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Fan C, Cahoon JL, Dinh BL, Ortega-Del Vecchyo D, Huber CD, Edge MD, Mancuso N, Chiang CWK. A likelihood-based framework for demographic inference from genealogical trees. Nat Genet 2025; 57:865-874. [PMID: 40113903 DOI: 10.1038/s41588-025-02129-x] [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: 10/23/2023] [Accepted: 02/14/2025] [Indexed: 03/22/2025]
Abstract
The demographic history of a population underlies patterns of genetic variation and is encoded in the gene-genealogical trees of the sampled haplotypes. Here we propose a demographic inference framework called the genealogical likelihood (gLike). Our method uses a graph-based structure to summarize the relationships among all lineages in a gene-genealogical tree with all possible trajectories of population memberships through time and derives the full likelihood across trees under a parameterized demographic model. We show through simulations and empirical applications that for populations that have experienced multiple admixtures, gLike can accurately estimate dozens of demographic parameters, including ancestral population sizes, admixture timing and admixture proportions, and it outperforms conventional demographic inference methods using the site frequency spectrum. Taken together, our proposed gLike framework harnesses underused genealogical information to offer high sensitivity and accuracy in inferring complex demographies for humans and other species.
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Affiliation(s)
- Caoqi Fan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
| | - Jordan L Cahoon
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Department of Computer Science, University of Southern California, Los Angeles, CA, USA
| | - Bryan L Dinh
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Diego Ortega-Del Vecchyo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Querétaro, México
| | - Christian D Huber
- Department of Biology, Penn State University, University Park, PA, USA
| | - Michael D Edge
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
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2
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Teo B, Bastide P, Ané C. Leveraging graphical model techniques to study evolution on phylogenetic networks. Philos Trans R Soc Lond B Biol Sci 2025; 380:20230310. [PMID: 39976402 PMCID: PMC11867149 DOI: 10.1098/rstb.2023.0310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 08/27/2024] [Accepted: 09/16/2024] [Indexed: 02/21/2025] Open
Abstract
The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture. Computing the likelihood of data observed at the leaves is costly as the size and complexity of the phylogeny grows. Efficient algorithms exist for trees, but cannot be applied to networks. We show that a vast array of models for trait evolution along phylogenetic networks can be reformulated as graphical models, for which efficient belief propagation algorithms exist. We provide a brief review of belief propagation on general graphical models, then focus on linear Gaussian models for continuous traits. We show how belief propagation techniques can be applied for exact or approximate (but more scalable) likelihood and gradient calculations, and prove novel results for efficient parameter inference of some models. We highlight the possible fruitful interactions between graphical models and phylogenetic methods. For example, approximate likelihood approaches have the potential to greatly reduce computational costs for phylogenies with reticulations.This article is part of the theme issue '"A mathematical theory of evolution": phylogenetic models dating back 100 years'.
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Affiliation(s)
- Benjamin Teo
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
| | - Paul Bastide
- IMAG, Université de Montpellier, CNRS, Montpellier, France
| | - Cécile Ané
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
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3
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Dimitriou AC, Maimaris G, Hadjipavlou G. Assessment of breeding nuclei contributions to the genetic diversity and population structure of the Cyprus Chios sheep. Sci Rep 2024; 14:29946. [PMID: 39623046 PMCID: PMC11612493 DOI: 10.1038/s41598-024-81678-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Accepted: 11/28/2024] [Indexed: 12/06/2024] Open
Abstract
Cyprus, facing climate change and desertification, has Europe's second highest population growth. Halloumi cheese's Protected Designation of Origin status boosted goat and sheep milk demand. Optimizing primary sector production is key to balancing food production and environmental sustainability. The present study aims to explore the genetic diversity and population structure of Cyprus Chios sheep, as well as the impact of existing breeding nuclei on the breed's gene pool. Two breeding nuclei aiming to preserve genetic diversity and boost local milk production and four private farms were sampled. Genome-wide data using Illumina 50 K arrays were generated, analyzing over 1000 animals from six farms. At least three distinct genetic groups were identified, two of which are represented by the nuclei's distinct genetic profiles and a third was found in private farms. Calculated metrics indicate a negative correlation of gene flow with geographic distance in case of the Eastern nucleus. Presented results support recent, though limited inbreeding (mean FROH=0.046), compared to other commercial breeds. Estimated effective population size reveals a stabilizing trend to a relatively high number (Ne ~ 200) which indicates relatively high diversity that allows further genetic improvement. Revealed genomic diversity highlights the necessity of such exploration before effectively implementing genomic evaluation programs.
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Affiliation(s)
- Andreas C Dimitriou
- Agricultural Research Institute, P.O. Box 22016, Lefkosia, 1516, Cyprus.
- Department of Biological Sciences, University of Cyprus, University Campus, 2109, Nicosia, Cyprus.
| | - Giannis Maimaris
- Agricultural Research Institute, P.O. Box 22016, Lefkosia, 1516, Cyprus
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4
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Larsson MNA, Morell Miranda P, Pan L, Başak Vural K, Kaptan D, Rodrigues Soares AE, Kivikero H, Kantanen J, Somel M, Özer F, Johansson AM, Storå J, Günther T. Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region. Genome Biol Evol 2024; 16:evae114. [PMID: 38795367 PMCID: PMC11162877 DOI: 10.1093/gbe/evae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 04/24/2024] [Accepted: 05/21/2024] [Indexed: 05/27/2024] Open
Abstract
Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centuries. North European short-tailed (NEST) breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia <6,000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and Åland, dating from the Late Neolithic (∼4,100 cal BP) to historical times (∼1,600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern NEST breeds, suggesting a substantial degree of long-term continuity of this sheep type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit relatively high genetic diversity when compared to modern NEST breeds, implying a loss of diversity in most breeds during the last centuries associated with breed formation and recent bottlenecks. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.
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Affiliation(s)
- Martin N A Larsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Pedro Morell Miranda
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Li Pan
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Damla Kaptan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | | | - Hanna Kivikero
- Department of Culture, University of Helsinki, Helsinki, Finland
| | - Juha Kantanen
- Natural Resources Institute Finland, Jokioinen, Finland
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Anna M Johansson
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Stockholm University, Stockholm, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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5
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Nguyen-Hoang A, Sandell FL, Himmelbauer H, Dohm JC. Spinach genomes reveal migration history and candidate genes for important crop traits. NAR Genom Bioinform 2024; 6:lqae034. [PMID: 38633427 PMCID: PMC11023180 DOI: 10.1093/nargab/lqae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 03/14/2024] [Accepted: 03/28/2024] [Indexed: 04/19/2024] Open
Abstract
Spinach (Spinacia oleracea) is an important leafy crop possessing notable economic value and health benefits. Current genomic resources include reference genomes and genome-wide association studies. However, the worldwide genetic relationships and the migration history of the crop remained uncertain, and genome-wide association studies have produced extensive gene lists related to agronomic traits. Here, we re-analysed the sequenced genomes of 305 cultivated and wild spinach accessions to unveil the phylogeny and history of cultivated spinach and to explore genetic variation in relation to phenotypes. In contrast to previous studies, we employed machine learning methods (based on Extreme Gradient Boosting, XGBoost) to detect variants that are collectively associated with agronomic traits. Variant-based cluster analyses revealed three primary spinach groups in the Middle East, Asia and Europe/US. Combining admixture analysis and allele-sharing statistics, migration routes of spinach from the Middle East to Europe and Asia are presented. Using XGBoost machine learning models we predict genomic variants influencing bolting time, flowering time, petiole color, and leaf surface texture and propose candidate genes for each trait. This study enhances our understanding of the history and phylogeny of domesticated spinach and provides valuable information on candidate genes for future genetic improvement of the crop.
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Affiliation(s)
- An Nguyen-Hoang
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Felix L Sandell
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
| | - Juliane C Dohm
- Institute of Computational Biology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, A-1190 Vienna, Austria
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6
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Salojärvi J, Rambani A, Yu Z, Guyot R, Strickler S, Lepelley M, Wang C, Rajaraman S, Rastas P, Zheng C, Muñoz DS, Meidanis J, Paschoal AR, Bawin Y, Krabbenhoft TJ, Wang ZQ, Fleck SJ, Aussel R, Bellanger L, Charpagne A, Fournier C, Kassam M, Lefebvre G, Métairon S, Moine D, Rigoreau M, Stolte J, Hamon P, Couturon E, Tranchant-Dubreuil C, Mukherjee M, Lan T, Engelhardt J, Stadler P, Correia De Lemos SM, Suzuki SI, Sumirat U, Wai CM, Dauchot N, Orozco-Arias S, Garavito A, Kiwuka C, Musoli P, Nalukenge A, Guichoux E, Reinout H, Smit M, Carretero-Paulet L, Filho OG, Braghini MT, Padilha L, Sera GH, Ruttink T, Henry R, Marraccini P, Van de Peer Y, Andrade A, Domingues D, Giuliano G, Mueller L, Pereira LF, Plaisance S, Poncet V, Rombauts S, Sankoff D, Albert VA, Crouzillat D, de Kochko A, Descombes P. The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars. Nat Genet 2024; 56:721-731. [PMID: 38622339 PMCID: PMC11018527 DOI: 10.1038/s41588-024-01695-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 02/23/2024] [Indexed: 04/17/2024]
Abstract
Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.
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Affiliation(s)
- Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
| | - Aditi Rambani
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Zhe Yu
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - Romain Guyot
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Susan Strickler
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Maud Lepelley
- Société des Produits Nestlé SA, Nestlé Research, Tours, France
| | - Cui Wang
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Sitaram Rajaraman
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniella Santos Muñoz
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - João Meidanis
- Institute of Computing, University of Campinas, Campinas, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science, The Federal University of Technology - Paraná (UTFPR), Cornélio Procópio, Brazil
| | - Yves Bawin
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | | | - Zhen Qin Wang
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Steven J Fleck
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Rudy Aussel
- Société des Produits Nestlé SA, Nestlé Research, Tours, France
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, Marseille, France
| | | | - Aline Charpagne
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Coralie Fournier
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Mohamed Kassam
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Gregory Lefebvre
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Sylviane Métairon
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Déborah Moine
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Michel Rigoreau
- Société des Produits Nestlé SA, Nestlé Research, Tours, France
| | - Jens Stolte
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland
| | - Perla Hamon
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | - Emmanuel Couturon
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | | | - Minakshi Mukherjee
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Tianying Lan
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jan Engelhardt
- Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Peter Stadler
- Department of Computer Science, University of Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | | | | | - Ucu Sumirat
- Indonesian Coffee and Cocoa Research Institute (ICCRI), Jember, Indonesia
| | - Ching Man Wai
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicolas Dauchot
- Research Unit in Plant Cellular and Molecular Biology, University of Namur, Namur, Belgium
| | - Simon Orozco-Arias
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Andrea Garavito
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Catherine Kiwuka
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Pascal Musoli
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Anne Nalukenge
- National Agricultural Research Organization (NARO), Entebbe, Uganda
| | - Erwan Guichoux
- Biodiversité Gènes & Communautés, INRA, Bordeaux, France
| | | | - Martin Smit
- Hortus Botanicus Amsterdam, Amsterdam, the Netherlands
| | | | - Oliveiro Guerreiro Filho
- Instituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil
| | - Masako Toma Braghini
- Instituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil
| | - Lilian Padilha
- Embrapa Café/Instituto Agronômico (IAC) Centro de Café 'Alcides Carvalho', Fazenda Santa Elisa, Campinas, Brazil
| | | | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Pierre Marraccini
- CIRAD - UMR DIADE (IRD-CIRAD-Université de Montpellier) BP 64501, Montpellier, France
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Alan Andrade
- Embrapa Café/Inovacafé Laboratory of Molecular Genetics Campus da UFLA-MG, Lavras, Brazil
| | - Douglas Domingues
- Group of Genomics and Transcriptomes in Plants, São Paulo State University, UNESP, Rio Claro, Brazil
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Casaccia Research Center, Rome, Italy
| | - Lukas Mueller
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Luiz Filipe Pereira
- Embrapa Café/Lab. Biotecnologia, Área de Melhoramento Genético, Londrina, Brazil
| | | | - Valerie Poncet
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
| | | | - Alexandre de Kochko
- Institut de Recherche pour le Développement (IRD), Université de Montpellier, Montpellier, France.
| | - Patrick Descombes
- Société des Produits Nestlé SA, Nestlé Research, Lausanne, Switzerland.
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Senczuk G, Macrì M, Di Civita M, Mastrangelo S, Del Rosario Fresno M, Capote J, Pilla F, Delgado JV, Amills M, Martínez A. The demographic history and adaptation of Canarian goat breeds to environmental conditions through the use of genome-wide SNP data. Genet Sel Evol 2024; 56:2. [PMID: 38172652 PMCID: PMC10763158 DOI: 10.1186/s12711-023-00869-0] [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: 08/04/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The presence of goats in the Canary Islands dates back to the late 1st millennium BC, which coincides with the colonization by the Amazigh settlers. However, the exact geographic origin of Canarian goats is uncertain since the Amazigh peoples were distributed over a wide spatial range. Nowadays, three Canarian breeds (Palmera, Majorera and Tinerfeña) are officially recognized, along with two distinct South and North Tinerfeña ecotypes, with the South Tinerfeña and Majorera goats thriving in arid and dry semi-desertic environments and the Palmera and North Tinerfeña goats are adapted to humid and temperate areas that are influenced by trade winds. Genotypes for 224 Canarian goats were generated using the Illumina Goat single nucleotide polymorphism (SNP)50 BeadChip. By merging these data with the genotypes from 1007 individuals of African and Southern European ancestry, our aim was to ascertain the geographic origin of the Canarian goats and identify genes associated with adaptation to diverse environmental conditions. RESULTS The diversity indices of the Canarian breeds align with most of those of the analyzed local breeds from Africa and Europe, except for the Palmera goats that showed lower levels of genetic variation. The Canarian breeds demonstrate a significant genetic differentiation compared to other populations, which indicates a history of prolonged geographic isolation. Moreover, the phylogenetic reconstruction indicated that the ancestry of the Canarian goats is fundamentally North African rather than West African. The ADMIXTURE and the TreeMix analyses showed no evidence of gene flow between Canarian goats and other continental breeds. The analysis of runs of homozygosity (ROH) identified 13 ROH islands while the window-based FST method detected 25 genomic regions under selection. Major signals of selection were found on Capra hircus (CHI) chromosomes 6, 7, and 10 using various comparisons and methods. CONCLUSIONS This genome-wide analysis sheds new light on the evolutionary history of the four breeds that inhabit the Canary Islands. Our findings suggest a North African origin of the Canarian goats. In addition, within the genomic regions highlighted by the ROH and FST approaches, several genes related to body size and heat tolerance were identified.
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Affiliation(s)
- Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy.
| | - Martina Macrì
- Animal Breeding Consulting S.L., 14014, Córdoba, Spain
- Universidad de Córdoba, 14071, Córdoba, Spain
| | - Marika Di Civita
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128, Palermo, Italy
| | | | - Juan Capote
- Instituto Canario de Investigaciones Científicas, 38260, Tenerife, Spain
| | - Fabio Pilla
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100, Campobasso, Italy
| | | | - Marcel Amills
- CRAG, CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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8
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Morell Miranda P, Soares AER, Günther T. Demographic reconstruction of the Western sheep expansion from whole-genome sequences. G3 (BETHESDA, MD.) 2023; 13:jkad199. [PMID: 37675574 PMCID: PMC11648245 DOI: 10.1093/g3journal/jkad199] [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: 06/09/2023] [Revised: 04/28/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023]
Abstract
As one of the earliest livestock, sheep (Ovis aries) were domesticated in the Fertile Crescent about 12,000-10,000 years ago and have a nearly worldwide distribution today. Most of our knowledge about the timing of their expansions stems from archaeological data but it is unclear how the genetic diversity of modern sheep fits with these dates. We used whole-genome sequencing data of 63 domestic breeds and their wild relatives, the Asiatic mouflon (O. gmelini, previously known as O. orientalis), to explore the demographic history of sheep. On the global scale, our analysis revealed geographic structuring among breeds with unidirectional recent gene flow from domestics into Asiatic mouflons. We then selected 4 representative breeds from Spain, Morocco, the United Kingdom, and Iran to build a comprehensive demographic model of the Western sheep expansion. We inferred a single domestication event around 11,000 years ago. The subsequent westward expansion is dated to approximately 7,000 years ago, later than the original Neolithic expansion of sheep and slightly predating the Secondary Product Revolution associated with wooly sheep. We see some signals of recent gene flow from an ancestral population into Southern European breeds which could reflect admixture with feral European mouflon. Furthermore, our results indicate that many breeds experienced a reduction of their effective population size during the last centuries, probably associated with modern breed development. Our study provides insights into the complex demographic history of Western Eurasian sheep, highlighting interactions between breeds and their wild counterparts.
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Affiliation(s)
- Pedro Morell Miranda
- Human Evolution, Department of Organismal Biology, Uppsala
University, SE-752 36 Uppsala, Sweden
| | - André E R Soares
- Human Evolution, Department of Organismal Biology, Uppsala
University, SE-752 36 Uppsala, Sweden
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory,
Department of Medical Biochemistry and Microbiology, Uppsala University,
SE-752 37 Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala
University, SE-752 36 Uppsala, Sweden
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9
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Coimbra RTF, Winter S, Muneza A, Fennessy S, Otiende M, Mijele D, Masiaine S, Stacy-Dawes J, Fennessy J, Janke A. Genomic analysis reveals limited hybridization among three giraffe species in Kenya. BMC Biol 2023; 21:215. [PMID: 37833744 PMCID: PMC10576358 DOI: 10.1186/s12915-023-01722-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa. RESULTS We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe. CONCLUSIONS Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.
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Affiliation(s)
- Raphael T F Coimbra
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany.
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | | | | | | | | | | | - Julian Fennessy
- Giraffe Conservation Foundation, Windhoek, Namibia
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany.
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany.
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10
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Flegontov P, Işıldak U, Maier R, Yüncü E, Changmai P, Reich D. Modeling of African population history using f-statistics is biased when applying all previously proposed SNP ascertainment schemes. PLoS Genet 2023; 19:e1010931. [PMID: 37676865 PMCID: PMC10508636 DOI: 10.1371/journal.pgen.1010931] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 09/19/2023] [Accepted: 08/21/2023] [Indexed: 09/09/2023] Open
Abstract
f-statistics have emerged as a first line of analysis for making inferences about demographic history from genome-wide data. Not only are they guaranteed to allow robust tests of the fits of proposed models of population history to data when analyzing full genome sequencing data-that is, all single nucleotide polymorphisms (SNPs) in the individuals being analyzed-but they are also guaranteed to allow robust tests of models for SNPs ascertained as polymorphic in a population that is an outgroup in a phylogenetic sense to all groups being analyzed. True "outgroup ascertainment" is in practice impossible in humans because our species has arisen from a substructured ancestral population that does not descend from a homogeneous ancestral population going back many hundreds of thousands of years into the past. However, initial studies suggested that non-outgroup-ascertainment schemes might produce robust enough results using f-statistics, and that motivated widespread fitting of models to data using non-outgroup-ascertained SNP panels such as the "Affymetrix Human Origins array" which has been genotyped on thousands of modern individuals from hundreds of populations, or the "1240k" in-solution enrichment reagent which has been the source of about 70% of published genome-wide data for ancient humans. In this study, we show that while analyses of population history using such panels work well for studies of relationships among non-African populations and one African outgroup, when co-modeling more than one sub-Saharan African and/or archaic human groups (Neanderthals and Denisovans), fitting of f-statistics to such SNP sets is expected to frequently lead to false rejection of true demographic histories, and failure to reject incorrect models. Analyzing panels of SNPs polymorphic in archaic humans, which has been suggested as a solution for the ascertainment problem, has limited statistical power and retains important biases. However, by carrying out simulations of diverse demographic histories, we show that bias in inferences based on f-statistics can be minimized by ascertaining on variants common in a union of diverse African groups; such ascertainment retains high statistical power while allowing co-analysis of archaic and modern groups.
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Affiliation(s)
- Pavel Flegontov
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Kalmyk Research Center of the Russian Academy of Sciences, Elista, Russia
| | - Ulaş Işıldak
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Robert Maier
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Eren Yüncü
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
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11
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Zhang L, Abhari N, Colijn C, Wu Y. A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings. Genome Res 2023; 33:1053-1060. [PMID: 37217252 PMCID: PMC10538497 DOI: 10.1101/gr.277669.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/16/2023] [Indexed: 05/24/2023]
Abstract
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the minimum phylogenetic network problem, in which phylogenetic trees are first inferred, and then the smallest phylogenetic network that displays all the trees is computed. The approach takes advantage of the fact that the theory of phylogenetic trees is mature, and there are excellent tools available for inferring phylogenetic trees from a large number of biomolecular sequences. A tree-child network is a phylogenetic network satisfying the condition that every nonleaf node has at least one child that is of indegree one. Here, we develop a new method that infers the minimum tree-child network by aligning lineage taxon strings in the phylogenetic trees. This algorithmic innovation enables us to get around the limitations of the existing programs for phylogenetic network inference. Our new program, named ALTS, is fast enough to infer a tree-child network with a large number of reticulations for a set of up to 50 phylogenetic trees with 50 taxa that have only trivial common clusters in about a quarter of an hour on average.
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Affiliation(s)
- Louxin Zhang
- Department of Mathematics and Centre for Data Science and Machine Learning, National University of Singapore, Singapore 119076, Singapore;
| | - Niloufar Abhari
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Yufeng Wu
- Department of Computer Science and Engineering and Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269, USA
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12
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Capodiferro MR, Chero Osorio AM, Rambaldi Migliore N, Tineo Tineo DH, Raveane A, Xavier C, Bodner M, Simão F, Ongaro L, Montinaro F, Lindo J, Huerta-Sanchez E, Politis G, Barbieri C, Parson W, Gusmão L, Achilli A. The multifaceted genomic history of Ashaninka from Amazonian Peru. Curr Biol 2023; 33:1573-1581.e5. [PMID: 36931272 DOI: 10.1016/j.cub.2023.02.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/14/2022] [Accepted: 02/14/2023] [Indexed: 03/18/2023]
Abstract
Despite its crucial location, the western side of Amazonia between the Andes and the source(s) of the Amazon River is still understudied from a genomic and archaeogenomic point of view, albeit possibly harboring essential information to clarify the complex genetic history of local Indigenous groups and their interactions with nearby regions,1,2,3,4,5,6,7,8 including central America and the Caribbean.9,10,11,12 Focusing on this key region, we analyzed the genome-wide profiles of 51 Ashaninka individuals from Amazonian Peru, observing an unexpected extent of genomic variation. We identified at least two Ashaninka subgroups with distinctive genomic makeups, which were differentially shaped by the degree and timing of external admixtures, especially with the Indigenous groups from the Andes and the Pacific coast. On a continental scale, Ashaninka ancestors probably derived from a south-north migration of Indigenous groups moving into the Amazonian rainforest from a southeastern area with contributions from the Southern Cone and the Atlantic coast. These ancestral populations diversified in the variegated geographic regions of interior South America, on the eastern side of the Andes, differentially interacting with surrounding coastal groups. In this complex scenario, we also revealed strict connections between the ancestors of present-day Ashaninka, who belong to the Arawakan language family,13 and those Indigenous groups that moved further north into the Caribbean, contributing to the early Ceramic (Saladoid) tradition in the islands.14,15.
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Affiliation(s)
- Marco Rosario Capodiferro
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy; Smurfit Institute of Genetics, Trinity College Dublin, D02 CX56 Dublin 2, Ireland.
| | - Ana María Chero Osorio
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Dean Herman Tineo Tineo
- Laboratorio de Biología Forense, Instituto de Medicina Legal y Ciencias Forenses, Ministerio Público, Lima 15033, Perú
| | | | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; I3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4099-002 Porto, Portugal
| | - Martin Bodner
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Filipa Simão
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro 23968-000, Brazil
| | - Linda Ongaro
- Smurfit Institute of Genetics, Trinity College Dublin, D02 CX56 Dublin 2, Ireland
| | - Francesco Montinaro
- Department of Biology-Genetics, University of Bari, 70125 Bari, Italy; Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Emilia Huerta-Sanchez
- Smurfit Institute of Genetics, Trinity College Dublin, D02 CX56 Dublin 2, Ireland; Ecology and Evolutionary Biology and Center for Computational and Molecular Biology, Brown University, Providence, RI 02906, USA
| | - Gustavo Politis
- INCUAPA-CONICET, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Olavarría 7400, Argentina
| | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland; Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; Forensic Science Program, Pennsylvania State University, State College, PA 16801, USA
| | - Leonor Gusmão
- Laboratório de Diagnóstico por DNA (LDD), Universidade do Estado do Rio de Janeiro, Rio de Janeiro 23968-000, Brazil
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy.
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13
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Nielsen SV, Vaughn AH, Leppälä K, Landis MJ, Mailund T, Nielsen R. Bayesian inference of admixture graphs on Native American and Arctic populations. PLoS Genet 2023; 19:e1010410. [PMID: 36780565 PMCID: PMC9956672 DOI: 10.1371/journal.pgen.1010410] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 02/24/2023] [Accepted: 01/23/2023] [Indexed: 02/15/2023] Open
Abstract
Admixture graphs are mathematical structures that describe the ancestry of populations in terms of divergence and merging (admixing) of ancestral populations as a graph. An admixture graph consists of a graph topology, branch lengths, and admixture proportions. The branch lengths and admixture proportions can be estimated using numerous numerical optimization methods, but inferring the topology involves a combinatorial search for which no polynomial algorithm is known. In this paper, we present a reversible jump MCMC algorithm for sampling high-probability admixture graphs and show that this approach works well both as a heuristic search for a single best-fitting graph and for summarizing shared features extracted from posterior samples of graphs. We apply the method to 11 Native American and Siberian populations and exploit the shared structure of high-probability graphs to characterize the relationship between Saqqaq, Inuit, Koryaks, and Athabascans. Our analyses show that the Saqqaq is not a good proxy for the previously identified gene flow from Arctic people into the Na-Dene speaking Athabascans.
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Affiliation(s)
- Svend V. Nielsen
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Andrew H. Vaughn
- Center for Computational Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Kalle Leppälä
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland
| | - Michael J. Landis
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Rasmus Nielsen
- Departments of Integrative Biology and Statistics, University of California Berkeley, Berkeley, California, United States of America
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
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14
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Daly KG, Arbuckle BS, Rossi C, Mattiangeli V, Lawlor PA, Mashkour M, Sauer E, Lesur J, Atici L, Erek CM, Bradley DG. A novel lineage of the Capra genus discovered in the Taurus Mountains of Turkey using ancient genomics. eLife 2022; 11:e82984. [PMID: 36190761 PMCID: PMC9529249 DOI: 10.7554/elife.82984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/09/2022] [Indexed: 11/13/2022] Open
Abstract
Direkli Cave, located in the Taurus Mountains of southern Turkey, was occupied by Late Epipaleolithic hunters-gatherers for the seasonal hunting and processing of game including large numbers of wild goats. We report genomic data from new and published Capra specimens from Direkli Cave and, supplemented with historic genomes from multiple Capra species, find a novel lineage best represented by a ~14,000 year old 2.59 X genome sequenced from specimen Direkli4. This newly discovered Capra lineage is a sister clade to the Caucasian tur species (Capra cylindricornis and Capra caucasica), both now limited to the Caucasus region. We identify genomic regions introgressed in domestic goats with high affinity to Direkli4, and find that West Eurasian domestic goats in the past, but not those today, appear enriched for Direkli4-specific alleles at a genome-wide level. This forgotten 'Taurasian tur' likely survived Late Pleistocene climatic change in a Taurus Mountain refuge and its genomic fate is unknown.
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Affiliation(s)
- Kevin G Daly
- Smurfit Institute of Genetics, Trinity College DublinDublinIreland
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Conor Rossi
- Smurfit Institute of Genetics, Trinity College DublinDublinIreland
| | | | - Phoebe A Lawlor
- Smurfit Institute of Genetics, Trinity College DublinDublinIreland
| | - Marjan Mashkour
- Centre National de Recherche Scientifique / Muséum national d'Histoire naturelle, Archéozoologie, ArchéobotaniqueParisFrance
- University of Tehran, Bioarchaeology Laboratory, (Central Laboratory), Archaeozoology sectionTehranIslamic Republic of Iran
| | - Eberhard Sauer
- School of History, Classics and Archaeology, University of EdinburghEdinburghUnited Kingdom
| | - Joséphine Lesur
- Centre National de Recherche Scientifique / Muséum national d'Histoire naturelle, Archéozoologie, ArchéobotaniqueParisFrance
| | - Levent Atici
- Department of Anthropology, University of Nevada, Las VegasLas VegasUnited States
| | - Cevdet Merih Erek
- Department of Archeology, Department of Prehistoric Archeology, Faculty of Letters, Ankara Hacı Bayram Veli UniversityAnkaraTurkey
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College DublinDublinIreland
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15
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Vallini L, Marciani G, Aneli S, Bortolini E, Benazzi S, Pievani T, Pagani L. Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa. Genome Biol Evol 2022; 14:evac045. [PMID: 35445261 PMCID: PMC9021735 DOI: 10.1093/gbe/evac045] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 11/14/2022] Open
Abstract
The population dynamics that followed the Out of Africa (OoA) expansion and the whereabouts of the early migrants before the differentiation that ultimately led to the formation of Oceanian, West and East Eurasian macropopulations have long been debated. Shedding light on these events may, in turn, provide clues to better understand the cultural evolution in Eurasia between 50 and 35 ka. Here, we analyze Eurasian Paleolithic DNA evidence to provide a comprehensive population model and validate it in light of available material culture. Leveraging on our integrated approach we propose the existence of a Eurasian population Hub, where Homo sapiens lived between the OoA and the broader colonization of Eurasia, which was characterized by multiple events of expansion and local extinction. A major population wave out of Hub, of which Ust'Ishim, Bacho Kiro, and Tianyuan are unadmixed representatives, is broadly associated with Initial Upper Paleolithic lithics and populated West and East Eurasia before or around 45 ka, before getting largely extinct in Europe. In this light, we suggest a parsimonious placement of Oase1 as an individual related to Bacho Kiro who experienced additional Neanderthal introgression. Another expansion, started before 38 ka, is broadly associated with Upper Paleolithic industries and repopulated Europe with sporadic admixtures with the previous wave (GoyetQ116-1) and more systematic ones, whereas moving through Siberia (Yana, Mal'ta). Before these events, we also confirm Zlatý Kůň as the most basal human lineage sequenced to date OoA, potentially representing an earlier wave of expansion out of the Hub.
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Affiliation(s)
| | - Giulia Marciani
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
- Department of Physical Sciences, Earth and Environment, University of Siena, Italy
| | - Serena Aneli
- Department of Biology, University of Padova, Italy
- Department of Public Health Sciences and Pediatrics, University of Turin, Italy
| | - Eugenio Bortolini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Luca Pagani
- Department of Biology, University of Padova, Italy
- Institute of Genomics, University of Tartu, Estonia
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16
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Librado P, Khan N, Fages A, Kusliy MA, Suchan T, Tonasso-Calvière L, Schiavinato S, Alioglu D, Fromentier A, Perdereau A, Aury JM, Gaunitz C, Chauvey L, Seguin-Orlando A, Der Sarkissian C, Southon J, Shapiro B, Tishkin AA, Kovalev AA, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Seregély T, Klassen L, Iversen R, Bignon-Lau O, Bodu P, Olive M, Castel JC, Boudadi-Maligne M, Alvarez N, Germonpré M, Moskal-del Hoyo M, Wilczyński J, Pospuła S, Lasota-Kuś A, Tunia K, Nowak M, Rannamäe E, Saarma U, Boeskorov G, Lōugas L, Kyselý R, Peške L, Bălășescu A, Dumitrașcu V, Dobrescu R, Gerber D, Kiss V, Szécsényi-Nagy A, Mende BG, Gallina Z, Somogyi K, Kulcsár G, Gál E, Bendrey R, Allentoft ME, Sirbu G, Dergachev V, Shephard H, Tomadini N, Grouard S, Kasparov A, Basilyan AE, Anisimov MA, Nikolskiy PA, Pavlova EY, Pitulko V, Brem G, Wallner B, Schwall C, Keller M, Kitagawa K, Bessudnov AN, Bessudnov A, Taylor W, Magail J, Gantulga JO, Bayarsaikhan J, Erdenebaatar D, Tabaldiev K, Mijiddorj E, Boldgiv B, Tsagaan T, Pruvost M, Olsen S, Makarewicz CA, Valenzuela Lamas S, Albizuri Canadell S, Nieto Espinet A, Iborra MP, Lira Garrido J, Rodríguez González E, Celestino S, Olària C, Arsuaga JL, Kotova N, Pryor A, Crabtree P, Zhumatayev R, et alLibrado P, Khan N, Fages A, Kusliy MA, Suchan T, Tonasso-Calvière L, Schiavinato S, Alioglu D, Fromentier A, Perdereau A, Aury JM, Gaunitz C, Chauvey L, Seguin-Orlando A, Der Sarkissian C, Southon J, Shapiro B, Tishkin AA, Kovalev AA, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Seregély T, Klassen L, Iversen R, Bignon-Lau O, Bodu P, Olive M, Castel JC, Boudadi-Maligne M, Alvarez N, Germonpré M, Moskal-del Hoyo M, Wilczyński J, Pospuła S, Lasota-Kuś A, Tunia K, Nowak M, Rannamäe E, Saarma U, Boeskorov G, Lōugas L, Kyselý R, Peške L, Bălășescu A, Dumitrașcu V, Dobrescu R, Gerber D, Kiss V, Szécsényi-Nagy A, Mende BG, Gallina Z, Somogyi K, Kulcsár G, Gál E, Bendrey R, Allentoft ME, Sirbu G, Dergachev V, Shephard H, Tomadini N, Grouard S, Kasparov A, Basilyan AE, Anisimov MA, Nikolskiy PA, Pavlova EY, Pitulko V, Brem G, Wallner B, Schwall C, Keller M, Kitagawa K, Bessudnov AN, Bessudnov A, Taylor W, Magail J, Gantulga JO, Bayarsaikhan J, Erdenebaatar D, Tabaldiev K, Mijiddorj E, Boldgiv B, Tsagaan T, Pruvost M, Olsen S, Makarewicz CA, Valenzuela Lamas S, Albizuri Canadell S, Nieto Espinet A, Iborra MP, Lira Garrido J, Rodríguez González E, Celestino S, Olària C, Arsuaga JL, Kotova N, Pryor A, Crabtree P, Zhumatayev R, Toleubaev A, Morgunova NL, Kuznetsova T, Lordkipanize D, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Clavel B, Lepetz S, Davoudi H, Mashkour M, Berezina NY, Stockhammer PW, Krause J, Haak W, Morales-Muñiz A, Benecke N, Hofreiter M, Ludwig A, Graphodatsky AS, Peters J, Kiryushin KY, Iderkhangai TO, Bokovenko NA, Vasiliev SK, Seregin NN, Chugunov KV, Plasteeva NA, Baryshnikov GF, Petrova E, Sablin M, Ananyevskaya E, Logvin A, Shevnina I, Logvin V, Kalieva S, Loman V, Kukushkin I, Merz I, Merz V, Sakenov S, Varfolomeyev V, Usmanova E, Zaibert V, Arbuckle B, Belinskiy AB, Kalmykov A, Reinhold S, Hansen S, Yudin AI, Vybornov AA, Epimakhov A, Berezina NS, Roslyakova N, Kosintsev PA, Kuznetsov PF, Anthony D, Kroonen GJ, Kristiansen K, Wincker P, Outram A, Orlando L. The origins and spread of domestic horses from the Western Eurasian steppes. Nature 2021; 598:634-640. [PMID: 34671162 PMCID: PMC8550961 DOI: 10.1038/s41586-021-04018-9] [Show More Authors] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/10/2021] [Indexed: 01/13/2023]
Abstract
Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2-4 at Botai, Central Asia around 3500 BC3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture11,12.
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Affiliation(s)
- Pablo Librado
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Naveed Khan
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France ,grid.440522.50000 0004 0478 6450Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Antoine Fages
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Mariya A. Kusliy
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France ,grid.415877.80000 0001 2254 1834Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Tomasz Suchan
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France ,grid.413454.30000 0001 1958 0162W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Laure Tonasso-Calvière
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Stéphanie Schiavinato
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Duha Alioglu
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Aurore Fromentier
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Aude Perdereau
- grid.460789.40000 0004 4910 6535Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université d’Evry, Université Paris-Saclay, Evry, France
| | - Charleen Gaunitz
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Lorelei Chauvey
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Andaine Seguin-Orlando
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Clio Der Sarkissian
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - John Southon
- grid.266093.80000 0001 0668 7243Earth System Science Department, University of California, Irvine, Irvine, CA USA
| | - Beth Shapiro
- grid.205975.c0000 0001 0740 6917Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA USA
| | - Alexey A. Tishkin
- grid.77225.350000000112611077Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Alexey A. Kovalev
- grid.465449.e0000 0001 1214 1108Department of Archaeological Heritage Preservation, Institute of Archaeology of the Russian Academy of Sciences, Moscow, Russia
| | - Saleh Alquraishi
- grid.56302.320000 0004 1773 5396Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed H. Alfarhan
- grid.56302.320000 0004 1773 5396Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Khaled A. S. Al-Rasheid
- grid.56302.320000 0004 1773 5396Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Timo Seregély
- grid.7359.80000 0001 2325 4853Institute for Archaeology, Heritage Conservation Studies and Art History, University of Bamberg, Bamberg, Germany
| | | | - Rune Iversen
- grid.5254.60000 0001 0674 042XSaxo Institute, section of Archaeology, University of Copenhagen, Copenhagen, Denmark
| | - Olivier Bignon-Lau
- grid.4444.00000 0001 2112 9282ArScAn-UMR 7041, Equipe Ethnologie préhistorique, CNRS, MSH-Mondes, Nanterre Cedex, France
| | - Pierre Bodu
- grid.4444.00000 0001 2112 9282ArScAn-UMR 7041, Equipe Ethnologie préhistorique, CNRS, MSH-Mondes, Nanterre Cedex, France
| | - Monique Olive
- grid.4444.00000 0001 2112 9282ArScAn-UMR 7041, Equipe Ethnologie préhistorique, CNRS, MSH-Mondes, Nanterre Cedex, France
| | | | - Myriam Boudadi-Maligne
- grid.412041.20000 0001 2106 639XUMR 5199 De la Préhistoire à l’Actuel : Culture, Environnement et Anthropologie (PACEA), CNRS, Université de Bordeaux, Pessac Cedex, France
| | - Nadir Alvarez
- grid.466902.f0000 0001 2248 6951Geneva Natural History Museum, Geneva, Switzerland ,grid.8591.50000 0001 2322 4988Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Mietje Germonpré
- grid.20478.390000 0001 2171 9581OD Earth & History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Magdalena Moskal-del Hoyo
- grid.413454.30000 0001 1958 0162W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Jarosław Wilczyński
- grid.413454.30000 0001 1958 0162Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Sylwia Pospuła
- grid.413454.30000 0001 1958 0162Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Anna Lasota-Kuś
- grid.413454.30000 0001 1958 0162Institute of Archaeology and Ethnology Polish Academy of Sciences, Kraków, Poland
| | - Krzysztof Tunia
- grid.413454.30000 0001 1958 0162Institute of Archaeology and Ethnology Polish Academy of Sciences, Kraków, Poland
| | - Marek Nowak
- grid.5522.00000 0001 2162 9631Institute of Archaeology, Jagiellonian University, Kraków, Poland
| | - Eve Rannamäe
- Department of Archaeology, Institute of History and Archaeology, Tartu, Estonia
| | - Urmas Saarma
- grid.10939.320000 0001 0943 7661Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Gennady Boeskorov
- Diamond and Precious Metals Geology Institute, SB RAS, Yakutsk, Russia
| | - Lembi Lōugas
- grid.8207.d0000 0000 9774 6466Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | - René Kyselý
- grid.447879.10000 0001 0792 540XDepartment of Natural Sciences and Archaeometry, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czechia
| | | | - Adrian Bălășescu
- grid.418333.e0000 0004 1937 1389Vasile Pârvan Institute of Archaeology, Department of Bioarchaeology, Romanian Academy, Bucharest, Romania
| | - Valentin Dumitrașcu
- grid.418333.e0000 0004 1937 1389Vasile Pârvan Institute of Archaeology, Department of Bioarchaeology, Romanian Academy, Bucharest, Romania
| | - Roxana Dobrescu
- grid.418333.e0000 0004 1937 1389Vasile Pârvan Institute of Archaeology, Department of Bioarchaeology, Romanian Academy, Bucharest, Romania
| | - Daniel Gerber
- grid.481823.4Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary ,grid.5591.80000 0001 2294 6276Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Viktória Kiss
- grid.481830.60000 0001 2238 5843Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary
| | - Anna Szécsényi-Nagy
- grid.481823.4Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary
| | - Balázs G. Mende
- grid.481823.4Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary
| | | | | | - Gabriella Kulcsár
- grid.481830.60000 0001 2238 5843Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary
| | - Erika Gál
- grid.481830.60000 0001 2238 5843Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary
| | - Robin Bendrey
- grid.4305.20000 0004 1936 7988School of History, Classics and Archaeology, University of Edinburgh, Old Medical School, Edinburgh, UK
| | - Morten E. Allentoft
- grid.1032.00000 0004 0375 4078Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia Australia ,grid.5254.60000 0001 0674 042XLundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ghenadie Sirbu
- grid.435140.7Department of Academic Management, Academy of Science of Moldova, Chișinău, Republic of Moldova
| | - Valentin Dergachev
- grid.435140.7Center of Archaeology, Institute of Cultural Heritage, Academy of Science of Moldova, Chișinău, Republic of Moldova
| | - Henry Shephard
- grid.446391.d0000 0001 2190 3450Archaeological Institute of America, Boston, MA USA
| | - Noémie Tomadini
- Centre National de Recherche Scientifique, Muséum national d’Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Sandrine Grouard
- Centre National de Recherche Scientifique, Muséum national d’Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Aleksei Kasparov
- grid.473277.20000 0001 2291 1890Institute for the History of Material Culture, Russian Academy of Sciences (IHMC RAS), St Petersburg, Russia
| | | | - Mikhail A. Anisimov
- grid.424187.c0000 0001 1942 9788Arctic and Antarctic Research Institute, St Petersburg, Russia
| | - Pavel A. Nikolskiy
- grid.465388.4Geological Institute, Russian Academy of Sciences, Moscow, Russia
| | - Elena Y. Pavlova
- grid.424187.c0000 0001 1942 9788Arctic and Antarctic Research Institute, St Petersburg, Russia
| | - Vladimir Pitulko
- grid.473277.20000 0001 2291 1890Institute for the History of Material Culture, Russian Academy of Sciences (IHMC RAS), St Petersburg, Russia
| | - Gottfried Brem
- grid.6583.80000 0000 9686 6466Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Barbara Wallner
- grid.6583.80000 0000 9686 6466Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Christoph Schwall
- grid.466489.10000 0001 2151 4674Department of Prehistory and Western Asian/Northeast African Archaeology, Austrian Archaeological Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Marcel Keller
- grid.10939.320000 0001 0943 7661Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia ,grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Keiko Kitagawa
- grid.10392.390000 0001 2190 1447SFB 1070 Resource Cultures, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany ,grid.4444.00000 0001 2112 9282UMR 7194 Muséum National d’Histoire Naturelle, CNRS, UPVD, Paris, France
| | - Alexander N. Bessudnov
- grid.459698.f0000 0000 8989 8101Semenov-Tyan-Shanskii Lipetsk State Pedagogical University, Lipetsk, Russia
| | - Alexander Bessudnov
- grid.473277.20000 0001 2291 1890Institute for the History of Material Culture, Russian Academy of Sciences (IHMC RAS), St Petersburg, Russia
| | - William Taylor
- grid.266190.a0000000096214564Museum of Natural History, University of Colorado-Boulder, Boulder, CO USA
| | - Jérome Magail
- Musée d’Anthropologie préhistorique de Monaco, Monaco, Monaco
| | - Jamiyan-Ombo Gantulga
- grid.425564.40000 0004 0587 3863Institute of Archaeology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Jamsranjav Bayarsaikhan
- grid.469873.70000 0004 4914 1197Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany ,Chinggis Khaan Museum, Ulaanbaatar, Mongolia
| | | | - Kubatbeek Tabaldiev
- grid.444269.90000 0004 0387 4627Department of History, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Enkhbayar Mijiddorj
- Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar, Mongolia
| | - Bazartseren Boldgiv
- grid.260731.10000 0001 2324 0259Department of Biology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Turbat Tsagaan
- grid.425564.40000 0004 0587 3863Institute of Archaeology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Mélanie Pruvost
- grid.412041.20000 0001 2106 639XUMR 5199 De la Préhistoire à l’Actuel : Culture, Environnement et Anthropologie (PACEA), CNRS, Université de Bordeaux, Pessac Cedex, France
| | - Sandra Olsen
- grid.266515.30000 0001 2106 0692Division of Archaeology, Biodiversity Institute, University of Kansas, Lawrence, KS USA
| | - Cheryl A. Makarewicz
- grid.9764.c0000 0001 2153 9986Institute for Prehistoric and Protohistoric Archaeology, Kiel University, Kiel, Germany ,grid.9764.c0000 0001 2153 9986ROOTS Excellence Cluster, Kiel University, Kiel, Germany
| | - Silvia Valenzuela Lamas
- grid.4711.30000 0001 2183 4846Archaeology of Social Dynamics, Institució Milà i Fontanals d’Humanitats, Consejo Superior de Investigaciones Científicas (IMF-CSIC), Barcelona, Spain
| | - Silvia Albizuri Canadell
- grid.5841.80000 0004 1937 0247Departament d’Història i Arqueologia–SERP, Universitat de Barcelona, Barcelona, Spain
| | - Ariadna Nieto Espinet
- grid.15043.330000 0001 2163 1432Grup d’Investigació Prehistòrica, Universitat de Lleida, PID2019-110022GB-I00, Lleida, Spain
| | | | - Jaime Lira Garrido
- grid.8393.10000000119412521Departamento de Medicina Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain ,Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain
| | | | - Sebastián Celestino
- grid.454770.50000 0001 1945 3489Instituto de Arqueología (CSIC–Junta de Extremadura), Mérida, Spain
| | - Carmen Olària
- grid.9612.c0000 0001 1957 9153Laboratori d’Arqueologia Prehistòrica, Universitat Jaume I, Castelló de la Plana, Spain
| | - Juan Luis Arsuaga
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain ,grid.4795.f0000 0001 2157 7667Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Nadiia Kotova
- grid.418751.e0000 0004 0385 8977Department of Eneolithic and Bronze Age, Institute of Archaeology National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alexander Pryor
- grid.8391.30000 0004 1936 8024Department of Archaeology, University of Exeter, Exeter, UK
| | - Pam Crabtree
- grid.137628.90000 0004 1936 8753Center for the Study of Human Origins, Anthropology Department, New York University, New York, NY USA
| | - Rinat Zhumatayev
- grid.77184.3d0000 0000 8887 5266Department of Archaeology, Ethnology and Museology, Al Farabi Kazakh National University, Almaty, Kazakhstan
| | - Abdesh Toleubaev
- grid.77184.3d0000 0000 8887 5266Department of Archaeology, Ethnology and Museology, Al Farabi Kazakh National University, Almaty, Kazakhstan
| | - Nina L. Morgunova
- grid.445474.20000 0001 1092 7131Scientific Research Department, Orenburg State Pedagogical University, Orenburg, Russia
| | - Tatiana Kuznetsova
- grid.14476.300000 0001 2342 9668Department of paleontology, Faculty of Geology, Moscow State University, Moscow, Russia ,grid.77268.3c0000 0004 0543 9688Institute of Geology and Petroleum Technologies, Kazan Federal University, Kazan, Russia
| | - David Lordkipanize
- grid.452450.20000 0001 0739 408XGeorgian National Museum, Tbilisi, Georgia ,grid.26193.3f0000 0001 2034 6082Tbilisi State University, Tbilisi, Georgia
| | - Matilde Marzullo
- grid.4708.b0000 0004 1757 2822Università degli Studi di Milano, Dipartimento di Beni Culturali e Ambientali, Milan, Italy
| | - Ornella Prato
- grid.4708.b0000 0004 1757 2822Università degli Studi di Milano, Dipartimento di Beni Culturali e Ambientali, Milan, Italy
| | - Giovanna Bagnasco Gianni
- grid.4708.b0000 0004 1757 2822Università degli Studi di Milano, Dipartimento di Beni Culturali e Ambientali, Milan, Italy
| | - Umberto Tecchiati
- grid.4708.b0000 0004 1757 2822Università degli Studi di Milano, Dipartimento di Beni Culturali e Ambientali, Milan, Italy
| | - Benoit Clavel
- Centre National de Recherche Scientifique, Muséum national d’Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Sébastien Lepetz
- Centre National de Recherche Scientifique, Muséum national d’Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Hossein Davoudi
- grid.46072.370000 0004 0612 7950University of Tehran, Central Laboratory, Bioarchaeology Laboratory, Archaeozoology Section, Tehran, Iran
| | - Marjan Mashkour
- Centre National de Recherche Scientifique, Muséum national d’Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France ,grid.46072.370000 0004 0612 7950University of Tehran, Central Laboratory, Bioarchaeology Laboratory, Archaeozoology Section, Tehran, Iran
| | - Natalia Ya. Berezina
- grid.14476.300000 0001 2342 9668Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | - Philipp W. Stockhammer
- grid.419518.00000 0001 2159 1813Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany ,grid.5252.00000 0004 1936 973XInstitute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, Munich, Munich, Germany
| | - Johannes Krause
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Wolfgang Haak
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany ,grid.1010.00000 0004 1936 7304School of Biological Sciences, The University of Adelaide, Adelaide, South Australia Australia
| | - Arturo Morales-Muñiz
- grid.5515.40000000119578126Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Norbert Benecke
- grid.424195.f0000 0001 2106 6832Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Michael Hofreiter
- grid.11348.3f0000 0001 0942 1117Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Mathematics and Science, University of Potsdam, Potsdam, Germany
| | - Arne Ludwig
- grid.418779.40000 0001 0708 0355Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany ,grid.7468.d0000 0001 2248 7639Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt University Berlin, Berlin, Germany
| | - Alexander S. Graphodatsky
- grid.415877.80000 0001 2254 1834Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Joris Peters
- grid.5252.00000 0004 1936 973XArchaeoBioCenter and Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, Munich, Germany ,grid.452781.d0000 0001 2203 6205SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany
| | - Kirill Yu. Kiryushin
- grid.77225.350000000112611077Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | | | - Nikolay A. Bokovenko
- grid.473277.20000 0001 2291 1890Institute for the History of Material Culture, Russian Academy of Sciences (IHMC RAS), St Petersburg, Russia
| | - Sergey K. Vasiliev
- grid.415877.80000 0001 2254 1834ArchaeoZOOlogy in Siberia and Central Asia—ZooSCAn International Research Laboratory, Institute of Archeology and Ethnography of the Siberian Branch of the RAS, Novosibirsk, Russia
| | - Nikolai N. Seregin
- grid.77225.350000000112611077Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Konstantin V. Chugunov
- grid.426493.e0000 0004 1800 742XDepartment of Eastern European and Siberian Archaeology, State Hermitage Museum, St Petersburg, Russia
| | - Natalya A. Plasteeva
- grid.482778.60000 0001 2197 0186Paleoecology Laboratory, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
| | - Gennady F. Baryshnikov
- grid.439287.30000 0001 2314 7601Zoological Institute, Russian Academy of Sciences, St Petersburg, Russia
| | - Ekaterina Petrova
- grid.6441.70000 0001 2243 2806Department of Archaeology, History Faculty, Vilnius University, Vilnius, Lithuania
| | - Mikhail Sablin
- grid.439287.30000 0001 2314 7601Zoological Institute, Russian Academy of Sciences, St Petersburg, Russia
| | - Elina Ananyevskaya
- grid.6441.70000 0001 2243 2806Department of Archaeology, History Faculty, Vilnius University, Vilnius, Lithuania
| | - Andrey Logvin
- grid.443586.8Laboratory for Archaeological Research, Faculty of History and Law, Kostanay State University, Kostanay, Kazakhstan
| | - Irina Shevnina
- grid.443586.8Laboratory for Archaeological Research, Faculty of History and Law, Kostanay State University, Kostanay, Kazakhstan
| | - Victor Logvin
- Department of History and Archaeology, Surgut Governmental University, Surgut, Russia
| | - Saule Kalieva
- Department of History and Archaeology, Surgut Governmental University, Surgut, Russia
| | - Valeriy Loman
- Saryarka Archaeological Institute, Buketov Karaganda University, Karaganda, Kazakhstan
| | - Igor Kukushkin
- Saryarka Archaeological Institute, Buketov Karaganda University, Karaganda, Kazakhstan
| | - Ilya Merz
- Toraighyrov University, Joint Research Center for Archeological Studies, Pavlodar, Kazakhstan
| | - Victor Merz
- Toraighyrov University, Joint Research Center for Archeological Studies, Pavlodar, Kazakhstan
| | - Sergazy Sakenov
- grid.55380.3b0000 0004 0398 5415Faculty of History, L. N. Gumilev Eurasian National University, Nur-Sultan, Kazakhstan
| | - Victor Varfolomeyev
- Saryarka Archaeological Institute, Buketov Karaganda University, Karaganda, Kazakhstan
| | - Emma Usmanova
- Saryarka Archaeological Institute, Buketov Karaganda University, Karaganda, Kazakhstan
| | - Viktor Zaibert
- grid.77184.3d0000 0000 8887 5266Institute of Archaeology and Steppe Civilizations, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Benjamin Arbuckle
- grid.10698.360000000122483208Department of Anthropology, Alumni Building, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | | | | | - Sabine Reinhold
- grid.424195.f0000 0001 2106 6832Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- grid.424195.f0000 0001 2106 6832Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Aleksandr I. Yudin
- Research Center for the Preservation of Cultural Heritage, Saratov, Russia
| | - Alekandr A. Vybornov
- grid.445790.b0000 0001 2218 2982Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - Andrey Epimakhov
- grid.440724.10000 0000 9958 5862Russian and Foreign History Department, South Ural State University, Chelyabinsk, Russia ,grid.465317.20000 0001 2224 8785South Ural Department, Institute of History and Archaeology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
| | - Natalia S. Berezina
- Archaeological School, Chuvash State Institute of Humanities, Cheboksary, Russia
| | - Natalia Roslyakova
- grid.445790.b0000 0001 2218 2982Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - Pavel A. Kosintsev
- grid.482778.60000 0001 2197 0186Paleoecology Laboratory, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia ,grid.412761.70000 0004 0645 736XDepartment of History of the Institute of Humanities, Ural Federal University, Ekaterinburg, Russia
| | - Pavel F. Kuznetsov
- grid.445790.b0000 0001 2218 2982Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - David Anthony
- grid.38142.3c000000041936754XDepartment of Human Evolutionary Biology, Harvard University, Cambridge, MA USA ,grid.418410.80000 0001 0115 6427Anthropology Faculty, Hartwick College, Oneonta NY, USA
| | - Guus J. Kroonen
- grid.5254.60000 0001 0674 042XDepartment of Nordic Studies and Linguistics, University of Copenhagen, Copenhagen, Denmark ,grid.5132.50000 0001 2312 1970Leiden University Center for Linguistics, Leiden University, Leiden, The Netherlands
| | - Kristian Kristiansen
- grid.8761.80000 0000 9919 9582Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden ,grid.452548.a0000 0000 9817 5300Present Address: Lundbeck Foundation GeoGenetics Centre, Copenhagen, Denmark
| | - Patrick Wincker
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université d’Evry, Université Paris-Saclay, Evry, France
| | - Alan Outram
- grid.8391.30000 0004 1936 8024Department of Archaeology, University of Exeter, Exeter, UK
| | - Ludovic Orlando
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
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