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Reynolds AW, Grote MN, Myrick JW, Al-Hindi DR, Siford RL, Mastoras M, Möller M, Henn BM. Persistence of Matrilocal Postmarital Residence Across Multiple Generations in Southern Africa. HUMAN NATURE (HAWTHORNE, N.Y.) 2023; 34:295-323. [PMID: 37310564 PMCID: PMC10353969 DOI: 10.1007/s12110-023-09452-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/24/2023] [Indexed: 06/14/2023]
Abstract
Factors such as subsistence turnover, warfare, or interaction between different groups can be major sources of cultural change in human populations. Global demographic shifts such as the transition to agriculture during the Neolithic and more recently the urbanization and globalization of the twentieth century have been major catalysts for cultural change. Here, we test whether cultural traits such as patri/matrilocality and postmarital migration persist in the face of social upheaval and gene flow during the past 150 years in postcolonial South Africa. The recent history of South Africa has seen major demographic shifts that resulted in the displacement and forced sedentism of indigenous Khoekhoe and San populations. During the expansion of the colonial frontier, the Khoe-San admixed with European colonists and enslaved individuals from West/Central Africa, Indonesia, and South Asia, introducing novel cultural norms. We conducted demographic interviews among Nama and Cederberg communities representing nearly 3,000 individuals across three generations. Despite the history of colonial expansion, and the subsequent incorporation of Khoe-San and Khoe-San-descendant communities into a colonial society with strong patrilocal norms, patrilocality is the least common postmarital residence pattern in our study populations today. Our results suggest that more recent forces of integration into the market economy are likely the primary drivers of change in the cultural traits examined in our study. Birthplace had a strong effect on an individual's odds of migration, distance moved, and postmarital residence form. These effects are at least partially explained by the population size of the birthplace. Our results suggest that market factors local to birthplaces are important drivers of residence decisions, although the frequency of matrilocal residence and a geographic and temporal cline in migration and residence patterns also indicate the persistence of some historic Khoe-San cultural traits in contemporary groups.
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Affiliation(s)
- Austin W Reynolds
- Department of Anthropology, Baylor University, Waco, TX, USA.
- Department of Anthropology, University of California (UC), Davis, CA, USA.
| | - Mark N Grote
- Department of Anthropology, University of California (UC), Davis, CA, USA
| | - Justin W Myrick
- Department of Anthropology, University of California (UC), Davis, CA, USA
| | - Dana R Al-Hindi
- Department of Anthropology, University of California (UC), Davis, CA, USA
| | - Rebecca L Siford
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Mira Mastoras
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
- UC Davis Genome Center, 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
| | - Brenna M Henn
- Department of Anthropology, University of California (UC), Davis, CA, USA
- UC Davis Genome Center, Davis, CA, USA
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Montinaro F, Capelli C. The evolutionary history of Southern Africa. Curr Opin Genet Dev 2018; 53:157-164. [PMID: 30522870 DOI: 10.1016/j.gde.2018.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 10/12/2018] [Accepted: 11/06/2018] [Indexed: 01/15/2023]
Abstract
The genomic variability of Southern African groups is characterized by an exceptional degree of diversity, which is the result of long-term local evolutionary history, migrations and gene-flow. Over the last few years several investigations have identified and described signatures related to these processes, revealing how ancient and more recent events have shaped the structure and ancestry composition of local populations. Here we discuss recent insights into the genetic history of the Southernmost part of the African continent provided by the analysis of modern and ancient genomes. Future work is expected to clarify the population dynamics associated with the emergence of Homo sapiens across Africa and the details of the process of dispersion and admixture associated with the arrival of Bantu-speaking groups in the region.
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Affiliation(s)
- Francesco Montinaro
- Department of Zoology, University of Oxford, UK; Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
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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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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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Larmuseau MHD, Ottoni C. Mediterranean Y-chromosome 2.0-why the Y in the Mediterranean is still relevant in the postgenomic era. Ann Hum Biol 2018; 45:20-33. [PMID: 29382278 DOI: 10.1080/03014460.2017.1402956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
CONTEXT Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour. OBJECTIVE For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available. METHODS A systematic literature search on Y-chromosomal studies in the Mediterranean was performed. RESULTS Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations. CONCLUSIONS There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.
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Affiliation(s)
- Maarten H D Larmuseau
- a KU Leuven, Forensic Biomedical Sciences , Department of Imaging & Pathology , Leuven , Belgium.,b KU Leuven, Laboratory of Socioecology and Social Evolution , Department of Biology , Leuven , Belgium
| | - Claudio Ottoni
- c Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences , University of Oslo , Oslo , Norway
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Marchi N, Mennecier P, Georges M, Lafosse S, Hegay T, Dorzhu C, Chichlo B, Ségurel L, Heyer E. Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy. Sci Rep 2018; 8:9397. [PMID: 29925873 PMCID: PMC6010435 DOI: 10.1038/s41598-018-27047-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 04/13/2018] [Indexed: 01/12/2023] Open
Abstract
When closely related individuals mate, they produce inbred offspring, which often have lower fitness than outbred ones. Geographical exogamy, by favouring matings between distant individuals, is thought to be an inbreeding avoidance mechanism; however, no data has clearly tested this prediction. Here, we took advantage of the diversity of matrimonial systems in humans to explore the impact of geographical exogamy on genetic diversity and inbreeding. We collected ethno-demographic data for 1,344 individuals in 16 populations from two Inner Asian cultural groups with contrasting dispersal behaviours (Turko-Mongols and Indo-Iranians) and genotyped genome-wide single nucleotide polymorphisms in 503 individuals. We estimated the population exogamy rate and confirmed the expected dispersal differences: Turko-Mongols are geographically more exogamous than Indo-Iranians. Unexpectedly, across populations, exogamy patterns correlated neither with the proportion of inbred individuals nor with their genetic diversity. Even more surprisingly, among Turko-Mongols, descendants from exogamous couples were significantly more inbred than descendants from endogamous couples, except for large distances (>40 km). Overall, 37% of the descendants from exogamous couples were closely inbred. This suggests that in Inner Asia, geographical exogamy is neither efficient in increasing genetic diversity nor in avoiding inbreeding, which might be due to kinship endogamy despite the occurrence of dispersal.
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Affiliation(s)
- Nina Marchi
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France.
| | - Philippe Mennecier
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France
| | - Myriam Georges
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France.,LM2E-UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, Institut Universitaire Européen de la Mer, Technopôle Brest-Iroise, Plouzane, 29280, France
| | - Sophie Lafosse
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France
| | - Tatyana Hegay
- Republican Scientific Center of Immunology, Ministry of Public Health, Tashkent, 100060, Uzbekistan
| | - Choduraa Dorzhu
- Department of biology and ecology, Tuvan State University, Kyzyl, 667000, Russia
| | - Boris Chichlo
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France
| | - Laure Ségurel
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France
| | - Evelyne Heyer
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, 75016, Paris, France.
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7
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Ly G, Alard B, Laurent R, Lafosse S, Toupance B, Monidarin C, Diffloth G, Bourdier F, Evrard O, Pavard S, Chaix R. Residence rule flexibility and descent groups dynamics shape uniparental genetic diversities in South East Asia. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 165:480-491. [PMID: 29359511 DOI: 10.1002/ajpa.23374] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 11/09/2017] [Accepted: 12/04/2017] [Indexed: 11/08/2022]
Abstract
OBJECTIVES Social organization plays a major role in shaping human population genetic diversity. In particular, matrilocal populations tend to exhibit less mitochondrial diversity than patrilocal populations, and the other way around for Y chromosome diversity. However, several studies have not replicated such findings. The objective of this study is to understand the reasons for such inconsistencies and further evaluate the influence of social organization on genetic diversity. MATERIALS AND METHODS We explored uniparental diversity patterns using mitochondrial HV1 sequences and 17 Y-linked short tandem repeats (STRs) in 12 populations (n = 619) from mainland South-East Asia exhibiting a wide range of social organizations, along with quantitative ethno-demographic information sampled at the individual level. RESULTS MtDNA diversity was lower in matrilocal than in multilocal and patrilocal populations while Y chromosome diversity was similar among these social organizations. The reasons for such asymmetry at the genetic level were understood by quantifying sex-specific migration rates from our ethno-demographic data: while female migration rates varied between social organizations, male migration rates did not. This unexpected lack of difference in male migrations resulted from a higher flexibility in residence rule in patrilocal than in matrilocal populations. In addition, our data suggested an impact of clan fission process on uniparental genetic patterns. CONCLUSIONS The observed lack of signature of patrilocality on Y chromosome patterns might be attributed to the higher residence flexibility in the studied patrilocal populations, thus providing a potential explanation for the apparent discrepancies between social and genetic structures. Altogether, this study highlights the need to quantify the actual residence and descent patterns to fit social to genetic structures.
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Affiliation(s)
- Goki Ly
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Paris, F-75016, France
| | - Bérénice Alard
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Paris, F-75016, France
| | - Romain Laurent
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Paris, F-75016, France
| | - Sophie Lafosse
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Paris, F-75016, France
| | - Bruno Toupance
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Paris, F-75016, France
| | - Chou Monidarin
- Faculty of Pharmacy and Rodolphe Mérieux Laboratory, University of Health Sciences, Phnom Penh, Cambodia
| | | | - Frédéric Bourdier
- Développement et Sociétés, UMR 201, Panthéon Sorbonne, IEDES, IRD, Paris, France
| | - Olivier Evrard
- Patrimoines Locaux et Gouvernance, UMR 208, IRD, MNHN, Paris, France
| | - Samuel Pavard
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Paris, F-75016, France
| | - Raphaëlle Chaix
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, Paris, F-75016, France
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8
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Marchi N, Hegay T, Mennecier P, Georges M, Laurent R, Whitten M, Endicott P, Aldashev A, Dorzhu C, Nasyrova F, Chichlo B, Ségurel L, Heyer E. Sex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 162:627-640. [PMID: 28158897 DOI: 10.1002/ajpa.23151] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 11/30/2016] [Accepted: 12/02/2016] [Indexed: 01/06/2023]
Abstract
OBJECTIVES Sex-specific genetic structures have been previously documented worldwide in humans, even though causal factors have not always clearly been identified. In this study, we investigated the impact of ethnicity, geography and social organization on the sex-specific genetic structure in Inner Asia. Furthermore, we explored the process of ethnogenesis in multiple ethnic groups. METHODS We sampled DNA in Central and Northern Asia from 39 populations of Indo-Iranian and Turkic-Mongolic native speakers. We focused on genetic data of the Y chromosome and mitochondrial DNA. First, we compared the frequencies of haplogroups to South European and East Asian populations. Then, we investigated the genetic differentiation for eight Y-STRs and the HVS1 region, and tested for the effect of geography and ethnicity on such patterns. Finally, we reconstructed the male demographic history, inferred split times and effective population sizes of different ethnic groups. RESULTS Based on the haplogroup data, we observed that the Indo-Iranian- and Turkic-Mongolic-speaking populations have distinct genetic backgrounds. However, each population showed consistent mtDNA and Y chromosome haplogroups patterns. As expected in patrilocal populations, we found that the Y-STRs were more structured than the HVS1. While ethnicity strongly influenced the genetic diversity on the Y chromosome, geography better explained that of the mtDNA. Furthermore, when looking at various ethnic groups, we systematically found a genetic split time older than historical records, suggesting a cultural rather than biological process of ethnogenesis. CONCLUSIONS This study highlights that, in Inner Asia, specific cultural behaviors, especially patrilineality and patrilocality, leave a detectable signature on the sex-specific genetic structure.
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Affiliation(s)
- Nina Marchi
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Tatyana Hegay
- Uzbek Academy of Sciences, Institute of Immunology, Tashkent, Uzbekistan
| | - Philippe Mennecier
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Myriam Georges
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Romain Laurent
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Mark Whitten
- MPRG on Comparative Population Linguistics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Philipp Endicott
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Almaz Aldashev
- Institute molecular biology and medicine, Bishkek, 720040, Kyrgyzstan
| | | | - Firuza Nasyrova
- Laboratory of Plant Genetics, Institute of Botany, Plant Physiology and Genetics, TAS, Dushanbe, 734063, Tajikistan
| | - Boris Chichlo
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Laure Ségurel
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Evelyne Heyer
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
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9
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Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations. Genetics 2016; 205:303-316. [PMID: 27838627 PMCID: PMC5223510 DOI: 10.1534/genetics.116.189209] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 10/13/2016] [Indexed: 12/19/2022] Open
Abstract
The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries.
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10
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The Y chromosome as the most popular marker in genetic genealogy benefits interdisciplinary research. Hum Genet 2016; 136:559-573. [DOI: 10.1007/s00439-016-1740-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/16/2016] [Indexed: 01/01/2023]
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11
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Niederstätter H, Berger B, Kayser M, Parson W. Differences in urbanization degree and consequences on the diversity of conventional vs. rapidly mutating Y-STRs in five municipalities from a small region of the Tyrolean Alps in Austria. Forensic Sci Int Genet 2016; 24:180-193. [DOI: 10.1016/j.fsigen.2016.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/23/2016] [Accepted: 07/17/2016] [Indexed: 12/09/2022]
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12
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Iacolina L, Brajković V, Canu A, Šprem N, Cubric-Curik V, Fontanesi L, Saarma U, Apollonio M, Scandura M. Novel Y-chromosome short tandem repeats in Sus scrofa and their variation in European wild boar and domestic pig populations. Anim Genet 2016; 47:682-690. [PMID: 27558303 DOI: 10.1111/age.12483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2016] [Indexed: 11/27/2022]
Abstract
Y-chromosome markers are important tools for studying male-specific gene flow within and between populations, hybridization patterns and kinship. However, their use in non-human mammals is often hampered by the lack of Y-specific polymorphic markers. We identified new male-specific short tandem repeats (STRs) in Sus scrofa using the available genome sequence. We selected four polymorphic loci (5-10 alleles per locus), falling in one duplicated and two single-copy regions. A total of 32 haplotypes were found by screening 211 individuals from eight wild boar populations across Europe and five domestic pig populations. European wild boar were characterized by significantly higher levels of haplotype diversity compared to European domestic pigs (HD = 0.904 ± 0.011 and HD = 0.491 ± 0.077 respectively). Relationships among STR haplotypes were investigated by combining them with single nucleotide polymorphisms at two linked genes (AMELY and UTY) in a network analysis. A differentiation between wild and domestic populations was observed (FST = 0.229), with commercial breeds sharing no Y haplotype with the sampled wild boar. Similarly, a certain degree of geographic differentiation was observed across Europe, with a number of local private haplotypes and high diversity in northern populations. The described Y-chromosome markers can be useful to track male inheritance and gene flow in wild and domestic populations, promising to provide insights into evolutionary and population genetics in Sus scrofa.
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Affiliation(s)
- L Iacolina
- Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy. .,Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, Aalborg, 9000, Denmark.
| | - V Brajković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, 10000, Croatia
| | - A Canu
- Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy
| | - N Šprem
- Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, 10000, Croatia
| | - V Cubric-Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, 10000, Croatia
| | - L Fontanesi
- Division of Animal Science, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna, I-40127, Italy
| | - U Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| | - M Apollonio
- Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy
| | - M Scandura
- Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy
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13
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Montinaro F, Davies J, Capelli C. Group membership, geography and shared ancestry: Genetic variation in the Basotho of Lesotho. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:156-61. [PMID: 26779678 DOI: 10.1002/ajpa.22933] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 11/16/2015] [Accepted: 12/14/2015] [Indexed: 11/10/2022]
Abstract
OBJECTIVES The investigation of the evolution of cultural and genetic traits and how they interact represents a vibrant area of research in evolutionary genetics, whose dynamics are particularly relevant for our species. One of the key assumptions of the "gene-culture coevolution" framework is the coinheritance of cultural and genetic traits. A corollary of the model is that culturally defined groups with a unique (or a limited number of) common origin(s) whose membership is inherited only through the male or female line are expected to show a relatively low intragroup variation for genetic markers similarly transmitted. Across human societies this is expected to be the case for cultural toponymies and family names within patrilineal and matrilineal groups considered in association with the nonrecombining region of the Y chromosome (NRY) and the mitochondrial DNA (mtDNA) portion of the genome, respectively. This study aims at exploring the degree of correlation between culture and genetics by investigating the genetic variation of culturally and geographically defined groups. METHODS We analyzed the genetic variation at NRY and mtDNA in 181 individuals from the Basotho, a Southern African patrilineal population from Lesotho, in combination with information about group membership and geographic origin. RESULTS Our results show that (a) the genetic distance between individuals belonging to the same culturally defined group is lower than the population as a whole when NRY markers are considered; (b) cultural traits have a bigger impact than geography for the within-group variation of Y chromosome, but not mtDNA; and (c) within-group genetic variation is compatible with a more homogeneous origin for less common groups. CONCLUSIONS Our results provided additional evidence for the relevance of the dual inheritance model (culture and genetics) in understanding the patterns of human genetic variation, as implied by gene-culture coevolution theory.
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Affiliation(s)
- Francesco Montinaro
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, Oxford, UK
| | - Joseph Davies
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, Oxford, UK
| | - Cristian Capelli
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, Oxford, UK
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14
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The Paternal Landscape along the Bight of Benin - Testing Regional Representativeness of West-African Population Samples Using Y-Chromosomal Markers. PLoS One 2015; 10:e0141510. [PMID: 26544036 PMCID: PMC4636292 DOI: 10.1371/journal.pone.0141510] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/08/2015] [Indexed: 11/19/2022] Open
Abstract
Patterns of genetic variation in human populations across the African continent are still not well studied in comparison with Eurasia and America, despite the high genetic and cultural diversity among African populations. In population and forensic genetic studies a single sample is often used to represent a complete African region. In such a scenario, inappropriate sampling strategies and/or the use of local, isolated populations may bias interpretations and pose questions of representativeness at a macrogeographic-scale. The non-recombining region of the Y-chromosome (NRY) has great potential to reveal the regional representation of a sample due to its powerful phylogeographic information content. An area poorly characterized for Y-chromosomal data is the West-African region along the Bight of Benin, despite its important history in the trans-Atlantic slave trade and its large number of ethnic groups, languages and lifestyles. In this study, Y-chromosomal haplotypes from four Beninese populations were determined and a global meta-analysis with available Y-SNP and Y-STR data from populations along the Bight of Benin and surrounding areas was performed. A thorough methodology was developed allowing comparison of population samples using Y-chromosomal lineage data based on different Y-SNP panels and phylogenies. Geographic proximity turned out to be the best predictor of genetic affinity between populations along the Bight of Benin. Nevertheless, based on Y-chromosomal data from the literature two population samples differed strongly from others from the same or neighbouring areas and are not regionally representative within large-scale studies. Furthermore, the analysis of the HapMap sample YRI of a Yoruban population from South-western Nigeria based on Y-SNPs and Y-STR data showed for the first time its regional representativeness, a result which is important for standard population and forensic genetic applications using the YRI sample. Therefore, the uniquely and powerful geographical information carried by the Y-chromosome makes it an important locus to test the representativeness of a certain sample even in the genomic era, especially in poorly investigated areas like Africa.
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15
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González-Santos M, Montinaro F, Oosthuizen O, Oosthuizen E, Busby GBJ, Anagnostou P, Destro-Bisol G, Pascali V, Capelli C. Genome-Wide SNP Analysis of Southern African Populations Provides New Insights into the Dispersal of Bantu-Speaking Groups. Genome Biol Evol 2015; 7:2560-8. [PMID: 26363465 PMCID: PMC4607521 DOI: 10.1093/gbe/evv164] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The expansion of Bantu-speaking agropastoralist populations had a great impact on the genetic, linguistic, and cultural variation of sub-Saharan Africa. It is generally accepted that Bantu languages originated in an area around the present border between Cameroon and Nigeria approximately 5,000 years ago, from where they spread South and East becoming the largest African linguistic branch. The demic consequences of this event are reflected in the relatively high genetic homogeneity observed across most of sub-Saharan Africa populations. In this work, we explored genome-wide single nucleotide polymorphism data from 28 populations to characterize the genetic components present in sub-Saharan African populations. Combining novel data from four Southern African populations with previously published results, we reject the hypothesis that the “non-Bantu” genetic component reported in South-Eastern Africa (Mozambique) reflects extensive gene flow between incoming agriculturalist and resident hunter-gatherer communities. We alternatively suggest that this novel component is the result of demographic dynamics associated with the Bantu dispersal.
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Affiliation(s)
| | - Francesco Montinaro
- Department of Zoology, University of Oxford, United Kingdom Institute of Legal Medicine, Catholic University, Rome, Italy
| | | | | | - George B J Busby
- Department of Zoology, University of Oxford, United Kingdom Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Paolo Anagnostou
- Dipartimento di Biologia Ambientale, Università "La Sapienza", Rome, Italy Istituto Italiano di Antropologia, Rome, Italy
| | - Giovanni Destro-Bisol
- Dipartimento di Biologia Ambientale, Università "La Sapienza", Rome, Italy Istituto Italiano di Antropologia, Rome, Italy
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16
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Kopp GH, Fischer J, Patzelt A, Roos C, Zinner D. Population genetic insights into the social organization of Guinea baboons (Papio papio): Evidence for female-biased dispersal. Am J Primatol 2015; 77:878-89. [PMID: 25864569 PMCID: PMC4654240 DOI: 10.1002/ajp.22415] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 03/06/2015] [Accepted: 03/17/2015] [Indexed: 01/23/2023]
Abstract
Sex differences in philopatry and dispersal have important consequences on the genetic structure of populations, social groups, and social relationships within groups. Among mammals, male dispersal and female philopatry are most common and closely related taxa typically exhibit similar dispersal patterns. However, among four well-studied species of baboons, only hamadryas baboons exhibit female dispersal, thus differing from their congenerics, which show female philopatry and close-knit female social relationships. Until recently, knowledge of the Guinea baboon social system and dispersal pattern remained sparse. Previous observations suggested that the high degree of tolerance observed among male Guinea baboons could be due to kinship. This led us to hypothesize that this species exhibits male philopatry and female dispersal, conforming to the hamadryas pattern. We genotyped 165 individuals from five localities in the Niokolo-Koba National Park, Senegal, at 14 autosomal microsatellite loci and sequenced a fragment of the mitochondrial hypervariable region I (HVRI) of 55 individuals. We found evidence for higher population structuring in males than in females, as expected if males are the more philopatric sex. A comparison of relatedness between male-male and female-female dyads within and among communities did not yield conclusive results. HVRI diversity within communities was high and did not differ between the sexes, also suggesting female gene flow. Our study is the first comprehensive analysis of the genetic population structure in Guinea baboons and provides evidence for female-biased dispersal in this species. In conjunction with their multilevel social organization, this finding parallels the observations for human hunter-gatherers and strengthens baboons as an intriguing model to elucidate the processes that shaped the highly cooperative societies of Homo.
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Affiliation(s)
- Gisela H Kopp
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Julia Fischer
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Annika Patzelt
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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17
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Tofanelli S, Brisighelli F, Anagnostou P, Busby GBJ, Ferri G, Thomas MG, Taglioli L, Rudan I, Zemunik T, Hayward C, Bolnick D, Romano V, Cali F, Luiselli D, Shepherd GB, Tusa S, Facella A, Capelli C. The Greeks in the West: genetic signatures of the Hellenic colonisation in southern Italy and Sicily. Eur J Hum Genet 2015; 24:429-36. [PMID: 26173964 DOI: 10.1038/ejhg.2015.124] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/29/2015] [Accepted: 05/06/2015] [Indexed: 11/09/2022] Open
Abstract
Greek colonisation of South Italy and Sicily (Magna Graecia) was a defining event in European cultural history, although the demographic processes and genetic impacts involved have not been systematically investigated. Here, we combine high-resolution surveys of the variability at the uni-parentally inherited Y chromosome and mitochondrial DNA in selected samples of putative source and recipient populations with forward-in-time simulations of alternative demographic models to detect signatures of that impact. Using a subset of haplotypes chosen to represent historical sources, we recover a clear signature of Greek ancestry in East Sicily compatible with the settlement from Euboea during the Archaic Period (eighth to fifth century BCE). We inferred moderate sex-bias in the numbers of individuals involved in the colonisation: a few thousand breeding men and a few hundred breeding women were the estimated number of migrants. Last, we demonstrate that studies aimed at quantifying Hellenic genetic flow by the proportion of specific lineages surviving in present-day populations may be misleading.
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Affiliation(s)
| | - Francesca Brisighelli
- Department of Zoology, University of Oxford, Oxford, UK.,Sezione di Medicina Legale-Istituto di Sanità Pubblica, Università Cattolica del Sacro Cuore, Roma, Italia
| | - Paolo Anagnostou
- Dipartimento di Biologia Ambientale, Università "La Sapienza", Roma, Italy.,Istituto Italiano di Antropologia, Roma, Italy
| | - George B J Busby
- Department of Zoology, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Gianmarco Ferri
- Dipartimento ad Attività Integrata di Laboratori, Anatomia Patologica, Medicina Legale, U.O. Struttura Complessa di Medicina Legale, Università di Modena e Reggio Emilia, Modena, Italy
| | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Luca Taglioli
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Igor Rudan
- Centre for Population Health Sciences, The University of Edinburgh Medical School, Scotland, UK
| | - Tatijana Zemunik
- Department of Medical Biology, University of Split, School of Medicine, Split, Croatia
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Deborah Bolnick
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Valentino Romano
- Dipartimento di Fisica e Chimica, Università di Palermo, Palermo, Italy.,Laboratorio di Genetica Molecolare, I.R.C.C.S. Associazione Oasi Maria SS., Troina, Italy
| | - Francesco Cali
- Dipartimento di Fisica e Chimica, Università di Palermo, Palermo, Italy
| | - Donata Luiselli
- Laboratorio di Antropologia Molecolare, Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Gillian B Shepherd
- A.D. Trendall Research Centre for Ancient Mediterranean Studies, La Trobe University, Melbourne, Victoria, Australia
| | | | - Antonino Facella
- Soprintendenza per i Beni Archeologici della Calabria, Reggio Calabria, Italy
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18
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Heyer E, Brandenburg JT, Leonardi M, Toupance B, Balaresque P, Hegay T, Aldashev A, Austerlitz F. Patrilineal populations show more male transmission of reproductive success than cognatic populations in Central Asia, which reduces their genetic diversity. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 157:537-43. [PMID: 25821184 DOI: 10.1002/ajpa.22739] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 02/19/2015] [Accepted: 02/22/2015] [Indexed: 11/10/2022]
Abstract
OBJECTIVE The extent to which social organization of human societies impacts the patterns of genetic diversity remains an open question. Here, we investigate the transmission of reproductive success in patrilineal and cognatic populations from Central Asia using a coalescent approach. METHODS We performed a study on the mitochondrial DNA (mtDNA) and Y chromosome polymorphism of patrilineal and cognatic populations from Central Asia. We reconstructed the gene genealogies in each population for both kind of markers and inferred the imbalance level of these genealogies, a parameter directly related to the level of transmission of reproductive success. RESULTS This imbalance level appeared much stronger for the Y chromosome in patrilineal populations than in cognatic populations, while no difference was found for mtDNA. Furthermore, we showed that this imbalance level correlates negatively with Y-chromosomal, mtDNA, and autosomal genetic diversity. CONCLUSIONS This shows that patrilineality might be one of the factors explaining the male transmission of reproductive success, which, in turn, lead to a reduction of genetic diversity. Thus, notwithstanding the fact that our population genetic approach clearly shows that there is a strong male-biased transmission of reproductive success in patrilineal societies, it also highlights the fact that a social process such as cultural transmission of reproductive success could play an important role in shaping human genetic diversity, although we cannot formally exclude that this transmission has also a genetic component.
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Affiliation(s)
- Evelyne Heyer
- Museum National D'histoire Naturelle, CNRS, Université Paris 7 Diderot, Sorbonne Paris Cité, Sorbonne Universités, Unité Eco-Anthropologie Et Ethnobiologie (UMR7206), Paris, France
| | - Jean-Tristan Brandenburg
- Museum National D'histoire Naturelle, CNRS, Université Paris 7 Diderot, Sorbonne Paris Cité, Sorbonne Universités, Unité Eco-Anthropologie Et Ethnobiologie (UMR7206), Paris, France.,INRA, UMR 0320/UMR 8120 Génétique Végétale, Ferme Du Moulon, Gif-sur-Yvette, 91190, France
| | - Michela Leonardi
- Museum National D'histoire Naturelle, CNRS, Université Paris 7 Diderot, Sorbonne Paris Cité, Sorbonne Universités, Unité Eco-Anthropologie Et Ethnobiologie (UMR7206), Paris, France.,Human Evolutionary Anthropology Group, Department of Anthropology, University College London, UK
| | - Bruno Toupance
- Museum National D'histoire Naturelle, CNRS, Université Paris 7 Diderot, Sorbonne Paris Cité, Sorbonne Universités, Unité Eco-Anthropologie Et Ethnobiologie (UMR7206), Paris, France
| | - Patricia Balaresque
- Laboratoire Anthropologie Moléculaire Et Imagerie De Synthèse, Unité Mixte De Recherche 5288 Centre National De La Recherche Scientifique-Université Paul Sabatier, Toulouse, 31073, France
| | - Tanya Hegay
- Academy of Sciences, Institute of Immunology, Tashkent, Uzbekistan
| | - Almaz Aldashev
- National Academy of Sciences of Kyrgyzstan, Bishkek, Kyrgyz Republic
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19
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Marks SJ, Montinaro F, Levy H, Brisighelli F, Ferri G, Bertoncini S, Batini C, Busby GBJ, Arthur C, Mitchell P, Stewart BA, Oosthuizen O, Oosthuizen E, D'Amato ME, Davison S, Pascali V, Capelli C. Static and moving frontiers: the genetic landscape of Southern African Bantu-speaking populations. Mol Biol Evol 2014; 32:29-43. [PMID: 25223418 DOI: 10.1093/molbev/msu263] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A consensus on Bantu-speaking populations being genetically similar has emerged in the last few years, but the demographic scenarios associated with their dispersal are still a matter of debate. The frontier model proposed by archeologists postulates different degrees of interaction among incoming agropastoralist and resident foraging groups in the presence of "static" and "moving" frontiers. By combining mitochondrial DNA and Y chromosome data collected from several southern African populations, we show that Bantu-speaking populations from regions characterized by a moving frontier developing after a long-term static frontier have larger hunter-gatherer contributions than groups from areas where a static frontier was not followed by further spatial expansion. Differences in the female and male components suggest that the process of assimilation of the long-term resident groups into agropastoralist societies was gender biased. Our results show that the diffusion of Bantu languages and culture in Southern Africa was a process more complex than previously described and suggest that the admixture dynamics between farmers and foragers played an important role in shaping the current patterns of genetic diversity.
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Affiliation(s)
- Sarah J Marks
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Francesco Montinaro
- Department of Zoology, University of Oxford, Oxford, United Kingdom Institute of Legal Medicine, Catholic University, Rome, Italy
| | - Hila Levy
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Gianmarco Ferri
- Dipartimento ad Attività Integrata di Laboratori, Anatomia Patologica, Medicina Legale, U.O. Struttura Complessa di Medicina Legale, Azienda Ospedaliero, Universitaria di Modena, Modena, Italy
| | | | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - George B J Busby
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Charles Arthur
- School of Archaeology, University of Oxford, Oxford, United Kingdom
| | - Peter Mitchell
- School of Archaeology, University of Oxford, Oxford, United Kingdom School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | | | - Maria Eugenia D'Amato
- Biotechnology Department, Forensic DNA Laboratory, University of the Western Cape, Bellville, South Africa
| | - Sean Davison
- Biotechnology Department, Forensic DNA Laboratory, University of the Western Cape, Bellville, South Africa
| | | | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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20
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Human migration patterns in Yemen and implications for reconstructing prehistoric population movements. PLoS One 2014; 9:e95712. [PMID: 24759992 PMCID: PMC3997431 DOI: 10.1371/journal.pone.0095712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 03/30/2014] [Indexed: 11/19/2022] Open
Abstract
Population migration has played an important role in human evolutionary history and in the patterning of human genetic variation. A deeper and empirically-based understanding of human migration dynamics is needed in order to interpret genetic and archaeological evidence and to accurately reconstruct the prehistoric processes that comprise human evolutionary history. Current empirical estimates of migration include either short time frames (i.e. within one generation) or partial knowledge about migration, such as proportion of migrants or distance of migration. An analysis of migration that includes both proportion of migrants and distance, and direction over multiple generations would better inform prehistoric reconstructions. To evaluate human migration, we use GPS coordinates from the place of residence of the Yemeni individuals sampled in our study, their birthplaces and their parents' and grandparents' birthplaces to calculate the proportion of migrants, as well as the distance and direction of migration events between each generation. We test for differences in these values between the generations and identify factors that influence the probability of migration. Our results show that the proportion and distance of migration between females and males is similar within generations. In contrast, the proportion and distance of migration is significantly lower in the grandparents' generation, most likely reflecting the decreasing effect of technology. Based on our results, we calculate the proportion of migration events (0.102) and mean and median distances of migration (96 km and 26 km) for the grandparent's generation to represent early times in human evolution. These estimates can serve to set parameter values of demographic models in model-based methods of prehistoric reconstruction, such as approximate Bayesian computation. Our study provides the first empirically-based estimates of human migration over multiple generations in a developing country and these estimates are intended to enable more precise reconstruction of the demographic processes that characterized human evolution.
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21
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Coia V, Capocasa M, Anagnostou P, Pascali V, Scarnicci F, Boschi I, Battaggia C, Crivellaro F, Ferri G, Alù M, Brisighelli F, Busby GBJ, Capelli C, Maixner F, Cipollini G, Viazzo PP, Zink A, Destro Bisol G. Demographic histories, isolation and social factors as determinants of the genetic structure of Alpine linguistic groups. PLoS One 2013; 8:e81704. [PMID: 24312576 PMCID: PMC3847036 DOI: 10.1371/journal.pone.0081704] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 10/15/2013] [Indexed: 11/25/2022] Open
Abstract
Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations we inferred that the joint effect of continued genetic isolation and reduced founding group size may explain the apportionment of genetic diversity observed in all groups. Extending the analysis to other continental populations, we observed that the genetic differentiation of Ladins and German speakers from Europeans is comparable or even greater to that observed for well known outliers like Sardinian and Basques. Finally, we found that in south Tyroleans, the social practice of Geschlossener Hof, a hereditary norm which might have favored male dispersal, coincides with a significant intra-group diversity for mtDNA but not for Y chromosome, a genetic pattern which is opposite to those expected among patrilocal populations. Together with previous evidence regarding the possible effects of “local ethnicity” on the genetic structure of German speakers that have settled in the eastern Italian Alps, this finding suggests that taking socio-cultural factors into account together with geographical variables and linguistic diversity may help unveil some yet to be understood aspects of the genetic structure of European populations.
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MESH Headings
- Chromosomes, Human, Y/genetics
- Demography/history
- Ethnicity/genetics
- Ethnicity/history
- Evolution, Molecular
- Female
- Gene Flow
- Genetic Variation
- History, 15th Century
- History, 16th Century
- History, 17th Century
- History, 18th Century
- History, 19th Century
- History, 20th Century
- History, 21st Century
- Humans
- Linguistics
- Male
- Mitochondria/genetics
- Polymorphism, Single Nucleotide
- White People/ethnology
- White People/genetics
- White People/history
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Affiliation(s)
- Valentina Coia
- Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy
- * E-mail: (VC); (GDB)
| | - Marco Capocasa
- Dipartimento Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
- Istituto Italiano di Antropologia, Rome, Italy
| | - Paolo Anagnostou
- Istituto Italiano di Antropologia, Rome, Italy
- Dipartimento Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Vincenzo Pascali
- Istituto di Medicina Legale e delle Assicurazioni, Università Cattolica di Roma, Rome, Italy
| | - Francesca Scarnicci
- Istituto di Medicina Legale e delle Assicurazioni, Università Cattolica di Roma, Rome, Italy
| | - Ilaria Boschi
- Istituto di Medicina Legale e delle Assicurazioni, Università Cattolica di Roma, Rome, Italy
| | - Cinzia Battaggia
- Dipartimento Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
| | - Federica Crivellaro
- Sezione di Antropologia, Museo Nazionale Preistorico Etnografico “Luigi Pigorini”, Rome, Italy
| | - Gianmarco Ferri
- Dipartimento Integrato di Servizi Diagnostici e di Laboratorio e di Medicina Legale, Università di Modena e Reggio Emilia, Modena, Italy
| | - Milena Alù
- Dipartimento Integrato di Servizi Diagnostici e di Laboratorio e di Medicina Legale, Università di Modena e Reggio Emilia, Modena, Italy
| | - Francesca Brisighelli
- Istituto di Medicina Legale e delle Assicurazioni, Università Cattolica di Roma, Rome, Italy
| | | | - Cristian Capelli
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Frank Maixner
- Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy
| | - Giovanna Cipollini
- Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy
| | - Pier Paolo Viazzo
- Dipartimento Culture, Politica e Società-Sezione Scienze Antropologiche, Università degli Studi di Torino, Turin, Italy
| | - Albert Zink
- Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy
| | - Giovanni Destro Bisol
- Istituto Italiano di Antropologia, Rome, Italy
- Dipartimento Biologia Ambientale, Sapienza Università di Roma, Rome, Italy
- * E-mail: (VC); (GDB)
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Berger B, Niederstätter H, Erhart D, Gassner C, Schennach H, Parson W. Reprint of: High resolution mapping of Y haplogroup G in Tyrol (Austria). Forensic Sci Int Genet 2013; 7:624-631. [DOI: 10.1016/j.fsigen.2013.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Berger B, Niederstätter H, Erhart D, Gassner C, Schennach H, Parson W. High resolution mapping of Y haplogroup G in Tyrol (Austria). Forensic Sci Int Genet 2013; 7:529-36. [PMID: 23948323 DOI: 10.1016/j.fsigen.2013.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 05/08/2013] [Accepted: 05/30/2013] [Indexed: 01/10/2023]
Abstract
The distribution of Y-chromosomal haplogroup G2a (G-P15) in present-day paternal lineages in Tyrol (Austria) was analyzed by applying a high-density regional sampling scheme that also covered remote mountain areas. There is evidence from ancient genetic data for a high frequency of Y-chromosomal haplogroup G in prehistoric populations of Central Europe, whilst nowadays levels well below 10% are routinely observed. A population sample comprising ∼3700 specimens was analyzed for Y-chromosomal variation by genotyping Y-SNPs and Y-STRs. The set of binary markers included nine SNPs specific for sub-lineages of haplogroup G. The frequency of haplogroup G in 2379 unrelated men born in Tyrol amounted to 11.3%. Nearly all of these Y chromosomes belonged to haplogroup G2a. The main sub-haplogroup within G2a was defined by the SNP L497 (G2a3b1c) and reached a population frequency of 8.6%. Although this average level is higher than reported for other countries the geographical distribution of haplogroup G-L497 showed a differentiated pattern with a clustered distribution within some alpine valleys, where maxima above 40% were found. Both, the estimation of coalescent times and a principle coordinates analysis based on RST values derived from Y-STR haplotypes from different sub-regions of Tyrol revealed evidence for an old settlement history associated with Y chromosomes belonging to haplogroup G in the Tyrolean Alps.
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Affiliation(s)
- Burkhard Berger
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria
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Destro Bisol G, Capocasa M, Anagnostou P. When gender matters: new insights into the relationships between social systems and the genetic structure of human populations. Mol Ecol 2013; 21:4917-20. [PMID: 23227491 DOI: 10.1111/mec.12001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Due to its important effects on the ecological dynamics and the genetic structure of species, biologists have long been interested in gender-biased dispersal, a condition where one gender is more prone to move from the natal site. More recently, this topic has attracted a great attention from human evolutionary geneticists. Considering the close relations between residential rules and social structure, gender-biased dispersal is, in fact, regarded as an important case study concerning the effects of socio-cultural factors on human genetic variation. It all started with the seminal paper by Mark Seielstad, Erich Minch and Luigi Luca Cavalli Sforza from Stanford University (Seielstad et al. 1998). They observed a larger differentiation for Y-chromosome than mitochondrial DNA between extant human populations, purportedly a consequence of the prevalence of long-term patrilocality in human societies. Subsequent studies, however, have highlighted the need to consider geographically close and culturally homogeneous groups, disentangle signals due to different peopling events and obtain unbiased estimates of genetic diversity. In this issue of Molecular Ecology, not only do Marks et al. (2012) adopt an experimental design which addresses these concerns, but they also take a further and important step forward by integrating the genetic analysis of two distant populations, the Basotho and Spanish, with data regarding migration rates and matrimonial distances. Using both empirical evidence and simulations, the authors show that female-biased migration due to patrilocality might shape the genetic structure of human populations only at short ranges and under substantial differences in migration rates between genders. Providing a quantitative framework for future studies of the effects of residential rules on the human genome, this study paves the way for further developments in the field. On a wider perspective, Marks et al.'s work demonstrates the power of approaches which integrate biological, cultural and demographic lines of evidence in the study of relations between social and genetic structures of human populations.
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Raaum RL, Al-Meeri A, Mulligan CJ. Culture modifies expectations of kinship and sex-biased dispersal patterns: A case study of patrilineality and patrilocality in tribal yemen. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 150:526-38. [PMID: 23359210 DOI: 10.1002/ajpa.22220] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 12/05/2012] [Indexed: 01/08/2023]
Affiliation(s)
| | - Ali Al-Meeri
- Department of Biochemistry and Molecular Biology; Sana'a University; Sana'a; Yemen
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