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Guyon L, Guez J, Toupance B, Heyer E, Chaix R. Patrilineal segmentary systems provide a peaceful explanation for the post-Neolithic Y-chromosome bottleneck. Nat Commun 2024; 15:3243. [PMID: 38658560 PMCID: PMC11043392 DOI: 10.1038/s41467-024-47618-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
Studies have found a pronounced decline in male effective population sizes worldwide around 3000-5000 years ago. This bottleneck was not observed for female effective population sizes, which continued to increase over time. Until now, this remarkable genetic pattern was interpreted as the result of an ancient structuring of human populations into patrilineal groups (gathering closely related males) violently competing with each other. In this scenario, violence is responsible for the repeated extinctions of patrilineal groups, leading to a significant reduction in male effective population size. Here, we propose an alternative hypothesis by modelling a segmentary patrilineal system based on anthropological literature. We show that variance in reproductive success between patrilineal groups, combined with lineal fission (i.e., the splitting of a group into two new groups of patrilineally related individuals), can lead to a substantial reduction in the male effective population size without resorting to the violence hypothesis. Thus, a peaceful explanation involving ancient changes in social structures, linked to global changes in subsistence systems, may be sufficient to explain the reported decline in Y-chromosome diversity.
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Affiliation(s)
- Léa Guyon
- Eco-Anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Paris, 75116, France.
| | - Jérémy Guez
- Eco-Anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Paris, 75116, France
- Université Paris-Saclay, CNRS, INRIA, Laboratoire Interdisciplinaire des Sciences du Numérique, Orsay, 91400, France
| | - Bruno Toupance
- Eco-Anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Paris, 75116, France
- Université Paris Cité, Eco-anthropologie, Paris, F-75006, France
| | - Evelyne Heyer
- Eco-Anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Paris, 75116, France
| | - Raphaëlle Chaix
- Eco-Anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Paris, 75116, France.
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2
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Karmin M, Flores R, Saag L, Hudjashov G, Brucato N, Crenna-Darusallam C, Larena M, Endicott PL, Jakobsson M, Lansing JS, Sudoyo H, Leavesley M, Metspalu M, Ricaut FX, Cox MP. Episodes of Diversification and Isolation in Island Southeast Asian and Near Oceanian Male Lineages. Mol Biol Evol 2022; 39:msac045. [PMID: 35294555 PMCID: PMC8926390 DOI: 10.1093/molbev/msac045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Island Southeast Asia (ISEA) and Oceania host one of the world's richest assemblages of human phenotypic, linguistic, and cultural diversity. Despite this, the region's male genetic lineages are globally among the last to remain unresolved. We compiled ∼9.7 Mb of Y chromosome (chrY) sequence from a diverse sample of over 380 men from this region, including 152 first reported here. The granularity of this data set allows us to fully resolve and date the regional chrY phylogeny. This new high-resolution tree confirms two main population bursts: multiple rapid diversifications following the region's initial settlement ∼50 kya, and extensive expansions <6 kya. Notably, ∼40-25 kya the deep rooting local lineages of C-M130, M-P256, and S-B254 show almost no further branching events in ISEA, New Guinea, and Australia, matching a similar pause in diversification seen in maternal mitochondrial DNA lineages. The main local lineages start diversifying ∼25 kya, at the time of the last glacial maximum. This improved chrY topology highlights localized events with important historical implications, including pre-Holocene contact between Mainland and ISEA, potential interactions between Australia and the Papuan world, and a sustained period of diversification following the flooding of the ancient Sunda and Sahul continents as the insular landscape observed today formed. The high-resolution phylogeny of the chrY presented here thus enables a detailed exploration of past isolation, interaction, and change in one of the world's least understood regions.
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Affiliation(s)
- Monika Karmin
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Rodrigo Flores
- Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Lauri Saag
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Georgi Hudjashov
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Nicolas Brucato
- Laboratoire Evolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, Toulouse, France
| | - Chelzie Crenna-Darusallam
- Genome Diversity and Disease Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Maximilian Larena
- Department of Organismal Biology, University of Uppsala, Uppsala, Sweden
| | - Phillip L Endicott
- Institute of Genomics, University of Tartu, Tartu, Estonia
- Department Hommes Natures Societies, Musée de l’Homme, Paris, France
| | - Mattias Jakobsson
- Department of Organismal Biology, University of Uppsala, Uppsala, Sweden
| | - J Stephen Lansing
- Complexity Science Hub Vienna, Vienna, Austria
- Santa Fe Institute Center for Advanced Study in the Behavioral Sciences, Stanford University, Santa Fe, USA
| | - Herawati Sudoyo
- Genome Diversity and Disease Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Matthew Leavesley
- School of Humanities and Social Sciences, University of Papua New Guinea, National Capital District, Papua New Guinea
- CABAH and College of Arts, Society and Education, James Cook University, Cairns, QLD, Australia
| | - Mait Metspalu
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - François-Xavier Ricaut
- Laboratoire Evolution et Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, Toulouse, France
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
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3
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Charles A, Penggoam S, Maskoen AM, Sahiratmadja E. Influence of TLR-8 Gene Polymorphisms (rs3764880 and rs3788935) Associated to Pulmonary Tuberculosis in Kupang, Indonesia. INDONESIAN JOURNAL OF TROPICAL AND INFECTIOUS DISEASE 2021. [DOI: 10.20473/ijtid.v9i1.22056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Toll-like receptor 8 (TLR-8) is known as part of intracellular signaling transduction for bacterial phagocytosis. Mycobacterium tuberculosis (Mtb) is intracellular pathogenic bacteria that is recognized by this receptor, and genetic variation of TLR-8 might alter susceptibility of the host towards pulmonary tuberculosis (PTB). This study aimed to determine whether TLR-8 gene polymorphisms were associated to PTB in Kupang, Indonesia. This case-control study compared demographic and clinical data between 115 PTB patients and 115 controls, then two TLR-8 single nucleotide polymorphisms (rs3764880 and rs3788935) were explored using the GoldenGate® Genotyping for VeraCode® / BeadXpress Illumina®. There is no significant difference between sex distribution of patient vs control groups. The polymorphisms (rs3764880 and rs3788935) are in Hardy-Weinberg Equilibrium in this population (p > 0.05). The distribution of major vs minor genotypes and alleles of TLR-8 polymorphisms in PTB patients were as followed: rs3764880 (GG vs GA vs AA, 50.0% vs 21.4% vs 28.6% ; G vs A, 60.9% vs 39.1% ) and rs3788935 (GG vs GA vs AA, 53.0% vs 21.7% vs 25.3%; G vs A, 62.9% vs 37.1%). Neither genotypes nor alleles were associated with PTB in this population (P > 0.05). Besides, when the analyses were stratified by gender, none of the alleles of polymorphism in both genders were associated with PTB cases. None of the TLR-8 polymorphisms have associated the risk of developing PTB in Kupang, East Nusa Tenggara population (as opposed to other studies in different ethnic groups). These might reflect the diversity of genetic polymorphisms in eastern Indonesia populations, suggesting different genetic backgrounds with western part of Indonesia.
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Ly G, Laurent R, Lafosse S, Monidarin C, Diffloth G, Bourdier F, Evrard O, Toupance B, Pavard S, Chaix R. From matrimonial practices to genetic diversity in Southeast Asian populations: the signature of the matrilineal puzzle. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180434. [PMID: 31303171 PMCID: PMC6664126 DOI: 10.1098/rstb.2018.0434] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2019] [Indexed: 01/27/2023] Open
Abstract
In matrilineal populations, the descent group affiliation is transmitted by women whereas the socio-political power frequently remains in the hands of men. This situation, named the 'matrilineal puzzle', is expected to promote local endogamy as a coping mechanism allowing men to maintain their decision-making power over their natal descent group. In this paper, we revisit this 'matrilineal puzzle' from a population genetics' point of view. Indeed, such tendency for local endogamy in matrilineal populations is expected to increase their genetic inbreeding and generate isolation-by-distance patterns between villages. To test this hypothesis, we collected ethno-demographic data for 3261 couples and high-density genetic data for 675 individuals from 11 Southeast Asian populations with a wide range of social organizations: matrilineal and matrilocal populations (M), patrilineal and patrilocal populations (P) or cognatic populations with predominant matrilocal residence (C). We observed that M and C populations have higher levels of village endogamy than P populations, and that such higher village endogamy leads to higher genetic inbreeding. M populations also exhibit isolation-by-distance patterns between villages. We interpret such genetic patterns as the signature of the 'matrilineal puzzle'. Notably, our results suggest that any form of matrilocal marriage (whatever the descent rule is) increases village endogamy. These findings suggest that male dominance, when combined with matrilocality, constrains inter-village migrations, and constitutes an underexplored cultural process shaping genetic patterns in human populations. This article is part of the theme issue 'The evolution of female-biased kinship in humans and other mammals'.
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Affiliation(s)
- Goki Ly
- Unité Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université de Paris, 17 place du Trocadéro, 75016 Paris, France
| | - Romain Laurent
- Unité Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université de Paris, 17 place du Trocadéro, 75016 Paris, France
| | - Sophie Lafosse
- Unité Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université de Paris, 17 place du Trocadéro, 75016 Paris, France
| | - Chou Monidarin
- Rodolphe Merieux Laboratory and Faculty of Pharmacy of University of Health Sciences, Phnom Penh, Cambodia
| | | | - Frédéric Bourdier
- Unité 201 Développement et Sociétés (DEVSOC), IEDES/IRD, Panthéon Sorbonne, Paris, France
| | - Olivier Evrard
- Unité Patrimoines Locaux et Gouvernance (PALOC), Muséum National d'Histoire Naturelle, CNRS, IRD, 75006 Paris, France
| | - Bruno Toupance
- Unité Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université de Paris, 17 place du Trocadéro, 75016 Paris, France
| | - Samuel Pavard
- Unité Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université de Paris, 17 place du Trocadéro, 75016 Paris, France
| | - Raphaëlle Chaix
- Unité Eco-anthropologie (EA), Muséum National d'Histoire Naturelle, CNRS, Université de Paris, 17 place du Trocadéro, 75016 Paris, France
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Chung NN, Jacobs GS, Sudoyo H, Malik SG, Chew LY, Lansing JS, Cox MP. Sex-linked genetic diversity originates from persistent sociocultural processes at microgeographic scales. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190733. [PMID: 31598251 PMCID: PMC6731738 DOI: 10.1098/rsos.190733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/26/2019] [Indexed: 06/10/2023]
Abstract
Population genetics has been successful at identifying the relationships between human groups and their interconnected histories. However, the link between genetic demography inferred at large scales and the individual human behaviours that ultimately generate that demography is not always clear. While anthropological and historical context are routinely presented as adjuncts in population genetic studies to help describe the past, determining how underlying patterns of human sociocultural behaviour impact genetics still remains challenging. Here, we analyse patterns of genetic variation in village-scale samples from two islands in eastern Indonesia, patrilocal Sumba and a matrilocal region of Timor. Adopting a 'process modelling' approach, we iteratively explore combinations of structurally different models as a thinking tool. We find interconnected socio-genetic interactions involving sex-biased migration, lineage-focused founder effects, and on Sumba, heritable social dominance. Strikingly, founder ideology, a cultural model derived from anthropological and archaeological studies at larger regional scales, has both its origins and impact at the scale of villages. Process modelling lets us explore these complex interactions, first by circumventing the complexity of formal inference when studying large datasets with many interacting parts, and then by explicitly testing complex anthropological hypotheses about sociocultural behaviour from a more familiar population genetic standpoint.
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Affiliation(s)
- Ning Ning Chung
- Complexity Institute, Nanyang Technological University, Singapore
- Centre for University Core, Singapore University of Social Sciences, Singapore
| | - Guy S. Jacobs
- Complexity Institute, Nanyang Technological University, Singapore
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
- Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
- Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Safarina G. Malik
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Lock Yue Chew
- Complexity Institute, Nanyang Technological University, Singapore
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - J. Stephen Lansing
- Santa Fe Institute, Santa Fe, NM 87501, USA
- Stockholm Resilience Center, Kräftriket, 10405 Stockholm, Sweden
| | - Murray P. Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand
- Te Pūnaha Matatini, Centre of Research Excellence for Complex Systems, Aukland, New Zealand
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6
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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: 14] [Impact Index Per Article: 2.0] [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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7
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Abstract
Associations between genes and languages occur even with sustained migration among communities. By comparing phylogenies of genes and languages, we identify one source of this association. In traditional tribal societies, marriage customs channel language transmission. When women remain in their natal community and men disperse (matrilocality), children learn their mothers’ language, and language correlates with maternally inherited mitochondrial DNA. For the converse kinship practice (patrilocality), language instead correlates with paternally inherited Y chromosome. Kinship rules dictating postmarital residence can persist for many generations and determine population genetic structure at the community scale. The long-term association of languages with genetic clades created by kinship systems provides information about language transmission, and about the structure and persistence of social groups. Languages are transmitted through channels created by kinship systems. Given sufficient time, these kinship channels can change the genetic and linguistic structure of populations. In traditional societies of eastern Indonesia, finely resolved cophylogenies of languages and genes reveal persistent movements between stable speech communities facilitated by kinship rules. When multiple languages are present in a region and postmarital residence rules encourage sustained directional movement between speech communities, then languages should be channeled along uniparental lines. We find strong evidence for this pattern in 982 individuals from 25 villages on two adjacent islands, where different kinship rules have been followed. Core groups of close relatives have stayed together for generations, while remaining in contact with, and marrying into, surrounding groups. Over time, these kinship systems shaped their gene and language phylogenies: Consistently following a postmarital residence rule turned social communities into speech communities.
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8
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Gomes SM, van Oven M, Souto L, Morreira H, Brauer S, Bodner M, Zimmermann B, Huber G, Strobl C, Röck AW, Côrte-Real F, Parson W, Kayser M. Lack of gene-language correlation due to reciprocal female but directional male admixture in Austronesians and non-Austronesians of East Timor. Eur J Hum Genet 2017; 25:246-252. [PMID: 27485412 PMCID: PMC5255940 DOI: 10.1038/ejhg.2016.101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 06/13/2016] [Accepted: 06/21/2016] [Indexed: 11/08/2022] Open
Abstract
Nusa Tenggara, including East Timor, located at the crossroad between Island Southeast Asia, Near Oceania, and Australia, are characterized by a complex cultural structure harbouring speakers from two different major linguistic groups of different geographic origins (Austronesian (AN) and non-Austronesian (NAN)). This provides suitable possibilities to study gene-language relationship; however, previous studies from other parts of Nusa Tenggara reported conflicting evidence about gene-language correlation in this region. Aiming to investigate gene-language relationships including sex-mediated aspects in East Timor, we analysed the paternally inherited non-recombining part of the Y chromosome (NRY) and the maternally inherited mitochondrial (mt) DNA in a representative collection of AN- and NAN-speaking groups. Y-SNP (single-nucleotide polymorphism) data were newly generated for 273 samples and combined with previously established Y-STR (short tandem repeat) data of the same samples, and with previously established mtDNA data of 290 different samples with, however, very similar representation of geographic and linguistic coverage of the country. We found NRY and mtDNA haplogroups of previously described putative East/Southeast Asian (E/SEA) and Near Oceanian (NO) origins in both AN and NAN speakers of East Timor, albeit in different proportions, suggesting reciprocal genetic admixture between both linguistic groups for females, but directional admixture for males. Our data underline the dual genetic origin of East Timorese in E/SEA and NO, and highlight that substantial genetic admixture between the two major linguistic groups had occurred, more so via women than men. Our study therefore provides another example where languages and genes do not conform due to sex-biased genetic admixture across major linguistic groups.
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Affiliation(s)
- Sibylle M Gomes
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal
| | - Mannis van Oven
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Luis Souto
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal
| | - Helena Morreira
- Department of Biology, University of Aveiro, Campus de Santiago, Aveiro, Portugal
| | - Silke Brauer
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Bettina Zimmermann
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Gabriela Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Christina Strobl
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexander W Röck
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
- Forensic Science Program, The Pennsylvania State University, University Park, PA, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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9
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Vallée F, Luciani A, Cox MP. Reconstructing Demography and Social Behavior During the Neolithic Expansion from Genomic Diversity Across Island Southeast Asia. Genetics 2016; 204:1495-1506. [PMID: 27683274 PMCID: PMC5161281 DOI: 10.1534/genetics.116.191379] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/16/2016] [Indexed: 11/18/2022] Open
Abstract
Archaeology, linguistics, and increasingly genetics are clarifying how populations moved from mainland Asia, through Island Southeast Asia, and out into the Pacific during the farming revolution. Yet key features of this process remain poorly understood, particularly how social behaviors intersected with demographic drivers to create the patterns of genomic diversity observed across Island Southeast Asia today. Such questions are ripe for computer modeling. Here, we construct an agent-based model to simulate human mobility across Island Southeast Asia from the Neolithic period to the present, with a special focus on interactions between individuals with Asian, Papuan, and mixed Asian-Papuan ancestry. Incorporating key features of the region, including its complex geography (islands and sea), demographic drivers (fecundity and migration), and social behaviors (marriage preferences), the model simultaneously tracks a full suite of genomic markers (autosomes, X chromosome, mitochondrial DNA, and Y chromosome). Using Bayesian inference, model parameters were determined that produce simulations that closely resemble the admixture profiles of 2299 individuals from 84 populations across Island Southeast Asia. The results highlight that greater propensity to migrate and elevated birth rates are related drivers behind the expansion of individuals with Asian ancestry relative to individuals with Papuan ancestry, that offspring preferentially resulted from marriages between Asian women and Papuan men, and that in contrast to current thinking, individuals with Asian ancestry were likely distributed across large parts of western Island Southeast Asia before the Neolithic expansion.
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Affiliation(s)
- François Vallée
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Aurélien Luciani
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
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10
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Creanza N, Feldman MW. Worldwide genetic and cultural change in human evolution. Curr Opin Genet Dev 2016; 41:85-92. [PMID: 27644074 DOI: 10.1016/j.gde.2016.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 08/04/2016] [Accepted: 08/19/2016] [Indexed: 01/04/2023]
Abstract
Both genetic variation and certain culturally transmitted phenotypes show geographic signatures of human demographic history. As a result of the human cultural predisposition to migrate to new areas, humans have adapted to a large number of different environments. Migration to new environments alters genetic selection pressures, and comparative genetic studies have pinpointed numerous likely targets of this selection. However, humans also exhibit many cultural adaptations to new environments, such as practices related to clothing, shelter, and food. Human culture interacts with genes and the environment in complex ways, and studying genes and culture together can deepen our understanding of human evolution.
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Affiliation(s)
- Nicole Creanza
- Department of Biology Stanford University, Gilbert Hall, 371 Serra Mall, Stanford, CA 94305, United States; Department of Biological Sciences, Vanderbilt University, 465 21st Ave. South, Nashville, TN 37212, United States.
| | - Marcus W Feldman
- Department of Biology Stanford University, Gilbert Hall, 371 Serra Mall, Stanford, CA 94305, United States
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11
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Cox MP, Hudjashov G, Sim A, Savina O, Karafet TM, Sudoyo H, Lansing JS. Small Traditional Human Communities Sustain Genomic Diversity over Microgeographic Scales despite Linguistic Isolation. Mol Biol Evol 2016; 33:2273-84. [PMID: 27274003 PMCID: PMC4989104 DOI: 10.1093/molbev/msw099] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
At least since the Neolithic, humans have largely lived in networks of small, traditional communities. Often socially isolated, these groups evolved distinct languages and cultures over microgeographic scales of just tens of kilometers. Population genetic theory tells us that genetic drift should act quickly in such isolated groups, thus raising the question: do networks of small human communities maintain levels of genetic diversity over microgeographic scales? This question can no longer be asked in most parts of the world, which have been heavily impacted by historical events that make traditional society structures the exception. However, such studies remain possible in parts of Island Southeast Asia and Oceania, where traditional ways of life are still practiced. We captured genome-wide genetic data, together with linguistic records, for a case-study system-eight villages distributed across Sumba, a small, remote island in eastern Indonesia. More than 4,000 years after these communities were established during the Neolithic period, most speak different languages and can be distinguished genetically. Yet their nuclear diversity is not reduced, instead being comparable to other, even much larger, regional groups. Modeling reveals a separation of time scales: while languages and culture can evolve quickly, creating social barriers, sporadic migration averaged over many generations is sufficient to keep villages linked genetically. This loosely-connected network structure, once the global norm and still extant on Sumba today, provides a living proxy to explore fine-scale genome dynamics in the sort of small traditional communities within which the most recent episodes of human evolution occurred.
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Affiliation(s)
- Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Georgi Hudjashov
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Andre Sim
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Olga Savina
- ARL Division of Biotechnology, University of Arizona
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Morrison MA, Magalhaes TR, Ramke J, Smith SE, Ennis S, Simpson CL, Portas L, Murgia F, Ahn J, Dardenne C, Mayne K, Robinson R, Morgan DJ, Brian G, Lee L, Woo SJ, Zacharaki F, Tsironi EE, Miller JW, Kim IK, Park KH, Bailey-Wilson JE, Farrer LA, Stambolian D, DeAngelis MM. Ancestry of the Timorese: age-related macular degeneration associated genotype and allele sharing among human populations from throughout the world. Front Genet 2015. [PMID: 26217379 PMCID: PMC4496576 DOI: 10.3389/fgene.2015.00238] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We observed that the third leading cause of blindness in the world, age-related macular degeneration (AMD), occurs at a very low documented frequency in a population-based cohort from Timor-Leste. Thus, we determined a complete catalog of the ancestry of the Timorese by analysis of whole exome chip data and haplogroup analysis of SNP genotypes determined by sequencing the Hypervariable I and II regions of the mitochondrial genome and 17 genotyped YSTR markers obtained from 535 individuals. We genotyped 20 previously reported AMD-associated SNPs in the Timorese to examine their allele frequencies compared to and between previously documented AMD cohorts of varying ethnicities. For those without AMD (average age > 55 years), genotype and allele frequencies were similar for most SNPs with a few exceptions. The major risk allele of HTRA1 rs11200638 (10q26) was at a significantly higher frequency in the Timorese, as well as 3 of the 5 protective CFH (1q32) SNPs (rs800292, rs2284664, and rs12066959). Additionally, the most commonly associated AMD-risk SNP, CFH rs1061170 (Y402H), was also seen at a much lower frequency in the Korean and Timorese populations than in the assessed Caucasian populations (C ~7 vs. ~40%, respectively). The difference in allele frequencies between the Timorese population and the other genotyped populations, along with the haplogroup analysis, also highlight the genetic diversity of the Timorese. Specifically, the most common ancestry groupings were Oceanic (Melanesian and Papuan) and Eastern Asian (specifically Han Chinese). The low prevalence of AMD in the Timorese population (2 of 535 randomly selected participants) may be due to the enrichment of protective alleles in this population at the 1q32 locus.
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Affiliation(s)
- Margaux A Morrison
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Tiago R Magalhaes
- National Children's Research Centre, Our Lady's Children's Hospital Dublin, Ireland ; Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin Dublin, Ireland
| | | | - Silvia E Smith
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Sean Ennis
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin Dublin, Ireland ; National Centre for Medical Genetics, Our Lady's Children's Hospital Dublin, Ireland
| | - Claire L Simpson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health Baltimore, MD, USA
| | - Laura Portas
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health Baltimore, MD, USA ; Institute of Population Genetics, The National Research Council Sassari, Italy
| | - Federico Murgia
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health Baltimore, MD, USA ; Institute of Population Genetics, The National Research Council Sassari, Italy
| | - Jeeyun Ahn
- Department of Ophthalmology, Seoul National University College of Medicine Seoul, South Korea ; Department of Ophthalmology, Seoul Metropolitan Government Seoul National University Boramae Medical Center Seoul, South Korea
| | - Caitlin Dardenne
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Katie Mayne
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Rosann Robinson
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Denise J Morgan
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
| | - Garry Brian
- The Fred Hollows Foundation New Zealand Auckland, New Zealand
| | - Lucy Lee
- The Fred Hollows Foundation New Zealand Auckland, New Zealand ; London School of Hygiene and Tropical Medicine, University of London London, UK
| | - Se J Woo
- Department of Ophthalmology, Seoul National University College of Medicine Seoul, South Korea ; Department of Ophthalmology, Seoul National University Bundang Hospital Seoungnam, South Korea
| | - Fani Zacharaki
- Department of Ophthalmology, University of Thessaly School of Medicine Larissa, Greece
| | - Evangelia E Tsironi
- Department of Ophthalmology, University of Thessaly School of Medicine Larissa, Greece
| | - Joan W Miller
- Retina Service and Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School Boston, MA, USA
| | - Ivana K Kim
- Retina Service and Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School Boston, MA, USA
| | - Kyu H Park
- Department of Ophthalmology, Seoul National University College of Medicine Seoul, South Korea ; Department of Ophthalmology, Seoul National University Bundang Hospital Seoungnam, South Korea
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health Baltimore, MD, USA
| | - Lindsay A Farrer
- Departments of Medicine, Ophthalmology, Neurology, Epidemiology, and Biostatistics, Boston University Schools of Medicine and Public Health Boston, MA, USA
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania Philadelphia, PA, USA
| | - Margaret M DeAngelis
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah Salt Lake City, UT, USA
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Maternal ancestry and population history from whole mitochondrial genomes. INVESTIGATIVE GENETICS 2015; 6:3. [PMID: 25798216 PMCID: PMC4367903 DOI: 10.1186/s13323-015-0022-2] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/04/2015] [Indexed: 01/12/2023]
Abstract
MtDNA has been a widely used tool in human evolutionary and population genetic studies over the past three decades. Its maternal inheritance and lack of recombination have offered the opportunity to explore genealogical relationships among individuals and to study the frequency differences of matrilineal clades among human populations at continental and regional scales. The whole mtDNA genome sequencing delivers molecular resolution that is sufficient to distinguish patterns that have arisen over thousands of years. However, mutation rate is highly variable among the functional and non-coding domains of mtDNA which makes it challenging to obtain accurate split dates of the mitochondrial clades. Due to the shallow coalescent time of mitochondrial TMRCA at approximately 100 to 200 thousand years (ky), mtDNA data have only limited power to inform us about the more distant past and the early stages of human evolutionary history. The variation shared by mitochondrial genomes of individuals drawn from different continents outside Africa has been used to illuminate the details of the colonization process of the Old World, whereas regional patterns of variation have been at the focus of studies addressing questions of a more recent time scale. In the era of whole nuclear genome sequencing, mitochondrial genomes are continuing to be informative as a unique tool for the assessment of female-specific aspects of the demographic history of human populations.
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