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Hajiesmaeil M, Ravasini F, Risi F, Magnarini G, Olivieri A, D'Atanasio E, Galehdari H, Trombetta B, Cruciani F. High incidence of AZF duplications in clan-structured Iranian populations detected through Y chromosome sequencing read depth analysis. Sci Rep 2023; 13:11857. [PMID: 37481605 PMCID: PMC10363161 DOI: 10.1038/s41598-023-39069-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/19/2023] [Indexed: 07/24/2023] Open
Abstract
The ampliconic region of the human Y chromosome consists of large duplicated sequences that can undergo non-allelic homologous recombination (NAHR), resulting in structural rearrangements that may cause infertility, especially when they occur in the azoospermia factor b/c (AZFb/c) region. Although AZF duplications have long been neglected due to the technical limitations of STS-based studies that focused mainly on deletions, recent next generation sequencing (NGS) technologies provided evidence for their importance in fertility. In this study, a NGS read depth approach was used to detect AZFb/c rearrangements in 87 Iranians from different ethnic groups. The duplication frequency in Iran proved to be twice as high as in the "1000 Genomes" dataset. Interestingly, most duplications were found in patrilineal ethnic groups, possibly as a consequence of their lower male effective population size which can counteract negative selection. Moreover, we found a large 8.0 Mb duplication, resulting in a fourfold increase in the copy number of AZFc genes, which to our knowledge is the largest duplication ever reported in this region. Overall, our results suggest that it is important to consider not only AZF deletions but also duplications to investigate the causes of male infertility, especially in patrilineal clan-based populations.
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Affiliation(s)
- Mogge Hajiesmaeil
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Francesco Ravasini
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Flavia Risi
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Giorgia Magnarini
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology 'Lazzaro Spallanzani', Pavia University, Pavia, Italy
- NBFC, National Biodiversity Future Center, 90133, Palermo, Italy
| | - Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology (IBPM), CNR, 00185, Rome, Italy
| | - Hamid Galehdari
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Beniamino Trombetta
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Fulvio Cruciani
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy.
- Institute of Molecular Biology and Pathology (IBPM), CNR, 00185, Rome, Italy.
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Guarino-Vignon P, Marchi N, Chimènes A, Monnereau A, Kroll S, Mashkour M, Lhuillier J, Bendezu-Sarmiento J, Heyer E, Bon C. Genetic analysis of a bronze age individual from Ulug-depe (Turkmenistan). Front Genet 2022; 13:884612. [PMID: 36072661 PMCID: PMC9441711 DOI: 10.3389/fgene.2022.884612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
The Oxus Civilisation (or Bactrio-Margian Archaeological Complex, BMAC) was the main archaeological culture of the Bronze Age in southern Central Asia. Paleogenetic analyses were previously conducted mainly on samples from the eastern part of BMAC. The population associated with BMAC descends from local Chalcolithic populations, with some outliers of steppe or South-Asian descent. Here, we present new genome-wide data for one individual from Ulug-depe (Turkmenistan), one of the main BMAC sites, located at the southwestern edge of the BMAC. We demonstrate that this individual genetically belongs to the BMAC cluster. Using this genome, we confirm that modern Indo-Iranian–speaking populations from Central Asia derive their ancestry from BMAC populations, with additional gene flow from the western and the Altai steppes in higher proportions among the Tajiks than the Yagnobi ethnic group.
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Affiliation(s)
- Perle Guarino-Vignon
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
- CAGT, UMR 5288, CNRS, Université Paul Sabatier Toulouse III, Toulouse, France
- *Correspondence: Perle Guarino-Vignon, ; Céline Bon,
| | - Nina Marchi
- CMPG, Institute of Ecology and Evolution, University of Berne, Berne, Switzerland
| | - Amélie Chimènes
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
| | - Aurore Monnereau
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
- BioArCh, Department of Archaeology, University of York, York, United Kingdom
| | - Sonja Kroll
- Archéozoologie, Archéobotanique Sociétés, Pratiques et Environnements (AASPE), Muséum National D'Histoire Naturelle, CNRS, Paris, France
| | - Marjan Mashkour
- Archéozoologie, Archéobotanique Sociétés, Pratiques et Environnements (AASPE), Muséum National D'Histoire Naturelle, CNRS, Paris, France
| | - Johanna Lhuillier
- Archéorient, Environnements et Sociétés de L'Orient Ancien, CNRS/Université Lyon 2, Lyon, France
| | - Julio Bendezu-Sarmiento
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
| | - Evelyne Heyer
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
| | - Céline Bon
- Eco-Anthropologie (EA), Muséum National D'Histoire Naturelle, CNRS, Université de Paris, Paris, France
- *Correspondence: Perle Guarino-Vignon, ; Céline Bon,
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3
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Lepers C, Billiard S, Porte M, Méléard S, Tran VC. Inference with selection, varying population size, and evolving population structure: application of ABC to a forward-backward coalescent process with interactions. Heredity (Edinb) 2021; 126:335-350. [PMID: 33128035 PMCID: PMC8027416 DOI: 10.1038/s41437-020-00381-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 10/15/2020] [Indexed: 11/08/2022] Open
Abstract
Genetic data are often used to infer demographic history and changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed a priori known, the evolution of the genetic composition of a population does not affect demography nor population structure, and there is no selection nor interaction between and within genetic strains. In this paper, we present a stochastic birth-death model with competitive interactions and asexual reproduction. We develop an inferential procedure for ecological, demographic, and genetic parameters. We first show how genetic diversity and genealogies are related to birth and death rates, and to how individuals compete within and between strains. This leads us to propose an original model of phylogenies, with trait structure and interactions, that allows multiple merging. Second, we develop an Approximate Bayesian Computation framework to use our model for analyzing genetic data. We apply our procedure to simulated data from a toy model, and to real data by analyzing the genetic diversity of microsatellites on Y-chromosomes sampled from Central Asia human populations in order to test whether different social organizations show significantly different fertilities.
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Affiliation(s)
| | - Sylvain Billiard
- Univ. Lille, CNRS, UMR 819 8 -Evo-Eco-Paleo, F-59000, Lille, France.
| | - Matthieu Porte
- IGN, Institut National de l'Information Géographique et Forestière, F-94165, Saint-Mandé, France.
| | - Sylvie Méléard
- CMAP, CNRS, Ecole Polytechnique, Institut polytechnique de Paris, route de Saclay, 91128, Palaiseau Cedex, France.
| | - Viet Chi Tran
- LAMA, Univ Gustave Eiffel, Univ Paris Est Creteil, CNRS, F-77454, Marne-la-Vallée, France.
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Bouakaze C, Delehelle F, Saenz-Oyhéréguy N, Moreira A, Schiavinato S, Croze M, Delon S, Fortes-Lima C, Gibert M, Bujan L, Huyghe E, Bellis G, Calderon R, Hernández CL, Avendaño-Tamayo E, Bedoya G, Salas A, Mazières S, Charioni J, Migot-Nabias F, Ruiz-Linares A, Dugoujon JM, Thèves C, Mollereau-Manaute C, Noûs C, Poulet N, King T, D'Amato ME, Balaresque P. Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters. Forensic Sci Int Genet 2020; 48:102342. [PMID: 32818722 DOI: 10.1016/j.fsigen.2020.102342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/24/2022]
Abstract
We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %). We observe heterogeneity in haplogroup assignation accuracy among classes, with most haplogroups having high prediction scores (99-100 %) and two (E1b1b and G) having lower scores (67 %). The small sample sizes of these classes explain the high tendency to misclassify the Y-profiles of these haplogroups; results were measurably improved as soon as more training data were added. We provide evidence that our ML approach is a robust method to accurately predict haplogroups when it is combined with a sufficient number of markers, well-balanced mutation rate Y-STR panels, and large ML training sets. Further research on confounding factors (such as CNV-STR or gene conversion) and ideal STR panels in regard to the branches analysed can be developed to help classifiers further optimize prediction scores.
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Affiliation(s)
- Caroline Bouakaze
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Franklin Delehelle
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France; REVA Unit, UMR 5505 - CNRS & Université de Toulouse, Institut de Recherche en Informatique de Toulouse, 31400 Toulouse, France
| | - Nancy Saenz-Oyhéréguy
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Andreia Moreira
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Stéphanie Schiavinato
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Myriam Croze
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Solène Delon
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Cesar Fortes-Lima
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Morgane Gibert
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Louis Bujan
- Equipe d'acceuil EA3694, Hôpital Paule de Viguier, 330 Avenue de Grande Bretagne, TSA 70034, 31059 Toulouse Cedex 9, France
| | - Eric Huyghe
- Equipe d'acceuil EA3694, Hôpital Paule de Viguier, 330 Avenue de Grande Bretagne, TSA 70034, 31059 Toulouse Cedex 9, France
| | - Gil Bellis
- INED Institut National d'Etudes Démographiques, 133 Boulevard Davout, 75980 Paris cedex 20, France
| | - Rosario Calderon
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University. 28040 Madrid, Spain
| | - Candela Lucia Hernández
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Complutense University. 28040 Madrid, Spain
| | - Efren Avendaño-Tamayo
- Grupo de Ciencias Básicas Aplicadas del Tecnológico de Antioquia, Tecnológico de Antioquia, Institución Universitaria, Medellín 050034, Colombia
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Instituto de Biología, Universidad de Antioquia Medellín Colombia, Colombia
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, GenPoB Research Group, Instituto de Investigaciones, Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | | | - Jacques Charioni
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France; Etablissement Français du Sang PACA Corse, Marseille, France
| | | | - Andres Ruiz-Linares
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France; Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jean-Michel Dugoujon
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Catherine Thèves
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Catherine Mollereau-Manaute
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Camille Noûs
- Laboratoire Cogitamous, CNRS & Université Toulouse III, 31000 Toulouse, France
| | - Nicolas Poulet
- Pôle écohydraulique AFB-IMT, allée du Pr Camille Soula, 31400 Toulouse, France
| | - Turi King
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Maria Eugenia D'Amato
- Forensic DNA Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of Western Cape, Cape Town, South Africa
| | - Patricia Balaresque
- Laboratoire d´Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288 - CNRS & Université Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France.
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5
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von Rueden C. Making and unmaking egalitarianism in small-scale human societies. Curr Opin Psychol 2020; 33:167-171. [DOI: 10.1016/j.copsyc.2019.07.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 07/20/2019] [Indexed: 11/28/2022]
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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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7
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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: 0.2] [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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8
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Zeng TC, Aw AJ, Feldman MW. Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck. Nat Commun 2018; 9:2077. [PMID: 29802241 PMCID: PMC5970157 DOI: 10.1038/s41467-018-04375-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 04/24/2018] [Indexed: 01/18/2023] Open
Abstract
In human populations, changes in genetic variation are driven not only by genetic processes, but can also arise from cultural or social changes. An abrupt population bottleneck specific to human males has been inferred across several Old World (Africa, Europe, Asia) populations 5000–7000 BP. Here, bringing together anthropological theory, recent population genomic studies and mathematical models, we propose a sociocultural hypothesis, involving the formation of patrilineal kin groups and intergroup competition among these groups. Our analysis shows that this sociocultural hypothesis can explain the inference of a population bottleneck. We also show that our hypothesis is consistent with current findings from the archaeogenetics of Old World Eurasia, and is important for conceptions of cultural and social evolution in prehistory. A population bottleneck 5000-7000 years ago in human males, but not females, has been inferred across several African, European and Asian populations. Here, Zeng and colleagues synthesize theory and data to suggest that competition among patrilineal kin groups produced the bottleneck pattern.
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Affiliation(s)
- Tian Chen Zeng
- Department of Sociology, Stanford University, Stanford, CA, 94305, USA.,Mathematical and Computational Science Program, Stanford University, Stanford, CA, 94305, USA
| | - Alan J Aw
- Mathematical and Computational Science Program, Stanford University, Stanford, CA, 94305, USA.,Department of Biology, Stanford University, Stanford, CA, USA
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9
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The Connection of the Genetic, Cultural and Geographic Landscapes of Transoxiana. Sci Rep 2017; 7:3085. [PMID: 28596519 PMCID: PMC5465200 DOI: 10.1038/s41598-017-03176-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 04/26/2017] [Indexed: 11/09/2022] Open
Abstract
We have analyzed Y-chromosomal variation in populations from Transoxiana, a historical region covering the southwestern part of Central Asia. We studied 780 samples from 10 regional populations of Kazakhs, Uzbeks, Turkmens, Dungans, and Karakalpaks using 35 SNP and 17 STR markers. Analysis of haplogroup frequencies using multidimensional scaling and principal component plots, supported by an analysis of molecular variance, showed that the geographic landscape of Transoxiana, despite its distinctiveness and diversity (deserts, fertile river basins, foothills and plains) had no strong influence on the genetic landscape. The main factor structuring the gene pool was the mode of subsistence: settled agriculture or nomadic pastoralism. Investigation of STR-based clusters of haplotypes and their ages revealed that cultural and demic expansions of Transoxiana were not closely connected with each other. The Arab cultural expansion introduced Islam to the region but did not leave a significant mark on the pool of paternal lineages. The Mongol expansion, in contrast, had enormous demic success, but did not impact cultural elements like language and religion. The genealogy of Muslim missionaries within the settled agricultural communities of Transoxiana was based on spiritual succession passed from teacher to disciple. However, among Transoxianan nomads, spiritual and biological succession became merged.
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10
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Marchi N, Hegay T, Mennecier P, Georges M, Laurent R, Whitten M, Endicott P, Aldashev A, Dorzhu C, Nasyrova F, Chichlo B, Ségurel L, Heyer E. Sex-specific genetic diversity is shaped by cultural factors in Inner Asian human populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 162:627-640. [PMID: 28158897 DOI: 10.1002/ajpa.23151] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 11/30/2016] [Accepted: 12/02/2016] [Indexed: 01/06/2023]
Abstract
OBJECTIVES Sex-specific genetic structures have been previously documented worldwide in humans, even though causal factors have not always clearly been identified. In this study, we investigated the impact of ethnicity, geography and social organization on the sex-specific genetic structure in Inner Asia. Furthermore, we explored the process of ethnogenesis in multiple ethnic groups. METHODS We sampled DNA in Central and Northern Asia from 39 populations of Indo-Iranian and Turkic-Mongolic native speakers. We focused on genetic data of the Y chromosome and mitochondrial DNA. First, we compared the frequencies of haplogroups to South European and East Asian populations. Then, we investigated the genetic differentiation for eight Y-STRs and the HVS1 region, and tested for the effect of geography and ethnicity on such patterns. Finally, we reconstructed the male demographic history, inferred split times and effective population sizes of different ethnic groups. RESULTS Based on the haplogroup data, we observed that the Indo-Iranian- and Turkic-Mongolic-speaking populations have distinct genetic backgrounds. However, each population showed consistent mtDNA and Y chromosome haplogroups patterns. As expected in patrilocal populations, we found that the Y-STRs were more structured than the HVS1. While ethnicity strongly influenced the genetic diversity on the Y chromosome, geography better explained that of the mtDNA. Furthermore, when looking at various ethnic groups, we systematically found a genetic split time older than historical records, suggesting a cultural rather than biological process of ethnogenesis. CONCLUSIONS This study highlights that, in Inner Asia, specific cultural behaviors, especially patrilineality and patrilocality, leave a detectable signature on the sex-specific genetic structure.
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Affiliation(s)
- Nina Marchi
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Tatyana Hegay
- Uzbek Academy of Sciences, Institute of Immunology, Tashkent, Uzbekistan
| | - Philippe Mennecier
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Myriam Georges
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Romain Laurent
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Mark Whitten
- MPRG on Comparative Population Linguistics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Philipp Endicott
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Almaz Aldashev
- Institute molecular biology and medicine, Bishkek, 720040, Kyrgyzstan
| | | | - Firuza Nasyrova
- Laboratory of Plant Genetics, Institute of Botany, Plant Physiology and Genetics, TAS, Dushanbe, 734063, Tajikistan
| | - Boris Chichlo
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Laure Ségurel
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | - Evelyne Heyer
- Eco-anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
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11
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Creanza N, Feldman MW. Worldwide genetic and cultural change in human evolution. Curr Opin Genet Dev 2016; 41:85-92. [PMID: 27644074 DOI: 10.1016/j.gde.2016.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 08/04/2016] [Accepted: 08/19/2016] [Indexed: 01/04/2023]
Abstract
Both genetic variation and certain culturally transmitted phenotypes show geographic signatures of human demographic history. As a result of the human cultural predisposition to migrate to new areas, humans have adapted to a large number of different environments. Migration to new environments alters genetic selection pressures, and comparative genetic studies have pinpointed numerous likely targets of this selection. However, humans also exhibit many cultural adaptations to new environments, such as practices related to clothing, shelter, and food. Human culture interacts with genes and the environment in complex ways, and studying genes and culture together can deepen our understanding of human evolution.
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Affiliation(s)
- Nicole Creanza
- Department of Biology Stanford University, Gilbert Hall, 371 Serra Mall, Stanford, CA 94305, United States; Department of Biological Sciences, Vanderbilt University, 465 21st Ave. South, Nashville, TN 37212, United States.
| | - Marcus W Feldman
- Department of Biology Stanford University, Gilbert Hall, 371 Serra Mall, Stanford, CA 94305, United States
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12
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Casarini L, Santi D, Marino M. Impact of gene polymorphisms of gonadotropins and their receptors on human reproductive success. Reproduction 2015; 150:R175-84. [PMID: 26370242 DOI: 10.1530/rep-15-0251] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2015] [Indexed: 12/17/2022]
Abstract
Gonadotropins and their receptors' genes carry several single-nucleotide polymorphisms resulting in endocrine genotypes modulating reproductive parameters, diseases, and lifespan leading to important implications for reproductive success and potential relevance during human evolution. Here we illustrate common genotypes of the gonadotropins and gonadotropin receptors' genes and their clinical implications in phenotypes relevant for reproduction such as ovarian cycle length, age of menopause, testosterone levels, polycystic ovary syndrome, and cancer. We then discuss their possible role in human reproduction and adaptation to the environment. Gonadotropins and their receptors' variants are differently distributed among human populations. Some hints suggest that they may be the result of natural selection that occurred in ancient times, increasing the individual chance of successful mating, pregnancy, and effective post-natal parental cares. The gender-related differences in the regulation of the reproductive endocrine systems imply that many of these genotypes may lead to sex-dependent effects, increasing the chance of mating and reproductive success in one sex at the expenses of the other sex. Also, we suggest that sexual conflicts within the FSH and LH-choriogonadotropin receptor genes contributed to maintain genotypes linked to subfertility among humans. Because the distribution of polymorphic markers results in a defined geographical pattern due to human migrations rather than natural selection, these polymorphisms may have had only a weak impact on reproductive success. On the contrary, such genotypes could acquire relevant consequences in the modern, developed societies in which parenthood attempts often occur at a later age, during a short, suboptimal reproductive window, making clinical fertility treatments necessary.
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Affiliation(s)
- Livio Casarini
- Unit of EndocrinologyDepartment of Biomedical, Metabolic and Neural SciencesCenter for Genomic ResearchUniversity of Modena and Reggio Emilia, Via G. Campi, 287, 41125 Modena, ItalyAzienda USL of ModenaNOCSAE, Via P. Giardini 1355, 41126 Modena, Italy Unit of EndocrinologyDepartment of Biomedical, Metabolic and Neural SciencesCenter for Genomic ResearchUniversity of Modena and Reggio Emilia, Via G. Campi, 287, 41125 Modena, ItalyAzienda USL of ModenaNOCSAE, Via P. Giardini 1355, 41126 Modena, Italy
| | - Daniele Santi
- Unit of EndocrinologyDepartment of Biomedical, Metabolic and Neural SciencesCenter for Genomic ResearchUniversity of Modena and Reggio Emilia, Via G. Campi, 287, 41125 Modena, ItalyAzienda USL of ModenaNOCSAE, Via P. Giardini 1355, 41126 Modena, Italy Unit of EndocrinologyDepartment of Biomedical, Metabolic and Neural SciencesCenter for Genomic ResearchUniversity of Modena and Reggio Emilia, Via G. Campi, 287, 41125 Modena, ItalyAzienda USL of ModenaNOCSAE, Via P. Giardini 1355, 41126 Modena, Italy
| | - Marco Marino
- Unit of EndocrinologyDepartment of Biomedical, Metabolic and Neural SciencesCenter for Genomic ResearchUniversity of Modena and Reggio Emilia, Via G. Campi, 287, 41125 Modena, ItalyAzienda USL of ModenaNOCSAE, Via P. Giardini 1355, 41126 Modena, Italy Unit of EndocrinologyDepartment of Biomedical, Metabolic and Neural SciencesCenter for Genomic ResearchUniversity of Modena and Reggio Emilia, Via G. Campi, 287, 41125 Modena, ItalyAzienda USL of ModenaNOCSAE, Via P. Giardini 1355, 41126 Modena, Italy
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