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Giesen A, Blanckenhorn WU, Schäfer MA, Shimizu KK, Shimizu-Inatsugi R, Misof B, Podsiadlowski L, Niehuis O, Lischer HEL, Aeschbacher S, Kapun M. Geographic Variation in Genomic Signals of Admixture Between Two Closely Related European Sepsid Fly Species. Evol Biol 2023; 50:395-412. [PMID: 37854269 PMCID: PMC10579158 DOI: 10.1007/s11692-023-09612-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The extent of interspecific gene flow and its consequences for the initiation, maintenance, and breakdown of species barriers in natural systems remain poorly understood. Interspecific gene flow by hybridization may weaken adaptive divergence, but can be overcome by selection against hybrids, which may ultimately promote reinforcement. An informative step towards understanding the role of gene flow during speciation is to describe patterns of past gene flow among extant species. We investigate signals of admixture between allopatric and sympatric populations of the two closely related European dung fly species Sepsis cynipsea and S. neocynipsea (Diptera: Sepsidae). Based on microsatellite genotypes, we first inferred a baseline demographic history using Approximate Bayesian Computation. We then used genomic data from pooled DNA of natural and laboratory populations to test for past interspecific gene flow based on allelic configurations discordant with the inferred population tree (ABBA-BABA test with D-statistic). Comparing the detected signals of gene flow with the contemporary geographic relationship among interspecific pairs of populations (sympatric vs. allopatric), we made two contrasting observations. At one site in the French Cevennes, we detected an excess of past interspecific gene flow, while at two sites in Switzerland we observed lower signals of past microsatellite genotypes gene flow among populations in sympatry compared to allopatric populations. These results suggest that the species boundaries between these two species depend on the past and/or present eco-geographic context in Europe, which indicates that there is no uniform link between contemporary geographic proximity and past interspecific gene flow in natural populations. Supplementary Information The online version contains supplementary material available at 10.1007/s11692-023-09612-5.
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Affiliation(s)
- Athene Giesen
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Wolf U. Blanckenhorn
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin A. Schäfer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | | | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University, Freiburg, Germany
| | - Heidi E. L. Lischer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Kapun
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Division of Cell & Developmental Biology, Medical University of Vienna, Vienna, Austria
- Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
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2
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Williams AC, Hill LJ. The 4 D's of Pellagra and Progress. Int J Tryptophan Res 2020; 13:1178646920910159. [PMID: 32327922 PMCID: PMC7163231 DOI: 10.1177/1178646920910159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/06/2020] [Indexed: 12/12/2022] Open
Abstract
Nicotinamide homeostasis is a candidate common denominator to explain smooth transitions, whether demographic, epidemiological or economic. This 'NAD world', dependent on hydrogen-based energy, is not widely recognised as it is neither measured nor viewed from a sufficiently multi-genomic or historical perspective. Reviewing the importance of meat and nicotinamide balances during our co-evolution, recent history suggests that populations only modernise and age well with low fertility on a suitably balanced diet. Imbalances on the low meat side lead to an excess of infectious disease, short lives and boom-bust demographics. On the high side, meat has led to an excess of degenerative, allergic and metabolic disease and low fertility. A 'Goldilocks' diet derived from mixed and sustainable farming (preserving the topsoil) allows for high intellectual capital, height and good health with controlled population growth resulting in economic growth and prosperity. Implementing meat equity worldwide could lead to progress for future generations on 'spaceship' earth by establishing control over population quality, thermostat and biodiversity, if it is not already too late.
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Affiliation(s)
- Adrian C Williams
- Department of Neurology, University
Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Lisa J Hill
- School of Biomedical Sciences, Institute
of Clinical Sciences, University of Birmingham, Birmingham, UK
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3
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Jay F, Boitard S, Austerlitz F. An ABC Method for Whole-Genome Sequence Data: Inferring Paleolithic and Neolithic Human Expansions. Mol Biol Evol 2020; 36:1565-1579. [PMID: 30785202 DOI: 10.1093/molbev/msz038] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Species generally undergo a complex demographic history consisting, in particular, of multiple changes in population size. Genome-wide sequencing data are potentially highly informative for reconstructing this demographic history. A crucial point is to extract the relevant information from these very large data sets. Here, we design an approach for inferring past demographic events from a moderate number of fully sequenced genomes. Our new approach uses Approximate Bayesian Computation, a simulation-based statistical framework that allows 1) identifying the best demographic scenario among several competing scenarios and 2) estimating the best-fitting parameters under the chosen scenario. Approximate Bayesian Computation relies on the computation of summary statistics. Using a cross-validation approach, we show that statistics such as the lengths of haplotypes shared between individuals, or the decay of linkage disequilibrium with distance, can be combined with classical statistics (e.g., heterozygosity and Tajima's D) to accurately infer complex demographic scenarios including bottlenecks and expansion periods. We also demonstrate the importance of simultaneously estimating the genotyping error rate. Applying our method on genome-wide human-sequence databases, we finally show that a model consisting in a bottleneck followed by a Paleolithic and a Neolithic expansion is the most relevant for Eurasian populations.
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Affiliation(s)
- Flora Jay
- Laboratoire EcoAnthropologie et Ethnobiologie, CNRS/MNHN/Université Paris Diderot, Paris, France.,Laboratoire de Recherche en Informatique, CNRS/Université Paris-Sud/Université Paris-Saclay, Orsay, France
| | - Simon Boitard
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, Castanet Tolosan, France
| | - Frédéric Austerlitz
- Laboratoire EcoAnthropologie et Ethnobiologie, CNRS/MNHN/Université Paris Diderot, Paris, France
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4
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Williams AC, Hill LJ. Nicotinamide as Independent Variable for Intelligence, Fertility, and Health: Origin of Human Creative Explosions? Int J Tryptophan Res 2019; 12:1178646919855944. [PMID: 31258332 PMCID: PMC6585247 DOI: 10.1177/1178646919855944] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 05/03/2019] [Indexed: 12/28/2022] Open
Abstract
Meat and nicotinamide acquisition was a defining force during the 2-million-year evolution of the big brains necessary for, anatomically modern, Homo sapiens to survive. Our next move was down the food chain during the Mesolithic 'broad spectrum', then horticultural, followed by the Neolithic agricultural revolutions and progressively lower average 'doses' of nicotinamide. We speculate that a fertility crisis and population bottleneck around 40 000 years ago, at the time of the Last Glacial Maximum, was overcome by Homo (but not the Neanderthals) by concerted dietary change plus profertility genes and intense sexual selection culminating in behaviourally modern Homo sapiens. Increased reliance on the 'de novo' synthesis of nicotinamide from tryptophan conditioned the immune system to welcome symbionts, such as TB (that excrete nicotinamide), and to increase tolerance of the foetus and thereby fertility. The trade-offs during the warmer Holocene were physical and mental stunting and more infectious diseases and population booms and busts. Higher nicotinamide exposure could be responsible for recent demographic and epidemiological transitions to lower fertility and higher longevity, but with more degenerative and auto-immune disease.
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Affiliation(s)
- Adrian C Williams
- Department of Neurology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Lisa J Hill
- School of Biomedical Sciences, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
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5
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Austerlitz F, Heyer E. Neutral Theory: From Complex Population History to Natural Selection and Sociocultural Phenomena in Human Populations. Mol Biol Evol 2018; 35:1304-1307. [PMID: 29659992 DOI: 10.1093/molbev/msy067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Here, we present a synthetic view on how Kimura's Neutral theory has helped us gaining insight on the different evolutionary forces that shape human evolution. We put this perspective in the frame of recent emerging challenges: the use of whole genome data for reconstructing population histories, natural selection on complex polygenic traits, and integrating cultural processes in human evolution.
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Affiliation(s)
- Frédéric Austerlitz
- UMR 7206 Eco-Anthropologie et Ethnobiologie, CNRS, MNHN, Université Paris Diderot, Paris, France
| | - Evelyne Heyer
- UMR 7206 Eco-Anthropologie et Ethnobiologie, CNRS, MNHN, Université Paris Diderot, Paris, France
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6
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Thouzeau V, Mennecier P, Verdu P, Austerlitz F. Genetic and linguistic histories in Central Asia inferred using approximate Bayesian computations. Proc Biol Sci 2018; 284:rspb.2017.0706. [PMID: 28835553 DOI: 10.1098/rspb.2017.0706] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/17/2017] [Indexed: 11/12/2022] Open
Abstract
Linguistic and genetic data have been widely compared, but the histories underlying these descriptions are rarely jointly inferred. We developed a unique methodological framework for analysing jointly language diversity and genetic polymorphism data, to infer the past history of separation, exchange and admixture events among human populations. This method relies on approximate Bayesian computations that enable the identification of the most probable historical scenario underlying each type of data, and to infer the parameters of these scenarios. For this purpose, we developed a new computer program PopLingSim that simulates the evolution of linguistic diversity, which we coupled with an existing coalescent-based genetic simulation program, to simulate both linguistic and genetic data within a set of populations. Applying this new program to a wide linguistic and genetic dataset of Central Asia, we found several differences between linguistic and genetic histories. In particular, we showed how genetic and linguistic exchanges differed in the past in this area: some cultural exchanges were maintained without genetic exchanges. The methodological framework and the linguistic simulation tool developed here can be used in future work for disentangling complex linguistic and genetic evolutions underlying human biological and cultural histories.
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Affiliation(s)
- Valentin Thouzeau
- CNRS, MNHN, Université Paris Diderot, UMR 7206 Eco-Anthropologie et Ethnobiologie, Paris 75016, France
| | - Philippe Mennecier
- CNRS, MNHN, Université Paris Diderot, UMR 7206 Eco-Anthropologie et Ethnobiologie, Paris 75016, France
| | - Paul Verdu
- CNRS, MNHN, Université Paris Diderot, UMR 7206 Eco-Anthropologie et Ethnobiologie, Paris 75016, France
| | - Frédéric Austerlitz
- CNRS, MNHN, Université Paris Diderot, UMR 7206 Eco-Anthropologie et Ethnobiologie, Paris 75016, France
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7
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Leonardi M, Barbujani G, Manica A. An earlier revolution: genetic and genomic analyses reveal pre-existing cultural differences leading to Neolithization. Sci Rep 2017; 7:3525. [PMID: 28615641 PMCID: PMC5471218 DOI: 10.1038/s41598-017-03717-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 05/02/2017] [Indexed: 01/28/2023] Open
Abstract
Archaeological evidence shows that, in the long run, Neolitization (the transition from foraging to food production) was associated with demographic growth. We used two methods (patterns of linkage disequilibrium from whole-genome SNPs and MSMC estimates on genomes) to reconstruct the demographic profiles for respectively 64 and 24 modern-day populations with contrasting lifestyles across the Old World (sub-Saharan Africa, south-eastern Asia, Siberia). Surprisingly, in all regions, food producers had larger effective population sizes (Ne) than foragers already 20 k years ago, well before the Neolithic revolution. As expected, this difference further increased ~12–10 k years ago, around or just before the onset of food production. Using paleoclimate reconstructions, we show that the early difference in Ne cannot be explained by food producers inhabiting more favorable regions. A number of mechanisms, including ancestral differences in census size, sedentism, exploitation of the natural resources, social stratification or connectivity between groups, might have led to the early differences in Ne detected in our analyses. Irrespective of the specific mechanisms involved, our results provide further evidence that long term cultural differences among populations of Palaeolithic hunter-gatherers are likely to have played an important role in the later Neolithization process.
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Affiliation(s)
- Michela Leonardi
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Borsari 44, 44121, Ferrara, Italy. .,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Oester Voldgade 5-7, DK-1350, Copenhagen, Denmark.
| | - Guido Barbujani
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Borsari 44, 44121, Ferrara, Italy
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing street, CB2 3EJ, Cambridge, UK
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8
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Experimental Study of the Biological Properties of Human Embryonic Stem Cell-Derived Retinal Progenitor Cells. Sci Rep 2017; 7:42363. [PMID: 28205557 PMCID: PMC5304228 DOI: 10.1038/srep42363] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 01/09/2017] [Indexed: 01/16/2023] Open
Abstract
Retinal degenerative diseases are among the leading causes of blindness worldwide, and cell replacement is considered as a promising therapeutic. However, the resources of seed cells are scarce. To further explore this type of therapy, we adopted a culture system that could harvest a substantial quantity of retinal progenitor cells (RPCs) from human embryonic stem cells (hESCs) within a relatively short period of time. Furthermore, we transplanted these RPCs into the subretinal spaces of Royal College of Surgeons (RCS) rats. We quantified the thickness of the treated rats' outer nuclear layers (ONLs) and explored the visual function via electroretinography (ERG). It was found that the differentiated cells expressed RPC markers and photoreceptor progenitor markers. The transplanted RPCs survived for at least 12 weeks, resulting in beneficial effects on the morphology of the host retina, and led to a significant improvement in the visual function of the treated animals. These therapeutic effects suggest that the hESCs-derived RPCs could delay degeneration of the retina and partially restore visual function.
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9
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Marchi N, Hegay T, Mennecier P, Georges M, Laurent R, Whitten M, Endicott P, Aldashev A, Dorzhu C, Nasyrova F, Chichlo B, Ségurel L, Heyer E. Sex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 162:627-640. [PMID: 28158897 DOI: 10.1002/ajpa.23151] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 11/30/2016] [Accepted: 12/02/2016] [Indexed: 01/06/2023]
Abstract
OBJECTIVES Sex-specific genetic structures have been previously documented worldwide in humans, even though causal factors have not always clearly been identified. In this study, we investigated the impact of ethnicity, geography and social organization on the sex-specific genetic structure in Inner Asia. Furthermore, we explored the process of ethnogenesis in multiple ethnic groups. METHODS We sampled DNA in Central and Northern Asia from 39 populations of Indo-Iranian and Turkic-Mongolic native speakers. We focused on genetic data of the Y chromosome and mitochondrial DNA. First, we compared the frequencies of haplogroups to South European and East Asian populations. Then, we investigated the genetic differentiation for eight Y-STRs and the HVS1 region, and tested for the effect of geography and ethnicity on such patterns. Finally, we reconstructed the male demographic history, inferred split times and effective population sizes of different ethnic groups. RESULTS Based on the haplogroup data, we observed that the Indo-Iranian- and Turkic-Mongolic-speaking populations have distinct genetic backgrounds. However, each population showed consistent mtDNA and Y chromosome haplogroups patterns. As expected in patrilocal populations, we found that the Y-STRs were more structured than the HVS1. While ethnicity strongly influenced the genetic diversity on the Y chromosome, geography better explained that of the mtDNA. Furthermore, when looking at various ethnic groups, we systematically found a genetic split time older than historical records, suggesting a cultural rather than biological process of ethnogenesis. CONCLUSIONS This study highlights that, in Inner Asia, specific cultural behaviors, especially patrilineality and patrilocality, leave a detectable signature on the sex-specific genetic structure.
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Affiliation(s)
- Nina Marchi
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Tatyana Hegay
- Uzbek Academy of Sciences, Institute of Immunology, Tashkent, Uzbekistan
| | - Philippe Mennecier
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Myriam Georges
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Romain Laurent
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Mark Whitten
- MPRG on Comparative Population Linguistics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Philipp Endicott
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Almaz Aldashev
- Institute molecular biology and medicine, Bishkek, 720040, Kyrgyzstan
| | | | - Firuza Nasyrova
- Laboratory of Plant Genetics, Institute of Botany, Plant Physiology and Genetics, TAS, Dushanbe, 734063, Tajikistan
| | - Boris Chichlo
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Laure Ségurel
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Evelyne Heyer
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
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10
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Aimé C, Austerlitz F. Different kinds of genetic markers permit inference of Paleolithic and Neolithic expansions in humans. Eur J Hum Genet 2016; 25:360-365. [PMID: 28000700 DOI: 10.1038/ejhg.2016.191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/12/2016] [Accepted: 11/22/2016] [Indexed: 11/09/2022] Open
Abstract
Recent population genetic studies have provided valuable insights on the demographic history of our species. However, some issues such as the dating of the first demographic expansions in human populations remain puzzling. Indeed, although a few genetic studies argued that the first human expansions were concomitant with the Neolithic transition, many others found signals of expansion events starting during the Palaeolithic. Here we performed a simulation study to show that these contradictory findings may result from the differences in the genetic markers used, especially if two successive expansion events occurred. For a large majority of replicates for each scenario tested, microsatellite data allow only detecting the recent expansion event in that case, whereas sequence data allow only detecting the ancient expansion. Combined with previous real data analyses, our results bring support to the ideas that (i) a first human expansions started during the Palaeolithic period, (ii) a second expansion event occurred later, concomitantly with the Neolithic transition.
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Affiliation(s)
- Carla Aimé
- UMR 7206, EcoAnthropologie et Ethnobiologie, CNRS/MNHN/Université Paris Diderot, Paris, France.,UMR 5554, Institut des Sciences de l'Évolution, CNRS-Université de Montpellier, Montpellier, France
| | - Frédéric Austerlitz
- UMR 7206, EcoAnthropologie et Ethnobiologie, CNRS/MNHN/Université Paris Diderot, Paris, France
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11
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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: 2.8] [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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12
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Zhan L, Paterson IG, Fraser BA, Watson B, Bradbury IR, Nadukkalam Ravindran P, Reznick D, Beiko RG, Bentzen P. megasat
: automated inference of microsatellite genotypes from sequence data. Mol Ecol Resour 2016; 17:247-256. [DOI: 10.1111/1755-0998.12561] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 05/31/2016] [Accepted: 05/31/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Luyao Zhan
- Faculty of Computer Science Dalhousie University 6050 University Avenue Halifax Nova Scotia B3H 4R2 Canada
| | - Ian G. Paterson
- Marine Gene Probe Laboratory Department of Biology Dalhousie University 1355 Oxford Street Halifax Nova Scotia B3H 4R2 Canada
| | - Bonnie A. Fraser
- Evolution Behaviour and Environment Group University of Sussex Sussex House Falmer Brighton BN1 9RH UK
| | - Beth Watson
- Marine Gene Probe Laboratory Department of Biology Dalhousie University 1355 Oxford Street Halifax Nova Scotia B3H 4R2 Canada
| | - Ian R. Bradbury
- Salmonids Section Science Branch Department of Fisheries and Oceans Canada 80 East White Hills Road St. John's Newfoundland A1C 5X1 Canada
| | | | - David Reznick
- Department of Biology University of California Riverside CA 92521 USA
| | - Robert G. Beiko
- Faculty of Computer Science Dalhousie University 6050 University Avenue Halifax Nova Scotia B3H 4R2 Canada
| | - Paul Bentzen
- Marine Gene Probe Laboratory Department of Biology Dalhousie University 1355 Oxford Street Halifax Nova Scotia B3H 4R2 Canada
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13
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Podgorná E, Diallo I, Vangenot C, Sanchez-Mazas A, Sabbagh A, Černý V, Poloni ES. Variation in NAT2 acetylation phenotypes is associated with differences in food-producing subsistence modes and ecoregions in Africa. BMC Evol Biol 2015; 15:263. [PMID: 26620671 PMCID: PMC4665893 DOI: 10.1186/s12862-015-0543-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 11/13/2015] [Indexed: 12/21/2022] Open
Abstract
Background Dietary changes associated to shifts in subsistence strategies during human evolution may have induced new selective pressures on phenotypes, as currently held for lactase persistence. Similar hypotheses exist for arylamine N-acetyltransferase 2 (NAT2) mediated acetylation capacity, a well-known pharmacogenetic trait with wide inter-individual variation explained by polymorphisms in the NAT2 gene. The environmental causative factor (if any) driving its evolution is as yet unknown, but significant differences in prevalence of acetylation phenotypes are found between hunter-gatherer and food-producing populations, both in sub-Saharan Africa and worldwide, and between agriculturalists and pastoralists in Central Asia. These two subsistence strategies also prevail among sympatric populations of the African Sahel, but knowledge on NAT2 variation among African pastoral nomads was up to now very scarce. Here we addressed the hypothesis of different selective pressures associated to the agriculturalist or pastoralist lifestyles having acted on the evolution of NAT2 by sequencing the gene in 287 individuals from five pastoralist and one agriculturalist Sahelian populations. Results We show that the significant NAT2 genetic structure of African populations is mainly due to frequency differences of three major haplotypes, two of which are categorized as decreased function alleles (NAT2*5B and NAT2*6A), particularly common in populations living in arid environments, and one fast allele (NAT2*12A), more frequently detected in populations living in tropical humid environments. This genetic structure does associate more strongly with a classification of populations according to ecoregions than to subsistence strategies, mainly because most Sahelian and East African populations display little to no genetic differentiation between them, although both regions hold nomadic or semi-nomadic pastoralist and sedentary agriculturalist communities. Furthermore, we found significantly higher predicted proportions of slow acetylators in pastoralists than in agriculturalists, but also among food-producing populations living in the Sahelian and dry savanna zones than in those living in humid environments, irrespective of their mode of subsistence. Conclusion Our results suggest a possible independent influence of both the dietary habits associated with subsistence modes and the chemical environment associated with climatic zones and biomes on the evolution of NAT2 diversity in sub-Saharan African populations. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0543-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eliška Podgorná
- Department of the Archaeology of Landscape and Archaeobiology, Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic. .,Department of Genetics and Evolution, Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, 12 Rue Gustave-Revilliod, 1211, Geneva 4, Switzerland.
| | - Issa Diallo
- Département de Linguistique et Langues Nationales, Institut des Sciences des Sociétés, CNRST, Ouagadougou, Burkina Faso.
| | - Christelle Vangenot
- Department of Genetics and Evolution, Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, 12 Rue Gustave-Revilliod, 1211, Geneva 4, Switzerland.
| | - Alicia Sanchez-Mazas
- Department of Genetics and Evolution, Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, 12 Rue Gustave-Revilliod, 1211, Geneva 4, Switzerland.
| | - Audrey Sabbagh
- IRD, UMR216, Mère et enfant face aux infections tropicales, Université Paris Descartes, Sorbonne Paris Cité, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France.
| | - Viktor Černý
- Department of the Archaeology of Landscape and Archaeobiology, Archaeogenetics Laboratory, Institute of Archaeology of the Academy of Sciences of the Czech Republic, Prague, Czech Republic.
| | - Estella S Poloni
- Department of Genetics and Evolution, Anthropology Unit, Laboratory of Anthropology, Genetics and Peopling History, University of Geneva, 12 Rue Gustave-Revilliod, 1211, Geneva 4, Switzerland.
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Suez M, Behdenna A, Brouillet S, Graça P, Higuet D, Achaz G. MicNeSs: genotyping microsatellite loci from a collection of (NGS) reads. Mol Ecol Resour 2015; 16:524-33. [DOI: 10.1111/1755-0998.12467] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/21/2015] [Accepted: 09/03/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Marie Suez
- UPMC Univ Paris 06; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’ Université Pierre et Marie Curie; Sorbonne Universités; Bat A Et 4 7 quai St Bernard F-75005 Paris France
- CNRS; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’; F-75005 Paris France
- Atelier de BioInformatique; Université Pierre et Marie Curie; 4, Place Jussieu F-75005 Paris France
| | - Abdelkader Behdenna
- UPMC Univ Paris 06; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’ Université Pierre et Marie Curie; Sorbonne Universités; Bat A Et 4 7 quai St Bernard F-75005 Paris France
- CNRS; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’; F-75005 Paris France
- Atelier de BioInformatique; Université Pierre et Marie Curie; 4, Place Jussieu F-75005 Paris France
- SMILE; CIRB (UMR 7241); Collège de France; 11, Place Marcelin Berthelot Paris Cedex 05 75231 Paris France
| | - Sophie Brouillet
- UPMC Univ Paris 06; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’ Université Pierre et Marie Curie; Sorbonne Universités; Bat A Et 4 7 quai St Bernard F-75005 Paris France
- CNRS; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’; F-75005 Paris France
- Atelier de BioInformatique; Université Pierre et Marie Curie; 4, Place Jussieu F-75005 Paris France
| | - Paula Graça
- UPMC Univ Paris 06; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’ Université Pierre et Marie Curie; Sorbonne Universités; Bat A Et 4 7 quai St Bernard F-75005 Paris France
- CNRS; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’; F-75005 Paris France
| | - Dominique Higuet
- UPMC Univ Paris 06; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’ Université Pierre et Marie Curie; Sorbonne Universités; Bat A Et 4 7 quai St Bernard F-75005 Paris France
- CNRS; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’; F-75005 Paris France
| | - Guillaume Achaz
- UPMC Univ Paris 06; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’ Université Pierre et Marie Curie; Sorbonne Universités; Bat A Et 4 7 quai St Bernard F-75005 Paris France
- CNRS; Institut de Biologie Paris-Seine; Evolution Paris-Seine (UMR 7138); Team ‘Eucaryotic Genome Evolution’; F-75005 Paris France
- Atelier de BioInformatique; Université Pierre et Marie Curie; 4, Place Jussieu F-75005 Paris France
- SMILE; CIRB (UMR 7241); Collège de France; 11, Place Marcelin Berthelot Paris Cedex 05 75231 Paris France
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15
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Aimé C, Heyer E, Austerlitz F. Inference of sex-specific expansion patterns in human populations from Y-chromosome polymorphism. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 157:217-25. [PMID: 25662940 DOI: 10.1002/ajpa.22707] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 01/13/2015] [Indexed: 11/10/2022]
Abstract
Studying the current distribution of genetic diversity in humans has important implications for our understanding of the history of our species. We analyzed a set of linked STR and SNP loci from the paternally inherited Y chromosome to infer the past demography of 55 African and Eurasian populations, using both the parametric and nonparametric coalescent-based methods implemented in the BEAST application. We inferred expansion events in most sedentary farmer populations, while we found constant effective population sizes for both nomadic hunter-gatherers and seminomadic herders. Our results differed, on several aspects, from previous results on mtDNA and autosomal markers. First, we found more recent expansion patterns in Eurasia than in Africa. This discrepancy, substantially stronger than the ones found with the other kind of markers, may result from a lower effective population size for men, which might have made male-transmitted markers more sensitive to the out-of-Africa bottleneck. Second, we found expansion signals only for sedentary farmers but not for nomadic herders in Central Asia, while these signals were found for both kind of populations in this area when using mtDNA or autosomal markers. Expansion signals in this area may result from spatial expansion processes and may have been erased for the Y chromosome among the herders because of restricted male gene flow.
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Affiliation(s)
- Carla Aimé
- Laboratoire d'Eco-Anthropologie et Ethnobiologie, UMR 7206 (Muséum National d'Histoire Naturelle-Centre National de la Recherche Scientifique-Université Paris 7 Diderot), Museum National d'Histoire Naturelle, F-75231, Paris, France
| | - Evelyne Heyer
- Laboratoire d'Eco-Anthropologie et Ethnobiologie, UMR 7206 (Muséum National d'Histoire Naturelle-Centre National de la Recherche Scientifique-Université Paris 7 Diderot), Museum National d'Histoire Naturelle, F-75231, Paris, France
| | - Frédéric Austerlitz
- Laboratoire d'Eco-Anthropologie et Ethnobiologie, UMR 7206 (Muséum National d'Histoire Naturelle-Centre National de la Recherche Scientifique-Université Paris 7 Diderot), Museum National d'Histoire Naturelle, F-75231, Paris, France
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