29367746 PMCID: PMC5784115 DOI: 10.1038/s41598-018-20020-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/11/2018] [Indexed: 11/11/2022] Open
Abstract
The Maniq and Mlabri are the only recorded nomadic hunter-gatherer groups in Thailand. Here, we sequenced complete mitochondrial (mt) DNA genomes and ~2.364 Mbp of non-recombining Y chromosome (NRY) to learn more about the origins of these two enigmatic populations. Both groups exhibited low genetic diversity compared to other Thai populations, and contrasting patterns of mtDNA and NRY diversity: there was greater mtDNA diversity in the Maniq than in the Mlabri, while the converse was true for the NRY. We found basal uniparental lineages in the Maniq, namely mtDNA haplogroups M21a, R21 and M17a, and NRY haplogroup K. Overall, the Maniq are genetically similar to other negrito groups in Southeast Asia. By contrast, the Mlabri haplogroups (B5a1b1 for mtDNA and O1b1a1a1b and O1b1a1a1b1a1 for the NRY) are common lineages in Southeast Asian non-negrito groups, and overall the Mlabri are genetically similar to their linguistic relatives (Htin and Khmu) and other groups from northeastern Thailand. In agreement with previous studies of the Mlabri, our results indicate that the Malbri do not directly descend from the indigenous negritos. Instead, they likely have a recent origin (within the past 1,000 years) by an extreme founder event (involving just one maternal and two paternal lineages) from an agricultural group, most likely the Htin or a closely-related group.
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22
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Enclaves of genetic diversity resisted Inca impacts on population history. Sci Rep 2017; 7:17411. [PMID: 29234095 PMCID: PMC5727115 DOI: 10.1038/s41598-017-17728-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/29/2017] [Indexed: 11/08/2022] Open
Abstract
The Inca Empire is claimed to have driven massive population movements in western South America, and to have spread Quechua, the most widely-spoken language family of the indigenous Americas. A test-case is the Chachapoyas region of northern Peru, reported as a focal point of Inca population displacements. Chachapoyas also spans the environmental, cultural and demographic divides between Amazonia and the Andes, and stands along the lowest-altitude corridor from the rainforest to the Pacific coast. Following a sampling strategy informed by linguistic data, we collected 119 samples, analysed for full mtDNA genomes and Y-chromosome STRs. We report a high indigenous component, which stands apart from the network of intense genetic exchange in the core central zone of Andean civilization, and is also distinct from neighbouring populations. This unique genetic profile challenges the routine assumption of large-scale population relocations by the Incas. Furthermore, speakers of Chachapoyas Quechua are found to share no particular genetic similarity or gene-flow with Quechua speakers elsewhere, suggesting that here the language spread primarily by cultural diffusion, not migration. Our results demonstrate how population genetics, when fully guided by the archaeological, historical and linguistic records, can inform multiple disciplines within anthropology.
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23
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Schlebusch CM, Malmström H, Günther T, Sjödin P, Coutinho A, Edlund H, Munters AR, Vicente M, Steyn M, Soodyall H, Lombard M, Jakobsson M. Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago. Science 2017; 358:652-655. [PMID: 28971970 DOI: 10.1126/science.aao6266] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/20/2017] [Indexed: 12/14/2022]
Abstract
Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. The remains of three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, and those of four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record.
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Affiliation(s)
- Carina M Schlebusch
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden.,Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa
| | - Helena Malmström
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden.,Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa
| | - Torsten Günther
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden
| | - Per Sjödin
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden
| | - Alexandra Coutinho
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden
| | - Hanna Edlund
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden
| | - Arielle R Munters
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden
| | - Mário Vicente
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden
| | - Maryna Steyn
- Human Variation and Identification Research Unit, School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, South Africa
| | - Himla Soodyall
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa
| | - Marlize Lombard
- Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa. .,Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Marais Street, Stellenbosch, 7600, South Africa
| | - Mattias Jakobsson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden. .,Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa.,Science for Life Laboratory (SciLife Lab), Uppsala, Sweden
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24
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Brunelli A, Kampuansai J, Seielstad M, Lomthaisong K, Kangwanpong D, Ghirotto S, Kutanan W. Y chromosomal evidence on the origin of northern Thai people. PLoS One 2017; 12:e0181935. [PMID: 28742125 PMCID: PMC5524406 DOI: 10.1371/journal.pone.0181935] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/10/2017] [Indexed: 01/11/2023] Open
Abstract
The Khon Mueang represent the major group of people present in today's northern Thailand. While linguistic and genetic data seem to support a shared ancestry between Khon Mueang and other Tai-Kadai speaking people, the possibility of an admixed origin with contribution from local Mon-Khmer population could not be ruled out. Previous studies conducted on northern Thai people did not provide a definitive answer and, in addition, have largely overlooked the distribution of paternal lineages in the area. In this work we aim to provide a comprehensive analysis of Y paternal lineages in northern Thailand and to explicitly model the origin of the Khon Mueang population. We obtained and analysed new Y chromosomal haplogroup data from more than 500 northern Thai individuals including Khon Mueang, Mon-Khmer and Tai-Kadai. We also explicitly simulated different demographic scenarios, developed to explain the Khon Mueang origin, employing an ABC simulation framework on both mitochondrial and Y microsatellites data. Our results highlighted a similar haplogroup composition of Khon Mueang and Tai-Kadai populations in northern Thailand, with shared high frequencies of haplogroups O-PK4, O-M117 and O-M111. Our ABC simulations also favoured a model in which the ancestors of modern Khon Mueang originated recently after a split from the other Tai-Kadai populations. Our different analyses concluded that the ancestors of Khon Mueang are likely to have originated from the same source of the other Tai-Kadai groups in southern China, with subsequent admixture events involving native Mon-Khmer speakers restricted to some specific populations.
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Affiliation(s)
- Andrea Brunelli
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Mark Seielstad
- Department of Laboratory Medicine & Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Khemika Lomthaisong
- Forensic Science Program, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Daoroong Kangwanpong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Silvia Ghirotto
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
- * E-mail: (SG); (WK)
| | - Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
- * E-mail: (SG); (WK)
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25
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Uren C, Möller M, van Helden PD, Henn BM, Hoal EG. Population structure and infectious disease risk in southern Africa. Mol Genet Genomics 2017; 292:499-509. [PMID: 28229227 DOI: 10.1007/s00438-017-1296-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 02/01/2017] [Indexed: 02/06/2023]
Abstract
The KhoeSan populations are the earliest known indigenous inhabitants of southern Africa. The relatively recent expansion of Bantu-speaking agropastoralists, as well as European colonial settlement along the south-west coast, dramatically changed patterns of genetic diversity in a region which had been largely isolated for thousands of years. Owing to this unique history, population structure in southern Africa reflects both the underlying KhoeSan genetic diversity as well as differential recent admixture. This population structure has a wide range of biomedical and sociocultural implications; such as changes in disease risk profiles. Here, we consolidate information from various population genetic studies that characterize admixture patterns in southern Africa with an aim to better understand differences in adverse disease phenotypes observed among groups. Our review confirms that ancestry has a direct impact on an individual's immune response to infectious diseases. In addition, we emphasize the importance of collaborative research, especially for populations in southern Africa that have a high incidence of potentially fatal infectious diseases such as HIV and tuberculosis.
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Affiliation(s)
- Caitlin Uren
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medical and Health Sciences, Stellenbosch University, Tygerberg, Parow, 7500, South Africa
| | - Marlo Möller
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medical and Health Sciences, Stellenbosch University, Tygerberg, Parow, 7500, South Africa
| | - Paul D van Helden
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medical and Health Sciences, Stellenbosch University, Tygerberg, Parow, 7500, South Africa
| | - Brenna M Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Eileen G Hoal
- SA MRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medical and Health Sciences, Stellenbosch University, Tygerberg, Parow, 7500, South Africa.
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26
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Rowold DJ, Perez-Benedico D, Stojkovic O, Alfonso-Sanchez MA, Garcia-Bertrand R, Herrera RJ. On the Bantu expansion. Gene 2016; 593:48-57. [PMID: 27451076 DOI: 10.1016/j.gene.2016.07.044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 07/18/2016] [Indexed: 10/21/2022]
Abstract
Here we report the results of fine resolution Y chromosomal analyses (Y-SNP and Y-STR) of 267 Bantu-speaking males from three populations located in the southeast region of Africa. In an effort to determine the relative Y chromosomal affinities of these three genotyped populations, the findings are interpreted in the context of 74 geographically and ethnically targeted African reference populations representing four major ethno-linguistic groups (Afro-Asiatic, Niger Kordofanin, Khoisan and Pygmoid). In this investigation, we detected a general similarity in the Y chromosome lineages among the geographically dispersed Bantu-speaking populations suggesting a shared heritage and the shallow time depth of the Bantu Expansion. Also, micro-variations in the Bantu Y chromosomal composition across the continent highlight location-specific gene flow patterns with non-Bantu-speaking populations (Khoisan, Pygmy, Afro-Asiatic). Our Y chromosomal results also indicate that the three Bantu-speaking Southeast populations genotyped exhibit unique gene flow patterns involving Eurasian populations but fail to reveal a prevailing genetic affinity to East or Central African Bantu-speaking groups. In addition, the Y-SNP data underscores a longitudinal partitioning in sub-Sahara Africa of two R1b1 subgroups, R1b1-P25* (west) and R1b1a2-M269 (east). No evidence was observed linking the B2a haplogroup detected in the genotyped Southeast African Bantu-speaking populations to gene flow from contemporary Khoisan groups.
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Affiliation(s)
- Daine J Rowold
- Foundation for Applied Molecular Evolution, Gainesville, FL 32601, USA
| | | | - Oliver Stojkovic
- Institute of Forensic Medicine, School of Medicine, University of Belgrade, Belgrade, Serbia
| | | | | | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO 80903, USA
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27
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Babić N, Dogan S, Čakar J, Pilav A, Marjanović D, Hadžiavdić V. Molecular diversity of 23 Y-chromosome short tandem repeat loci in the population of Tuzla Canton, Bosnia and Herzegovina. Ann Hum Biol 2016; 44:419-426. [PMID: 27826995 DOI: 10.1080/03014460.2016.1259430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Tuzla Canton is the most populated region in the ethnically mixed territory of Bosnia and Herzegovina, whose genetic analysis could provide an insight into past demographic events. AIM Analysis of 23 Y-chromosome STR markers in the population of Tuzla Canton and investigation of the genetic relationship of the male population of the Tuzla Canton and that of the larger Bosnian and Herzegovinian population as well as neighbouring and other European populations. SUBJECTS AND METHODS The study was conducted among 100 unrelated healthy adult males from Tuzla Canton that have been genotyped using 23 Y-STR loci included in the PowerPlex Y23 kit. Statistical parameters such as haplotype diversity and allele frequencies were calculated, as well as the Rst-based genetic distances between the new dataset and those from Bosnia and Herzegovina and elsewhere, which were then visualised through multi-dimensional scaling plot and neighbour-joining phylogenetic tree analyses. RESULTS The PowerPlex Y23 kit has shown high discrimination capacity, as all 100 individuals have unique haplotypes. The newly incorporated loci seem to be highly informative. Population comparison reveals no statistically significant differences between the study population and the general Bosnian-Herzegovinian population, and between the study population and neighbouring populations. CONCLUSION These results could be used as an additional investigation of the genetic relationship between the regional populations in Bosnia and Herzegovina and neighbouring human populations, as well as for further human population and forensic genetics studies.
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Affiliation(s)
- Naida Babić
- a Department of Biology, Faculty of Natural Sciences and Mathematics , University of Tuzla , Tuzla , Bosnia and Herzegovina
| | - Serkan Dogan
- b Department of Genetics and Bioengineering , International Burch University , Sarajevo , Bosnia and Herzegovina
| | - Jasmina Čakar
- c Institute for Genetic Engineering and Biotechnology, University of Sarajevo , Sarajevo , Bosnia and Herzegovina
| | - Amela Pilav
- c Institute for Genetic Engineering and Biotechnology, University of Sarajevo , Sarajevo , Bosnia and Herzegovina
| | - Damir Marjanović
- b Department of Genetics and Bioengineering , International Burch University , Sarajevo , Bosnia and Herzegovina.,d Institute for Anthropological Researches , Zagreb , Croatia
| | - Vesna Hadžiavdić
- a Department of Biology, Faculty of Natural Sciences and Mathematics , University of Tuzla , Tuzla , Bosnia and Herzegovina
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