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Boucher RD, Wittig RM, Lemoine SRT, Maro A, Wang X, Koch PL, Oelze VM. Strontium isotopes track female dispersal in Taï chimpanzees. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 184:e24981. [PMID: 38828504 DOI: 10.1002/ajpa.24981] [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] [Received: 12/23/2023] [Revised: 04/08/2024] [Accepted: 05/14/2024] [Indexed: 06/05/2024]
Abstract
OBJECTIVES Chimpanzees (Pan troglodytes) are patrilocal, with males remaining in their natal community and females dispersing when they reach sexual maturity. However, the details of female chimpanzee dispersal, such as their possible origin, are difficult to assess, even in habituated communities. This study investigates the utility of 87Sr/86Sr analysis for (1) assessing Sr baseline differences between chimpanzee territories and (2) identifying the status (immigrant or natal) of females of unknown origin within the territories of five neighboring communities in Taï National Park (Côte d'Ivoire). MATERIALS AND METHODS To create a local Sr isoscape for the Taï Chimpanzee Project (TCP) study area, we sampled environmental samples from TCP-established territories (n = 35). To assess dispersal patterns, 34 tooth enamel samples (one per individual) were selected from the Taï chimpanzee skeletal collection. 87Sr/86Sr analysis was performed on all 69 samples at the W.M. Keck Lab. The theoretical density and overlap of chimpanzee communities as well as generalized linear mixed models (GLMMs) were used to test each question. RESULTS 87Sr/86Sr ratios for natal male chimpanzees ranged from 0.71662 to 0.72187, which is well within the corresponding environmental baseline range of 0.70774-0.73460. The local Sr isoscapes fit was estimated with the root-mean-square error value, which was 0.0048 (22% of the whole 87Sr/86Sr data range). GLMMs identified significant differences in 87Sr/86Sr ratios between natal and unknown North community origin groups, suggesting that after 1980, females of unknown origin could be immigrants to North community (n = 7, z-ratio = -4.08, p = 0.0001, power = 0.94). DISCUSSION This study indicates that 87Sr/86This study indicates that 87Sr/86Sr analysis can successfully identify immigrant females in skeletal collections obtained from wild chimpanzee communities, enabling the tracking of female dispersal patterns historically. There are, however, significant limitations within the scope of this study, such as (1) the absence of reliable maps for the TCP study area, (2) limited capacity for environmental sampling, (3) small sample sizes, and (4) tooth formation in wild chimpanzees.
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Affiliation(s)
- Renee D Boucher
- Department of Anthropology, University of California, Santa Cruz, California, USA
| | - Roman M Wittig
- Institute for Cognitive Sciences, UMR5229 CNRS, University of Lyon 1, Bron cedex, France
- Taï Chimpanzee Project, CSRS, Abidjan, Côte d'Ivoire
| | | | - Aleksey Maro
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Xueye Wang
- Department of Anthropology, University of California, Santa Cruz, California, USA
- Center for Archaeological Science, Sichuan University, Chengdu, China
| | - Paul L Koch
- Department of Earth and Planetary Sciences, University of California, Santa Cruz, California, USA
| | - Vicky M Oelze
- Department of Anthropology, University of California, Santa Cruz, California, USA
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2
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Hamilton MI, Copeland SR, Nelson SV. A reanalysis of strontium isotope ratios as indicators of dispersal in South African hominins. J Hum Evol 2024; 187:103480. [PMID: 38159536 DOI: 10.1016/j.jhevol.2023.103480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024]
Abstract
Dispersal patterns in primates have major implications for behavior and sociality but are difficult to reconstruct for fossil species. This study applies novel strontium isotope methodologies that have reliably predicted philopatry and dispersal patterns in chimpanzees and other modern primates to previously published strontium isotope ratios (87Sr/86Sr) of two South African hominins, Australopithecus africanus and Australopithecus robustus. In this study, the difference or 'offset' was calculated between the 87Sr/86Sr of each fossil tooth compared to local bioavailable 87Sr/86Sr as defined by cluster analysis of modern plant isotope ratios. Large teeth (presumably belonging to males) have low offsets from local 87Sr/86Sr proxies, while small teeth (presumably from females) have greater offsets from local 87Sr/86Sr proxies. This supports previous conclusions of male philopatry and female dispersal in both A. africanus and A. robustus. Furthermore, A. robustus shows more extreme differences between presumed males and females compared to A. africanus. This is analogous to differences seen in modern olive baboons compared to chimpanzees and suggests that A. africanus may have had a larger home range than A. robustus. Neither hominin species has 87Sr/86Sr consistent with riparian habitat preferences despite the demonstrated presence of riparian habitats in South Africa at the time.
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Affiliation(s)
- Marian I Hamilton
- University of New Mexico, Department of Anthropology, MSC01-1040 1, Albuquerque, NM, 87131, USA; University of Northern Colorado, Department of Anthropology, Candelaria Hall 2200, Campus Box 90, Greeley, CO, 80639, USA.
| | - Sandi R Copeland
- Environmental Stewardship Group, Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, NM, 87545, USA
| | - Sherry V Nelson
- University of New Mexico, Department of Anthropology, MSC01-1040 1, Albuquerque, NM, 87131, USA
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3
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Cotter DJ, Webster TH, Wilson MA. Genomic and demographic processes differentially influence genetic variation across the human X chromosome. PLoS One 2023; 18:e0287609. [PMID: 37910456 PMCID: PMC10619814 DOI: 10.1371/journal.pone.0287609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/08/2023] [Indexed: 11/03/2023] Open
Abstract
Many forces influence genetic variation across the genome including mutation, recombination, selection, and demography. Increased mutation and recombination both lead to increases in genetic diversity in a region-specific manner, while complex demographic patterns shape patterns of diversity on a more global scale. While these processes act across the entire genome, the X chromosome is particularly interesting because it contains several distinct regions that are subject to different combinations and strengths of these forces: the pseudoautosomal regions (PARs) and the X-transposed region (XTR). The X chromosome thus can serve as a unique model for studying how genetic and demographic forces act in different contexts to shape patterns of observed variation. We therefore sought to explore diversity, divergence, and linkage disequilibrium in each region of the X chromosome using genomic data from 26 human populations. Across populations, we find that both diversity and substitution rate are consistently elevated in PAR1 and the XTR compared to the rest of the X chromosome. In contrast, linkage disequilibrium is lowest in PAR1, consistent with the high recombination rate in this region, and highest in the region of the X chromosome that does not recombine in males. However, linkage disequilibrium in the XTR is intermediate between PAR1 and the autosomes, and much lower than the non-recombining X. Finally, in addition to these global patterns, we also observed variation in ratios of X versus autosomal diversity consistent with population-specific evolutionary history as well. While our results were generally consistent with previous work, two unexpected observations emerged. First, our results suggest that the XTR does not behave like the rest of the recombining X and may need to be evaluated separately in future studies. Second, the different regions of the X chromosome appear to exhibit unique patterns of linked selection across different human populations. Together, our results highlight profound regional differences across the X chromosome, simultaneously making it an ideal system for exploring the action of evolutionary forces as well as necessitating its careful consideration and treatment in genomic analyses.
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Affiliation(s)
- Daniel J. Cotter
- Department of Genetics, Stanford University, Stanford, CA, United States of America
| | - Timothy H. Webster
- Department of Anthropology, University of Utah, Salt Lake City, UT, United States of America
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
- Center for Evolution and Medicine, Biodesign Institute, Arizona State University, Tempe, AZ, United States of America
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4
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Korunes KL, Soares-Souza GB, Bobrek K, Tang H, Araújo II, Goldberg A, Beleza S. Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans. G3 (BETHESDA, MD.) 2022; 12:jkac183. [PMID: 35861404 PMCID: PMC9526050 DOI: 10.1093/g3journal/jkac183] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/21/2022] [Indexed: 11/22/2022]
Abstract
Genetic data can provide insights into population history, but first, we must understand the patterns that complex histories leave in genomes. Here, we consider the admixed human population of Cabo Verde to understand the patterns of genetic variation left by social and demographic processes. First settled in the late 1400s, Cabo Verdeans are admixed descendants of Portuguese colonizers and enslaved West African people. We consider Cabo Verde's well-studied historical record alongside genome-wide SNP data from 563 individuals from 4 regions within the archipelago. We use genetic ancestry to test for patterns of nonrandom mating and sex-specific gene flow, and we examine the consequences of these processes for common demographic inference methods and genetic patterns. Notably, multiple population genetic tools that assume random mating underestimate the timing of admixture, but incorporating nonrandom mating produces estimates more consistent with historical records. We consider how admixture interrupts common summaries of genomic variation such as runs of homozygosity. While summaries of runs of homozygosity may be difficult to interpret in admixed populations, differentiating runs of homozygosity by length class shows that runs of homozygosity reflect historical differences between the islands in their contributions from the source populations and postadmixture population dynamics. Finally, we find higher African ancestry on the X chromosome than on the autosomes, consistent with an excess of European males and African females contributing to the gene pool. Considering these genomic insights into population history in the context of Cabo Verde's historical record, we can identify how assumptions in genetic models impact inference of population history more broadly.
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Affiliation(s)
| | | | - Katherine Bobrek
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Isabel Inês Araújo
- Faculdade de Ciências e Tecnologia, Universidade de Cabo Verde (Uni-CV), Praia, Ilha de Santiago CP 379C, Cabo Verde
| | - Amy Goldberg
- Evolutionary Anthropology, Duke University, Durham, NC 27705, USA
| | - Sandra Beleza
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
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5
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Huszar TI, Bodmer WF, Hutnik K, Wetton JH, Jobling MA. Sequencing of autosomal, mitochondrial and Y-chromosomal forensic markers in the People of the British Isles cohort detects population structure dominated by patrilineages. Forensic Sci Int Genet 2022; 59:102725. [DOI: 10.1016/j.fsigen.2022.102725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/08/2022] [Accepted: 05/13/2022] [Indexed: 11/27/2022]
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6
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Ji T, Zhang H, Pagel M, Mace R. A phylogenetic analysis of dispersal norms, descent and subsistence in Sino-Tibetans. EVOL HUM BEHAV 2022. [DOI: 10.1016/j.evolhumbehav.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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7
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Sirak KA, Fernandes DM, Lipson M, Mallick S, Mah M, Olalde I, Ringbauer H, Rohland N, Hadden CS, Harney É, Adamski N, Bernardos R, Broomandkhoshbacht N, Callan K, Ferry M, Lawson AM, Michel M, Oppenheimer J, Stewardson K, Zalzala F, Patterson N, Pinhasi R, Thompson JC, Van Gerven D, Reich D. Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia. Nat Commun 2021; 12:7283. [PMID: 34907168 PMCID: PMC8671435 DOI: 10.1038/s41467-021-27356-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 11/16/2021] [Indexed: 12/23/2022] Open
Abstract
Relatively little is known about Nubia's genetic landscape prior to the influence of the Islamic migrations that began in the late 1st millennium CE. Here, we increase the number of ancient individuals with genome-level data from the Nile Valley from three to 69, reporting data for 66 individuals from two cemeteries at the Christian Period (~650-1000 CE) site of Kulubnarti, where multiple lines of evidence suggest social stratification. The Kulubnarti Nubians had ~43% Nilotic-related ancestry (individual variation between ~36-54%) with the remaining ancestry consistent with being introduced through Egypt and ultimately deriving from an ancestry pool like that found in the Bronze and Iron Age Levant. The Kulubnarti gene pool - shaped over a millennium - harbors disproportionately female-associated West Eurasian-related ancestry. Genetic similarity among individuals from the two cemeteries supports a hypothesis of social division without genetic distinction. Seven pairs of inter-cemetery relatives suggest fluidity between cemetery groups. Present-day Nubians are not directly descended from the Kulubnarti Nubians, attesting to additional genetic input since the Christian Period.
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Affiliation(s)
- Kendra A Sirak
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
- Department of Anthropology, Emory University, Atlanta, GA, 30322, USA.
- Earth Institute and School of Archaeology, University College Dublin, Dublin, 4, Ireland.
| | - Daniel M Fernandes
- Earth Institute and School of Archaeology, University College Dublin, Dublin, 4, Ireland
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
- CIAS, Department of Life Sciences, University of Coimbra, 3000-456, Coimbra, Portugal
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Harald Ringbauer
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Carla S Hadden
- Center for Applied Isotope Studies, University of Georgia, Athens, GA, 30602, USA
| | - Éadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Anthropology, University of California, Santa Cruz, CA, 95064, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - Ron Pinhasi
- Earth Institute and School of Archaeology, University College Dublin, Dublin, 4, Ireland
- Department of Evolutionary Anthropology, University of Vienna, Vienna, 1090, Austria
| | - Jessica C Thompson
- Department of Anthropology, Emory University, Atlanta, GA, 30322, USA
- Department of Anthropology, Yale University, New Haven, CT, 06511, USA
- Yale Peabody Museum of Natural History, New Haven, CT, 06511, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ, 85287, USA
| | - Dennis Van Gerven
- Department of Anthropology, University of Colorado at Boulder, Boulder, CO, 80309, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
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8
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Scorrano G, Yediay FE, Pinotti T, Feizabadifarahani M, Kristiansen K. The genetic and cultural impact of the Steppe migration into Europe. Ann Hum Biol 2021; 48:223-233. [PMID: 34459341 DOI: 10.1080/03014460.2021.1942984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND During the early 3rd millennium BCE migration from Pontic Steppe, mainly related to Yamnaya culture, has affected European populations both culturally and genetically, however, it has long been debated to what extent this migration was male-driven, and how this replacement process took place which eliminated partially/largely Neolithic male lines over time. AIM This paper aims to evaluate the influence of the Steppe migration on European Bronze Age populations by calculating both male and female genetic contributions of the Steppe-related ancestry to the European Bronze Age populations. With this approach, we will be able to clarify the hypotheses on whether it was male-biased migration or not. SUBJECTS AND METHODS To evaluate the genetic impact and the proportion of the Steppe-related ancestry to the European Bronze Age populations, we performed PCA and qpAdm analyses by using published genome-wide data. In addition, we quantified male and female genetic contribution into Europe by using the analysis of uniparental markers and the X-chromosome. RESULTS The Steppe migration had a considerable impact on the genetic makeup of the Bronze Age European populations. The data suggest that the Steppe-related ancestry arriving into Central Europe was male-driven, dominantly in the Corded Ware culture populations and lesser in the Bell Beaker populations. In fact, there is no evidence that this migration had a significant input on the mitochondrial genetic pool of all European Bronze Age populations. CONCLUSIONS Our analyses suggest that the Steppe-related ancestry had genetic impact on mainly Central-Eastern Europe. Moreover, this migration was male-driven for most of the Central European populations belonging to the Corded Ware groups, and to a lesser extent for the Bell Beaker groups.
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Affiliation(s)
- Gabriele Scorrano
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Fulya Eylem Yediay
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thomaz Pinotti
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Laboratório de Biodiversidade e Evolução Molecular (LBEM), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Kristian Kristiansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
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9
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Cotter DJ, Severson AL, Rosenberg NA. The effect of consanguinity on coalescence times on the X chromosome. Theor Popul Biol 2021; 140:32-43. [PMID: 33901539 DOI: 10.1016/j.tpb.2021.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 10/21/2022]
Abstract
Consanguineous unions increase the frequency at which identical genomic segments are inherited along separate paths of descent, decreasing coalescence times for pairs of alleles drawn from an individual who is the offspring of a consanguineous pair. For an autosomal locus, it has recently been shown that the mean time to the most recent common ancestor (TMRCA) for two alleles in the same individual and the mean TMRCA for two alleles in two separate individuals both decrease with increasing consanguinity in a population. Here, we extend this analysis to the X chromosome, considering X-chromosomal coalescence times under a coalescent model with diploid, male-female mating pairs. We examine four possible first-cousin mating schemes that are equivalent in their effects on autosomes, but that have differing effects on the X chromosome: patrilateral-parallel, patrilateral-cross, matrilateral-parallel, and matrilateral-cross. In each mating model, we calculate mean TMRCA for X-chromosomal alleles sampled either within or between individuals. We describe a consanguinity effect on X-chromosomal TMRCA that differs from the autosomal pattern under matrilateral but not under patrilateral first-cousin mating. For matrilateral first cousins, the effect of consanguinity in reducing TMRCA is stronger on the X chromosome than on the autosomes, with an increased effect of parallel-cousin mating compared to cross-cousin mating. The theoretical computations support the utility of the model in understanding patterns of genomic sharing on the X chromosome.
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Affiliation(s)
- Daniel J Cotter
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.
| | - Alissa L Severson
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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10
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Hamilton MI, Fernandez DP, Nelson SV. Using strontium isotopes to determine philopatry and dispersal in primates: a case study from Kibale National Park. ROYAL SOCIETY OPEN SCIENCE 2021; 8:200760. [PMID: 33972840 PMCID: PMC8074638 DOI: 10.1098/rsos.200760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 01/15/2021] [Indexed: 06/12/2023]
Abstract
Strontium isotope ratios (87Sr/86Sr) allow researchers to track changes in mobility throughout an animal's life and could theoretically be used to reconstruct sex-biases in philopatry and dispersal patterns in primates. Dispersal patterns are a life-history variable that correlate with numerous aspects of behaviour and socio-ecology that are elusive in the fossil record. The present study demonstrates that the standard archaeological method used to differentiate between 'local' and 'non-local' individuals, which involves comparing faunal isotopic ratios with environmental isotopic minima and maxima, is not always reliable; aspects of primate behaviour, local environments, geologic heterogeneity and the availability of detailed geologic maps may compromise its utility in certain situations. This study instead introduces a different methodological approach: calculating offset values to compare 87Sr/86Sr of teeth with that of bone or local environments. We demonstrate this method's effectiveness using data from five species of primates, including chimpanzees, from Kibale National Park, Uganda. Tooth-to-bone offsets reliably indicate sex-biases in dispersal for primates with small home ranges while tooth-to-environment offset comparisons are more reliable for primates with larger home ranges. Overall, tooth-to-environment offsets yield the most reliable predictions of species' sex-biases in dispersal.
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Affiliation(s)
- Marian I. Hamilton
- Department of Anthropology, University of Northern Colorado, Greeley, CO, 80639-6900, USA
- Department of Anthropology, University of New Mexico, Albuquerque, NM, 87111, USA
| | - Diego P. Fernandez
- Department of Geology and Geochemistry, University of Utah, Salt Lake City, UT, USA
| | - Sherry V. Nelson
- Department of Anthropology, University of New Mexico, Albuquerque, NM, 87111, USA
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11
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Lall GM, Larmuseau MHD, Wetton JH, Batini C, Hallast P, Huszar TI, Zadik D, Aase S, Baker T, Balaresque P, Bodmer W, Børglum AD, de Knijff P, Dunn H, Harding SE, Løvvik H, Dupuy BM, Pamjav H, Tillmar AO, Tomaszewski M, Tyler-Smith C, Verdugo MP, Winney B, Vohra P, Story J, King TE, Jobling MA. Subdividing Y-chromosome haplogroup R1a1 reveals Norse Viking dispersal lineages in Britain. Eur J Hum Genet 2020; 29:512-523. [PMID: 33139852 PMCID: PMC7940619 DOI: 10.1038/s41431-020-00747-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/08/2020] [Accepted: 10/07/2020] [Indexed: 12/16/2022] Open
Abstract
The influence of Viking-Age migrants to the British Isles is obvious in archaeological and place-names evidence, but their demographic impact has been unclear. Autosomal genetic analyses support Norse Viking contributions to parts of Britain, but show no signal corresponding to the Danelaw, the region under Scandinavian administrative control from the ninth to eleventh centuries. Y-chromosome haplogroup R1a1 has been considered as a possible marker for Viking migrations because of its high frequency in peninsular Scandinavia (Norway and Sweden). Here we select ten Y-SNPs to discriminate informatively among hg R1a1 sub-haplogroups in Europe, analyse these in 619 hg R1a1 Y chromosomes including 163 from the British Isles, and also type 23 short-tandem repeats (Y-STRs) to assess internal diversity. We find three specifically Western-European sub-haplogroups, two of which predominate in Norway and Sweden, and are also found in Britain; star-like features in the STR networks of these lineages indicate histories of expansion. We ask whether geographical distributions of hg R1a1 overall, and of the two sub-lineages in particular, correlate with regions of Scandinavian influence within Britain. Neither shows any frequency difference between regions that have higher (≥10%) or lower autosomal contributions from Norway and Sweden, but both are significantly overrepresented in the region corresponding to the Danelaw. These differences between autosomal and Y-chromosomal histories suggest either male-specific contribution, or the influence of patrilocality. Comparison of modern DNA with recently available ancient DNA data supports the interpretation that two sub-lineages of hg R1a1 spread with the Vikings from peninsular Scandinavia.
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Affiliation(s)
| | - Maarten H D Larmuseau
- Department of Human Genetics, KU Leuven-University of Leuven, Leuven, Belgium.,Laboratory of Socioecology and Social Evolution, KU Leuven-University of Leuven, Leuven, Belgium.,Histories vzw, Zoutwerf 5, 2800, Mechelen, Belgium
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,School of History, Politics and International Relations, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Pille Hallast
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, 50411, Estonia
| | - Tunde I Huszar
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK
| | - Daniel Zadik
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | | | - Tina Baker
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Patricia Balaresque
- UMR5288, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, Université Paul Sabatier, Toulouse, France
| | - Walter Bodmer
- Department of Oncology, University of Oxford, Oxford, UK
| | - Anders D Børglum
- Department of Biomedicine & Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Hayley Dunn
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, Sutton Bonington Campus, Loughborough, UK.,Museum of Cultural History, University of Oslo, Oslo, Norway
| | | | - Berit Myhre Dupuy
- Division of Forensic Sciences, Norwegian Institute of Public Health, Oslo, Norway
| | - Horolma Pamjav
- Hungarian Institute for Forensic Sciences, Institute of Forensic Genetics, Budapest, Hungary
| | - Andreas O Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Division of Medicine and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust Manchester, Manchester, UK
| | | | - Marta Pereira Verdugo
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.,Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
| | - Bruce Winney
- Department of Oncology, University of Oxford, Oxford, UK
| | - Pragya Vohra
- School of History, Politics and International Relations, University of Leicester, Leicester, UK.,Department of History, University of York, Heslington, York, UK
| | - Joanna Story
- School of History, Politics and International Relations, University of Leicester, Leicester, UK
| | - Turi E King
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
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12
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Kutanan W, Shoocongdej R, Srikummool M, Hübner A, Suttipai T, Srithawong S, Kampuansai J, Stoneking M. Cultural variation impacts paternal and maternal genetic lineages of the Hmong-Mien and Sino-Tibetan groups from Thailand. Eur J Hum Genet 2020; 28:1563-1579. [PMID: 32690935 PMCID: PMC7576213 DOI: 10.1038/s41431-020-0693-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 06/17/2020] [Accepted: 06/26/2020] [Indexed: 11/09/2022] Open
Abstract
The Hmong-Mien (HM) and Sino-Tibetan (ST) speaking groups are known as hill tribes in Thailand; they were the subject of the first studies to show an impact of patrilocality vs. matrilocality on patterns of mitochondrial (mt) DNA vs. male-specific portion of the Y chromosome (MSY) variation. However, HM and ST groups have not been studied in as much detail as other Thai groups; here we report and analyze 234 partial MSY sequences (∼2.3 mB) and 416 complete mtDNA sequences from 14 populations that, when combined with our previous published data, provides the largest dataset yet for the hill tribes. We find a striking difference between Hmong and IuMien (Mien-speaking) groups: the Hmong are genetically different from both the IuMien and all other Thai groups, whereas the IuMien are genetically more similar to other linguistic groups than to the Hmong. In general, we find less of an impact of patrilocality vs. matrilocality on patterns of mtDNA vs. MSY variation than previous studies. However, there is a dramatic difference in the frequency of MSY and mtDNA lineages of Northeast Asian (NEA) origin vs. Southeast Asian (SEA) origin in HM vs. ST groups: HM groups have high frequencies of NEA MSY lineages but lower frequencies of NEA mtDNA lineages, while ST groups show the opposite. A potential explanation is that the ancestors of Thai HM groups were patrilocal, while the ancestors of Thai ST groups were matrilocal. Overall, these results attest to the impact of cultural practices on patterns of mtDNA vs. MSY variation.
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Affiliation(s)
- Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand. .,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
| | - Rasmi Shoocongdej
- Department of Archaeology, Faculty of Archaeology, Silpakorn University, Bangkok, 10200, Thailand
| | - Metawee Srikummool
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany
| | - Thanatip Suttipai
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Suparat Srithawong
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, 50202, Thailand.,Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, 50202, Thailand
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
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13
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Abstract
Despite the efforts made to reconstruct the history of modern humans, there are still poorly explored regions that are key for understanding the phylogeography of our species. One of them is the Philippines, which is crucial to unravel the colonization of Southeast Asia and Oceania but where little is known about when and how the first humans arrived. In order to shed light into this settlement, we collected samples from 157 individuals of the Philippines with the four grandparents belonging to the same region and mitochondrial variants older than 20,000 years. Next, we analyzed the hypervariable I mtDNA region by approximate Bayesian computation based on extensive spatially explicit computer simulations to select among several migration routes towards the Philippines and to estimate population genetic parameters of this colonization. We found that the colonization of the Philippines occurred more than 60,000 years ago, with long-distance dispersal and from both north and south migration routes. Our results also suggest an environmental scenario especially optimal for humans, with large carrying capacity and population growth, in comparison to other regions of Asia. In all, our study suggests a rapid expansion of modern humans towards the Philippines that could be associated with the establisment of maritime technologies and favorable environmental conditions.
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14
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Micheletti AJC, Ruxton GD, Gardner A. The demography of human warfare can drive sex differences in altruism. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e7. [PMID: 37588371 PMCID: PMC10427324 DOI: 10.1017/ehs.2020.5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Recent years have seen great interest in the suggestion that between-group aggression and within-group altruism have coevolved. However, these efforts have neglected the possibility that warfare - via its impact on demography - might influence human social behaviours more widely, not just those directly connected to success in war. Moreover, the potential for sex differences in the demography of warfare to translate into sex differences in social behaviour more generally has remained unexplored. Here, we develop a kin-selection model of altruism performed by men and women for the benefit of their groupmates in a population experiencing intergroup conflict. We find that warfare can promote altruistic, helping behaviours as the additional reproductive opportunities winners obtain in defeated groups decrease harmful competition between kin. Furthermore, we find that sex can be a crucial modulator of altruism, with there being a tendency for the sex that competes more intensely with relatives to behave more altruistically and for the sex that competes more intensely with non-relatives in defeated groups to receive more altruism. In addition, there is also a tendency for the less-dispersing sex to both give and receive more altruism. We discuss implications for our understanding of observed sex differences in cooperation in human societies.
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Affiliation(s)
- Alberto J. C. Micheletti
- School of Biology, University of St Andrews, Dyers Brae, St AndrewsKY16 9TH, UK
- Institute for Advanced Study in Toulouse, Université Toulouse 1 Capitole, 1 esplanade de l'Université, 31080 Toulouse Cedex 06, France
| | - Graeme D. Ruxton
- School of Biology, University of St Andrews, Dyers Brae, St AndrewsKY16 9TH, UK
| | - Andy Gardner
- School of Biology, University of St Andrews, Dyers Brae, St AndrewsKY16 9TH, UK
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15
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Kutanan W, Kampuansai J, Srikummool M, Brunelli A, Ghirotto S, Arias L, Macholdt E, Hübner A, Schröder R, Stoneking M. Contrasting Paternal and Maternal Genetic Histories of Thai and Lao Populations. Mol Biol Evol 2020; 36:1490-1506. [PMID: 30980085 PMCID: PMC6573475 DOI: 10.1093/molbev/msz083] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The human demographic history of Mainland Southeast Asia (MSEA) has not been well studied; in particular, there have been very few sequence-based studies of variation in the male-specific portions of the Y chromosome (MSY). Here, we report new MSY sequences of ∼2.3 mB from 914 males and combine these with previous data for a total of 928 MSY sequences belonging to 59 populations from Thailand and Laos who speak languages belonging to three major Mainland Southeast Asia families: Austroasiatic, Tai-Kadai, and Sino-Tibetan. Among the 92 MSY haplogroups, two main MSY lineages (O1b1a1a* [O-M95*] and O2a* [O-M324*]) contribute substantially to the paternal genetic makeup of Thailand and Laos. We also analyze complete mitochondrial DNA genome sequences published previously from the same groups and find contrasting pattern of male and female genetic variation and demographic expansions, especially for the hill tribes, Mon, and some major Thai groups. In particular, we detect an effect of postmarital residence pattern on genetic diversity in patrilocal versus matrilocal groups. Additionally, both male and female demographic expansions were observed during the early Mesolithic (∼10 ka), with two later major male-specific expansions during the Neolithic period (∼4–5 ka) and the Bronze/Iron Age (∼2.0–2.5 ka). These two later expansions are characteristic of the modern Austroasiatic and Tai-Kadai groups, respectively, consistent with recent ancient DNA studies. We simulate MSY data based on three demographic models (continuous migration, demic diffusion, and cultural diffusion) of major Thai groups and find different results from mitochondrial DNA simulations, supporting contrasting male and female genetic histories.
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Affiliation(s)
- Wibhu Kutanan
- Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Metawee Srikummool
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Andrea Brunelli
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Silvia Ghirotto
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Leonardo Arias
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Enrico Macholdt
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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16
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Abstract
The rapidly decreasing costs of generating genetic data sequencing and the ease of new DNA collection technologies have opened up new opportunities for anthropologists to conduct field-based genetic studies. An exciting aspect of this work comes from linking genetic data with the kinds of individual-level traits evolutionary anthropologists often rely on, such as those collected in long-term demographic and ethnographic studies. However, combining these two types of data raises a host of ethical questions related to the collection, analysis and reporting of such data. Here we address this conundrum by examining one particular case, the collection and analysis of paternity data. We are particularly interested in the logistics and ethics involved in genetic paternity testing in the localized settings where anthropologists often work. We discuss the particular issues related to paternity testing in these settings, including consent and disclosure, consideration of local identity and beliefs and developing a process of continued community engagement. We then present a case study of our own research in Namibia, where we developed a multi-tiered strategy for consent and community engagement, built around a double-blind procedure for data collection, analysis and reporting. Paternity testing in anthropology raises ethical and methodological issues. We summarize these and describe a novel double-blind method used in our work.
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17
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18
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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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19
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Abstract
The population of the Mediterranean island of Sardinia has made important contributions to genome-wide association studies of complex disease traits and, based on ancient DNA (aDNA) studies of mainland Europe, Sardinia is hypothesized to be a unique refuge for early Neolithic ancestry. To provide new insights on the genetic history of this flagship population, we analyzed 3,514 whole-genome sequenced individuals from Sardinia. We find Sardinian samples show elevated levels of shared ancestry with Basque individuals, especially samples from the more historically isolated regions of Sardinia. Our analysis also uniquely illuminates how levels of genetic similarity with mainland aDNA samples varies subtly across the island. Together, our results indicate within-island sub-structure and sex-biased processes have substantially impacted the genetic history of Sardinia. These results give new insight to the demography of ancestral Sardinians and help further the understanding of sharing of disease risk alleles between Sardinia and mainland populations.
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20
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Inferring sex-specific demographic history from SNP data. PLoS Genet 2018; 14:e1007191. [PMID: 29385127 PMCID: PMC5809101 DOI: 10.1371/journal.pgen.1007191] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 02/12/2018] [Accepted: 01/08/2018] [Indexed: 12/04/2022] Open
Abstract
The relative female and male contributions to demography are of great importance to better understand the history and dynamics of populations. While earlier studies relied on uniparental markers to investigate sex-specific questions, the increasing amount of sequence data now enables us to take advantage of tens to hundreds of thousands of independent loci from autosomes and the X chromosome. Here, we develop a novel method to estimate effective sex ratios or ESR (defined as the female proportion of the effective population) from allele count data for each branch of a rooted tree topology that summarizes the history of the populations of interest. Our method relies on Kimura’s time-dependent diffusion approximation for genetic drift, and is based on a hierarchical Bayesian model to integrate over the allele frequencies along the branches. We show via simulations that parameters are inferred robustly, even under scenarios that violate some of the model assumptions. Analyzing bovine SNP data, we infer a strongly female-biased ESR in both dairy and beef cattle, as expected from the underlying breeding scheme. Conversely, we observe a strongly male-biased ESR in early domestication times, consistent with an easier taming and management of cows, and/or introgression from wild auroch males, that would both cause a relative increase in male effective population size. In humans, analyzing a subsample of non-African populations, we find a male-biased ESR in Oceanians that may reflect complex marriage patterns in Aboriginal Australians. Because our approach relies on allele count data, it may be applied on a wide range of species. The history of populations and their social organization is often intricate due to breeding structures, migration patterns or population bottlenecks. Estimation of the female proportion of the effective population (sex ratio) is therefore important to better understand this underlying social structure and dynamics. This question has been mainly investigated so far by comparing genetic variation of mitochondrial DNA and the Y chromosome, two uniparentally inherited markers that reflect the demographic history of females and males, respectively. To overcome the intrinsic limitations of these genetic markers, and to take advantage of the increasing amount of sequence data, we propose a new approach that uses large numbers of independent polymorphisms from autosomes and the X chromosome to estimate sex ratios, throughout the history of populations. This method allows us to confirm a strongly female-biased sex ratio in modern dairy and beef cattle breeds. Yet, we find a strongly male-biased sex ratio during domestication times, consistent with an easier taming and management of cows, and/or introgression from wild auroch males. Analyzing human data from a sample of non-African populations, we find a male bias in Oceanians, possibly indicating complex marriage patterns among Aboriginal Australian groups.
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21
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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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22
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Ancient X chromosomes reveal contrasting sex bias in Neolithic and Bronze Age Eurasian migrations. Proc Natl Acad Sci U S A 2017; 114:2657-2662. [PMID: 28223527 DOI: 10.1073/pnas.1616392114] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Dramatic events in human prehistory, such as the spread of agriculture to Europe from Anatolia and the late Neolithic/Bronze Age migration from the Pontic-Caspian Steppe, can be investigated using patterns of genetic variation among the people who lived in those times. In particular, studies of differing female and male demographic histories on the basis of ancient genomes can provide information about complexities of social structures and cultural interactions in prehistoric populations. We use a mechanistic admixture model to compare the sex-specifically-inherited X chromosome with the autosomes in 20 early Neolithic and 16 late Neolithic/Bronze Age human remains. Contrary to previous hypotheses suggested by the patrilocality of many agricultural populations, we find no evidence of sex-biased admixture during the migration that spread farming across Europe during the early Neolithic. For later migrations from the Pontic Steppe during the late Neolithic/Bronze Age, however, we estimate a dramatic male bias, with approximately five to 14 migrating males for every migrating female. We find evidence of ongoing, primarily male, migration from the steppe to central Europe over a period of multiple generations, with a level of sex bias that excludes a pulse migration during a single generation. The contrasting patterns of sex-specific migration during these two migrations suggest a view of differing cultural histories in which the Neolithic transition was driven by mass migration of both males and females in roughly equal numbers, perhaps whole families, whereas the later Bronze Age migration and cultural shift were instead driven by male migration, potentially connected to new technology and conquest.
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23
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Webster TH, Wilson Sayres MA. Genomic signatures of sex-biased demography: progress and prospects. Curr Opin Genet Dev 2016; 41:62-71. [PMID: 27599147 DOI: 10.1016/j.gde.2016.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/06/2016] [Accepted: 08/02/2016] [Indexed: 01/09/2023]
Abstract
Sex-biased demographic events have played a crucial role in shaping human history. Many of these processes affect genetic variation and can therefore leave detectable signatures in the genome because autosomal, X-linked, Y-linked, and mitochondrial DNA inheritance differ between sexes. Here, we discuss how sex-biased processes shape patterns of genetic diversity across the genome, review recent genomic evidence for sex-biased demography in modern human populations, and suggest directions for future research.
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Affiliation(s)
- Timothy H Webster
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | - Melissa A Wilson Sayres
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA; Center for Evolution and Medicine, The Biodesign Institute at Arizona State University, Tempe, AZ 85287, USA.
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24
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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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Abstract
Sex-biased demography, in which parameters governing migration and population size differ between females and males, has been studied through comparisons of X chromosomes, which are inherited sex-specifically, and autosomes, which are not. A common form of sex bias in humans is sex-biased admixture, in which at least one of the source populations differs in its proportions of females and males contributing to an admixed population. Studies of sex-biased admixture often examine the mean ancestry for markers on the X chromosome in relation to the autosomes. A simple framework noting that in a population with equally many females and males, two-thirds of X chromosomes appear in females, suggests that the mean X-chromosomal admixture fraction is a linear combination of female and male admixture parameters, with coefficients 2/3 and 1/3, respectively. Extending a mechanistic admixture model to accommodate the X chromosome, we demonstrate that this prediction is not generally true in admixture models, although it holds in the limit for an admixture process occurring as a single event. For a model with constant ongoing admixture, we determine the mean X-chromosomal admixture, comparing admixture on female and male X chromosomes to corresponding autosomal values. Surprisingly, in reanalyzing African-American genetic data to estimate sex-specific contributions from African and European sources, we find that the range of contributions compatible with the excess African ancestry on the X chromosome compared to autosomes has a wide spread, permitting scenarios either without male-biased contributions from Europe or without female-biased contributions from Africa.
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Primate sociality to human cooperation. Why us and not them? HUMAN NATURE-AN INTERDISCIPLINARY BIOSOCIAL PERSPECTIVE 2015; 25:28-48. [PMID: 24307447 DOI: 10.1007/s12110-013-9184-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Developmental psychologists identify propensities for social engagement in human infants that are less evident in other apes; Sarah Hrdy links these social propensities to novel features of human childrearing. Unlike other ape mothers, humans can bear a new baby before the previous child is independent because they have help. This help alters maternal trade-offs and so imposes new selection pressures on infants and young children to actively engage their caretakers' attention and commitment. Such distinctive childrearing is part of our grandmothering life history. While consequences for other cooperative activities must surely follow, the novel rearing environments set up by helpful grandmothering can explain why natural selection escalated preferences and motivations for interactivity in our lineage in the first place, and why, unlike other aspects of infant development, social sensitivities are not delayed in humans compared with genus Pan.
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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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Fine-scale genetic assessment of sex-specific dispersal patterns in a multilevel primate society. J Hum Evol 2014; 78:103-13. [PMID: 25466516 DOI: 10.1016/j.jhevol.2014.10.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 10/29/2014] [Accepted: 10/30/2014] [Indexed: 11/23/2022]
Abstract
Like humans, hamadryas baboons (Papio hamadryas) are unusual among primates in having a multilevel social system and stable pair bonds, and are thus a useful model for the evolution of human sociality. While the kinship structure and sex-biased dispersal patterns that underlie human social organization have been extensively elucidated, the impact of these factors on the social system of hamadryas baboons is currently unclear. Here we use genetic analysis of individuals to elucidate the patterns of male and female dispersal across multiple levels of society in a wild population of hamadryas baboons. We characterized 244 members of five hamadryas bands at Filoha, Ethiopia by genotyping one Y-linked and 23 autosomal microsatellite loci and sequencing part of the mitochondrial hypervariable control region I. We found both male and female dispersal to be limited at the level of the band, with more movement of females than males among bands. By integrating long-term behavioral data for Band 1, we also found evidence for male and female philopatry at the clan level. We speculate that male philopatry at the clan level and female dispersal across one-male units and clans may enable both kin-based cooperation among males and the maintenance of kin bonds among females after dispersal. This would mean that, as in humans, kin bonds within both sexes are a core feature of the hamadryas social system, thus contributing to our understanding of the evolution of social organization in humans.
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Brandt G, Szécsényi-Nagy A, Roth C, Alt KW, Haak W. Human paleogenetics of Europe--the known knowns and the known unknowns. J Hum Evol 2014; 79:73-92. [PMID: 25467114 DOI: 10.1016/j.jhevol.2014.06.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/25/2014] [Accepted: 06/19/2014] [Indexed: 12/01/2022]
Abstract
The number of ancient human DNA studies has drastically increased in recent years. This results in a substantial record of mitochondrial sequences available from many prehistoric sites across Western Eurasia, but also growing Y-chromosome and autosomal sequence data. We review the current state of research with specific emphasis on the Holocene population events that likely have shaped the present-day genetic variation in Europe. We reconcile observations from the genetic data with hypotheses about the peopling and settlement history from anthropology and archaeology for various key regions, and also discuss the data in light of evidence from related disciplines, such as modern human genetics, climatology and linguistics.
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Affiliation(s)
- Guido Brandt
- Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany
| | - Anna Szécsényi-Nagy
- Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany; Archaeological Institute, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1014 Budapest, Hungary
| | - Christina Roth
- Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany
| | - Kurt Werner Alt
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Heritage Museum, Richard-Wagner-Straße 9, D-06114 Halle, Germany; Institute for Prehistory and Archaeological Science, Basel University, Petersplatz 1, 4003 Basel, Switzerland; Danube Private University, Faculty of Medicine and Dentistry, Doktor-Karl-Dorrek-Straße 23, 3500 Krems an der Donau, Austria
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, The University of Adelaide, North Terrace Campus, SA-5005 Adelaide, Australia.
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30
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Abstract
Sex-biased admixture has been observed in a wide variety of admixed populations. Genetic variation in sex chromosomes and functions of quantities computed from sex chromosomes and autosomes have often been examined to infer patterns of sex-biased admixture, typically using statistical approaches that do not mechanistically model the complexity of a sex-specific history of admixture. Here, expanding on a model of Verdu and Rosenberg (2011) that did not include sex specificity, we develop a model that mechanistically examines sex-specific admixture histories. Under the model, multiple source populations contribute to an admixed population, potentially with their male and female contributions varying over time. In an admixed population descended from two source groups, we derive the moments of the distribution of the autosomal admixture fraction from a specific source population as a function of sex-specific introgression parameters and time. Considering admixture processes that are constant in time, we demonstrate that surprisingly, although the mean autosomal admixture fraction from a specific source population does not reveal a sex bias in the admixture history, the variance of autosomal admixture is informative about sex bias. Specifically, the long-term variance decreases as the sex bias from a contributing source population increases. This result can be viewed as analogous to the reduction in effective population size for populations with an unequal number of breeding males and females. Our approach suggests that it may be possible to use the effect of sex-biased admixture on autosomal DNA to assist with methods for inference of the history of complex sex-biased admixture processes.
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Kim PS, McQueen JS, Coxworth JE, Hawkes K. Grandmothering drives the evolution of longevity in a probabilistic model. J Theor Biol 2014; 353:84-94. [PMID: 24637003 DOI: 10.1016/j.jtbi.2014.03.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 03/05/2014] [Accepted: 03/06/2014] [Indexed: 11/27/2022]
Abstract
We present a mathematical model based on the Grandmother Hypothesis to simulate how human post-menopausal longevity could have evolved as ancestral grandmothers began to assist the reproductive success of younger females by provisioning grandchildren. Grandmothers׳ help would allow mothers to give birth to subsequent offspring sooner without risking the survival of existing offspring. Our model is an agent-based model (ABM), in which the population evolves according to probabilistic rules governing interactions among individuals. The model is formulated according to the Gillespie algorithm of determining the times to next events. Grandmother effects drive the population from an equilibrium representing a great-ape-like average adult lifespan in the lower twenties to a new equilibrium with a human-like average adult lifespan in the lower forties. The stochasticity of the ABM allows the possible coexistence of two locally-stable equilibria, corresponding to great-ape-like and human-like lifespans. Populations with grandmothering that escape the ancestral condition then shift to human-like lifespan, but the transition takes longer than previous models (Kim et al., 2012). Our simulations are consistent with the possibility that distinctive longevity is a feature of genus Homo that long antedated the appearance of our species.
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Affiliation(s)
- Peter S Kim
- School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia.
| | - John S McQueen
- School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia.
| | - James E Coxworth
- Department of Anthropology, University of Utah, Salt Lake City, UT 84112, USA; Utah Population Database, University of Utah, Salt Lake City, UT 84112, USA.
| | - Kristen Hawkes
- Department of Anthropology, University of Utah, Salt Lake City, UT 84112, USA.
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Inoue E, Akomo-Okoue EF, Ando C, Iwata Y, Judai M, Fujita S, Hongo S, Nze-Nkogue C, Inoue-Murayama M, Yamagiwa J. Male genetic structure and paternity in western lowland gorillas (Gorilla gorilla gorilla). AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 151:583-8. [PMID: 23868171 DOI: 10.1002/ajpa.22312] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 05/03/2013] [Indexed: 11/11/2022]
Abstract
The male dispersal patterns of western lowland gorillas (WLGs, Gorilla gorilla gorilla) are not well understood. To determine whether most silverbacks stay close to their relatives, we analyzed autosomal and Y-chromosomal microsatellites (STRs) in wild WLGs at Moukalaba, Gabon. We obtained STR genotypes for 38 individuals, including eight silverbacks and 12 adult females in an approximately 40 km(2) area. Among them, 20 individuals were members of one identified group (Group Gentil; GG), including one silverback and six adult females. The silverback sired all 13 of the offspring in GG and no Y-STR polymorphism within GG was found, as expected in a one-male group structure. Over all silverbacks sampled, Y-STR diversity was high considering the limited sampling area, and silverbacks with similar Y-STR haplotypes were not always located in nearby areas. Although the misclassification rate of kinship estimates in this study was not negligible, there were no kin dyads among all silverbacks sampled. These results suggest that silverbacks born in the same group do not stay close to each other after maturation. The Y-STR diversity in this study was similar to that of a previous study conducted in an area that was approximately 150 times larger than our study area. Similarity of WLG Y-STR diversity between studies at different sampling scales suggests that male gene flow may not be geographically limited. These results suggest that WLG males normally disperse from their natal areas after maturation, at least, in Moukalaba.
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Affiliation(s)
- Eiji Inoue
- Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan.
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35
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Mona S, Mordret E, Veuille M, Tommaseo-Ponzetta M. Investigating sex-specific dynamics using uniparental markers: West New Guinea as a case study. Ecol Evol 2013; 3:2647-60. [PMID: 24567829 PMCID: PMC3930047 DOI: 10.1002/ece3.660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 05/27/2013] [Accepted: 05/31/2013] [Indexed: 12/24/2022] Open
Abstract
Mitochondrial DNA (mtDNA) and Y chromosome (NRY) genetic markers have been often contrasted to investigate sex-specific dynamics. Traditionally, isolation by distance, intrapopulation genetic diversity and population differentiation are estimated from both markers and compared. Two possible sources of bias are often neglected. First, kilometric distances are frequently used as predictor of the connectivity between groups, hiding the role played by environmental features at a microgeographic scale. Second, the comparison of intrapopulation diversity and population differentiation between mtDNA and NRY is hampered by their different mutational mechanisms and rates. Here, we show how to account for these biases by analyzing from a different perspective a published dataset of eight West New Guinea (WNG) populations for which mtDNA control region sequences and seven linked NRY microsatellites had been typed. First, we modeled the connectivity among sampled populations by computing the number of days required to travel between groups. Then, we investigated the differences between the two sexes accounting for the molecular characteristics of the markers examined to obtain estimates on the product of the effective population size and the migration rate among demes (Nm). We achieved this goal by studying the shape of the gene genealogy at several sampling levels and using spatial explicit simulations. Both the direction and the rate of migration differ between male and females, with an Nm estimated to be >6 times higher in the latter under many evolutionary scenarios. We finally highlight the importance of applying metapopulation models when analyzing the genetic diversity of a species. We have applied the prediction of the sampling theory in a meta-population and we have corroborated our finding using spatial explicit simulations. Both approaches are fundamentally meant to deal with structured populations: we strongly believe in the importance of tacking structure into account when inferring the demographic history of a species.
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Affiliation(s)
- Stefano Mona
- Laboratoire Biologie intégrative des populations, Ecole Pratique des Hautes Etudes 46 rue de Lille, 75007, Paris, France ; CNRS UMR 7205, Muséum National d'Histoire Naturelle Rue Buffon, 75005, Paris, France
| | - Ernest Mordret
- Laboratoire Biologie intégrative des populations, Ecole Pratique des Hautes Etudes 46 rue de Lille, 75007, Paris, France ; CNRS UMR 7205, Muséum National d'Histoire Naturelle Rue Buffon, 75005, Paris, France
| | - Michel Veuille
- Laboratoire Biologie intégrative des populations, Ecole Pratique des Hautes Etudes 46 rue de Lille, 75007, Paris, France ; CNRS UMR 7205, Muséum National d'Histoire Naturelle Rue Buffon, 75005, Paris, France
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Sanchez-Faddeev H, Pijpe J, van der Hulle T, Meij HJ, van der Gaag KJ, Slagboom PE, Westendorp RGJ, de Knijff P. The influence of clan structure on the genetic variation in a single Ghanaian village. Eur J Hum Genet 2013; 21:1134-9. [PMID: 23443025 PMCID: PMC3778349 DOI: 10.1038/ejhg.2013.12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 12/18/2012] [Accepted: 01/10/2013] [Indexed: 11/09/2022] Open
Abstract
Socioeconomic and cultural factors are thought to have an important role in influencing human population genetic structure. To explain such population structure differences, most studies analyse genetic differences among widely dispersed human populations. In contrast, we have studied the genetic structure of an ethnic group occupying a single village in north-eastern Ghana. We found a markedly skewed male population substructure because of an almost complete lack of male gene flow among Bimoba clans in this village. We also observed a deep male substructure within one of the clans in this village. Among all males, we observed only three Y-single-nucleotide polymorphism (SNP) haplogroups: E1b1a*-M2, E1b1a7a*-U174 and E1b1a8a*-U209, P277, P278. In contrast to the marked Y-chromosomal substructure, mitochondrial DNA HVS-1 sequence variation and autosomal short-tandem repeats variation patterns indicate high genetic diversities and a virtually random female-mediated gene flow among clans. On the extreme micro-geographical scale of this single Bimoba village, correspondence between the Y-chromosome lineages and clan membership could be due to the combined effects of the strict patrilocal and patrilineal structure. If translated to larger geographic scales, our results would imply that the extent of variation in uniparentally inherited genetic markers, which are typically associated with historical migration on a continental scale, could equally likely be the result of many small and different cumulative effects of social factors such as clan membership that act at a local scale. Such local scale effects should therefore be considered in genetic studies, especially those that use uniparental markers, before making inferences about human history at large.
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Affiliation(s)
- Hernando Sanchez-Faddeev
- 1] Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands [2] Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
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37
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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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Montano V, Marcari V, Pavanello M, Anyaele O, Comas D, Destro-Bisol G, Batini C. The influence of habitats on female mobility in Central and Western Africa inferred from human mitochondrial variation. BMC Evol Biol 2013; 13:24. [PMID: 23360301 PMCID: PMC3605107 DOI: 10.1186/1471-2148-13-24] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 01/25/2013] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND When studying the genetic structure of human populations, the role of cultural factors may be difficult to ascertain due to a lack of formal models. Linguistic diversity is a typical example of such a situation. Patrilocality, on the other hand, can be integrated into a biological framework, allowing the formulation of explicit working hypotheses. The present study is based on the assumption that patrilocal traditions make the hypervariable region I of the mtDNA a valuable tool for the exploration of migratory dynamics, offering the opportunity to explore the relationships between genetic and linguistic diversity. We studied 85 Niger-Congo-speaking patrilocal populations that cover regions from Senegal to Central African Republic. A total of 4175 individuals were included in the study. RESULTS By combining a multivariate analysis aimed at investigating the population genetic structure, with a Bayesian approach used to test models and extent of migration, we were able to detect a stepping-stone migration model as the best descriptor of gene flow across the region, with the main discontinuities corresponding to forested areas. CONCLUSIONS Our analyses highlight an aspect of the influence of habitat variation on human genetic diversity that has yet to be understood. Rather than depending simply on geographic linear distances, patterns of female genetic variation vary substantially between savannah and rainforest environments. Our findings may be explained by the effects of recent gene flow constrained by environmental factors, which superimposes on a background shaped by pre-agricultural peopling.
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Affiliation(s)
- Valeria Montano
- Dipartimento di Biologia Ambientale, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy.
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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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Verdu P, Becker NSA, Froment A, Georges M, Grugni V, Quintana-Murci L, Hombert JM, Van der Veen L, Le Bomin S, Bahuchet S, Heyer E, Austerlitz F. Sociocultural behavior, sex-biased admixture, and effective population sizes in Central African Pygmies and non-Pygmies. Mol Biol Evol 2013; 30:918-37. [PMID: 23300254 DOI: 10.1093/molbev/mss328] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Sociocultural phenomena, such as exogamy or phylopatry, can largely determine human sex-specific demography. In Central Africa, diverging patterns of sex-specific genetic variation have been observed between mobile hunter-gatherer Pygmies and sedentary agricultural non-Pygmies. However, their sex-specific demography remains largely unknown. Using population genetics and approximate Bayesian computation approaches, we inferred male and female effective population sizes, sex-specific migration, and admixture rates in 23 Central African Pygmy and non-Pygmy populations, genotyped for autosomal, X-linked, Y-linked, and mitochondrial markers. We found much larger effective population sizes and migration rates among non-Pygmy populations than among Pygmies, in agreement with the recent expansions and migrations of non-Pygmies and, conversely, the isolation and stationary demography of Pygmy groups. We found larger effective sizes and migration rates for males than for females for Pygmies, and vice versa for non-Pygmies. Thus, although most Pygmy populations have patrilocal customs, their sex-specific genetic patterns resemble those of matrilocal populations. In fact, our results are consistent with a lower prevalence of polygyny and patrilocality in Pygmies compared with non-Pygmies and a potential female transmission of reproductive success in Pygmies. Finally, Pygmy populations showed variable admixture levels with the non-Pygmies, with often much larger introgression from male than from female lineages. Social discrimination against Pygmies triggering complex movements of spouses in intermarriages can explain these male-biased admixture patterns in a patrilocal context. We show how gender-related sociocultural phenomena can determine highly variable sex-specific demography among populations, and how population genetic approaches contrasting chromosomal types allow inferring detailed human sex-specific demographic history.
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Affiliation(s)
- Paul Verdu
- Department of Biology, Stanford University, USA.
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Pardiñas AF, Roca A, García-Vazquez E, López B. Assessing the genetic influence of ancient sociopolitical structure: micro-differentiation patterns in the population of Asturias (Northern Spain). PLoS One 2012; 7:e50206. [PMID: 23209673 PMCID: PMC3507697 DOI: 10.1371/journal.pone.0050206] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/16/2012] [Indexed: 11/18/2022] Open
Abstract
The human populations of the Iberian Peninsula are the varied result of a complex mixture of cultures throughout history, and are separated by clear social, cultural, linguistic or geographic barriers. The stronger genetic differences between closely related populations occur in the northern third of Spain, a phenomenon commonly known as "micro-differentiation". It has been argued and discussed how this form of genetic structuring can be related to both the rugged landscape and the ancient societies of Northern Iberia, but this is difficult to test in most regions due to the intense human mobility of previous centuries. Nevertheless, the Spanish autonomous community of Asturias shows a complex history which hints of a certain isolation of its population. This, joined together with a difficult terrain full of deep valleys and steep mountains, makes it suitable for performing a study of genetic structure, based on mitochondrial DNA and Y-Chromosome markers. Our analyses do not only show that there are micro-differentiation patterns inside the Asturian territory, but that these patterns are strikingly similar between both uniparental markers. The inference of barriers to gene flow also indicates that Asturian populations from the coastal north and the mountainous south seem to be relatively isolated from the rest of the territory. These findings are discussed in light of historic and geographic data and, coupled with previous evidence, show that the origin of the current genetic patterning might indeed lie in Roman and Pre-Roman sociopolitical divisions.
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Affiliation(s)
- Antonio F. Pardiñas
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Asturias, Spain
| | - Agustín Roca
- Departamento de Biología Funcional, Universidad de Oviedo, Asturias, Spain
| | - Eva García-Vazquez
- Departamento de Biología Funcional, Universidad de Oviedo, Asturias, Spain
| | - Belén López
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Asturias, Spain
- * E-mail:
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Favre M, Sornette D. Strong gender differences in reproductive success variance, and the times to the most recent common ancestors. J Theor Biol 2012; 310:43-54. [PMID: 22743131 DOI: 10.1016/j.jtbi.2012.06.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 06/11/2012] [Accepted: 06/17/2012] [Indexed: 10/28/2022]
Abstract
The Time to the Most Recent Common Ancestor (TMRCA) based on human mitochondrial DNA (mtDNA) is estimated to be twice that based on the non-recombining part of the Y chromosome (NRY). These TMRCAs have special demographic implications because mtDNA is transmitted only from mother to child, while NRY is passed along from father to son. Therefore, the former locus reflects female history, and the latter, male history. To investigate what caused the two-to-one female-male TMRCA ratio r(F/M)=T(F)/T(M) in humans, we develop a forward-looking agent-based model (ABM) with overlapping generations. Our ABM simulates agents with individual life cycles, including life events such as reaching maturity or menopause. We implemented two main mating systems: polygynandry and polygyny with different degrees in between. In each mating system, the male population can be either homogeneous or heterogeneous. In the latter case, some males are 'alphas' and others are 'betas', which reflects the extent to which they are favored by female mates. A heterogeneous male population implies a competition among males with the purpose of signaling as alpha males. The introduction of a heterogeneous male population is found to reduce by a factor 2 the probability of finding equal female and male TMRCAs and shifts the distribution of r(F/M) to higher values. In order to account for the empirical observation of the factor 2, a high level of heterogeneity in the male population is needed: less than half the males can be alphas and betas can have at most half the fitness of alphas for the TMRCA ratio to depart significantly from 1. In addition, we find that, in the modes that maximize the probability of having 1.5<r(F/M)<2.5, the present generation has 1.4 times as many female as male ancestors. We also tested the effect of sex-biased migration and sex-specific death rates and found that these are unlikely to explain alone the sex-biased TMRCA ratio observed in humans. Our results support the view that we are descended from males who were successful in a highly competitive context, while females were facing a much smaller female-female competition.
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Affiliation(s)
- Maroussia Favre
- Department of Management, Technology and Economics, Swiss Federal Institute of Technology, ETH Zurich, Scheuchzerstrasse 7, CH-8092 Zurich, Switzerland.
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Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S. A high-coverage genome sequence from an archaic Denisovan individual. Science 2012; 338:222-6. [PMID: 22936568 DOI: 10.1126/science.1224344] [Citation(s) in RCA: 1090] [Impact Index Per Article: 90.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.
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Affiliation(s)
- Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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Marks SJ, Levy H, Martinez-Cadenas C, Montinaro F, Capelli C. Migration distance rather than migration rate explains genetic diversity in human patrilocal groups. Mol Ecol 2012; 21:4958-69. [PMID: 22765647 DOI: 10.1111/j.1365-294x.2012.05689.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Sarah J Marks
- Department of Zoology, University of Oxford, Oxford, UK
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ARORA N, Van NOORDWIJK MA, ACKERMANN C, WILLEMS EP, NATER A, GREMINGER M, NIETLISBACH P, DUNKEL LP, UTAMI ATMOKO SS, PAMUNGKAS JOKO, PERWITASARI-FARAJALLAH DYAH, Van SCHAIK CP, KRÜTZEN M. Parentage-based pedigree reconstruction reveals female matrilineal clusters and male-biased dispersal in nongregarious Asian great apes, the Bornean orang-utans (Pongo pygmaeus). Mol Ecol 2012; 21:3352-62. [DOI: 10.1111/j.1365-294x.2012.05608.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Community differentiation and kinship among Europe's first farmers. Proc Natl Acad Sci U S A 2012; 109:9326-30. [PMID: 22645332 DOI: 10.1073/pnas.1113710109] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Community differentiation is a fundamental topic of the social sciences, and its prehistoric origins in Europe are typically assumed to lie among the complex, densely populated societies that developed millennia after their Neolithic predecessors. Here we present the earliest, statistically significant evidence for such differentiation among the first farmers of Neolithic Europe. By using strontium isotopic data from more than 300 early Neolithic human skeletons, we find significantly less variance in geographic signatures among males than we find among females, and less variance among burials with ground stone adzes than burials without such adzes. From this, in context with other available evidence, we infer differential land use in early Neolithic central Europe within a patrilocal kinship system.
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48
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Jobling MA. The impact of recent events on human genetic diversity. Philos Trans R Soc Lond B Biol Sci 2012; 367:793-9. [PMID: 22312046 DOI: 10.1098/rstb.2011.0297] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The historical record tells us stories of migrations, population expansions and colonization events in the last few thousand years, but what was their demographic impact? Genetics can throw light on this issue, and has mostly done so through the maternally inherited mitochondrial DNA (mtDNA) and the male-specific Y chromosome. However, there are a number of problems, including marker ascertainment bias, possible influences of natural selection, and the obscuring layers of the palimpsest of historical and prehistorical events. Y-chromosomal lineages are particularly affected by genetic drift, which can be accentuated by recent social selection. A diversity of approaches to expansions in Europe is yielding insights into the histories of Phoenicians, Roma, Anglo-Saxons and Vikings, and new methods for producing and analysing genome-wide data hold much promise. The field would benefit from more consensus on appropriate methods, and better communication between geneticists and experts in other disciplines, such as history, archaeology and linguistics.
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Affiliation(s)
- Mark A Jobling
- Department of Genetics, University of Leicester, Leicester, UK.
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He JD, Peng MS, Quang HH, Dang KP, Trieu AV, Wu SF, Jin JQ, Murphy RW, Yao YG, Zhang YP. Patrilineal perspective on the Austronesian diffusion in Mainland Southeast Asia. PLoS One 2012; 7:e36437. [PMID: 22586471 PMCID: PMC3346718 DOI: 10.1371/journal.pone.0036437] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 04/02/2012] [Indexed: 01/22/2023] Open
Abstract
The Cham people are the major Austronesian speakers of Mainland Southeast Asia (MSEA) and the reconstruction of the Cham population history can provide insights into their diffusion. In this study, we analyzed non-recombining region of the Y chromosome markers of 177 unrelated males from four populations in MSEA, including 59 Cham, 76 Kinh, 25 Lao, and 17 Thai individuals. Incorporating published data from mitochondrial DNA (mtDNA), our results indicated that, in general, the Chams are an indigenous Southeast Asian population. The origin of the Cham people involves the genetic admixture of the Austronesian immigrants from Island Southeast Asia (ISEA) with the local populations in MSEA. Discordance between the overall patterns of Y chromosome and mtDNA in the Chams is evidenced by the presence of some Y chromosome lineages that prevail in South Asians. Our results suggest that male-mediated dispersals via the spread of religions and business trade might play an important role in shaping the patrilineal gene pool of the Cham people.
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Affiliation(s)
- Jun-Dong He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
- Graduate University of the Chinese Academy of Sciences, Beijing, China
| | - Huy Ho Quang
- Department of Immunology, Hanoi Medical University, Hanoi, Vietnam
| | - Khoa Pham Dang
- Department of Immunology, Hanoi Medical University, Hanoi, Vietnam
| | - An Vu Trieu
- Department of Immunology, Hanoi Medical University, Hanoi, Vietnam
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Robert W. Murphy
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Canada
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, China
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China
- * E-mail:
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Rasteiro R, Bouttier PA, Sousa VC, Chikhi L. Investigating sex-biased migration during the Neolithic transition in Europe, using an explicit spatial simulation framework. Proc Biol Sci 2012; 279:2409-16. [PMID: 22298848 DOI: 10.1098/rspb.2011.2323] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cultural practices can deeply influence genetic diversity patterns. The Neolithic transitions that took place at different times and locations around the world led to major cultural and demographic changes that influenced and therefore left their marks on human genetic diversity patterns. Several studies on the European Neolithic transition suggest that mitochondrial DNA (mtDNA) and Y-chromosome data can exhibit different patterns, which could be owing to different demographic histories for females and males. Archaeological and anthropological data suggest that the transition from hunter-gatherers (HGs) to farmers' societies is probably associated with changes in social organization, particularly in post-marital residence (PMR) rules (i.e. patrilocality, matrilocality or bilocality). The movements of humans and genes associated with these rules can be seen as sex-biased short-range migrations. We developed a new individual-based simulation approach to explore the genetic consequences of 45 different scenarios, where we varied the patterns of PMR and admixture between HGs and farmers. We recorded mtDNA and Y-chromosome data and analysed their diversity patterns within and between populations, through time and space. We also collected published mtDNA and Y-chromosome data from European and Near-Eastern populations in order to identify the scenarios that would best explain them. We show that: (i) different PMR systems can lead to different patterns of genetic diversity and differentiation, (ii) asymmetries between mtDNA and Y-chromosome can be owing to different behaviours between males and females, but also to different mutations rates, and (iii) patrilocality in farmers explains the present patterns of genetic diversity better than matrilocality or bilocality. Moreover, we found that (iv) the genetic diversity of farmers change depending on the HGs PMR rules even though they are assumed to disappear more than 5000 years ago in our simulations.
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