Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions
Nijman I.J. Rosen B.D. Bardou P. Faraut T. Cumer T. Daly K.G. Zheng Z. Cai Y. Asadollahpour H. Kul B.Ç. Zhang W.-Y. Guangxin E. Ayin A. Baird H. Bakhtin M. Bâlteanu V.A. Barfield D. Berger B. Blichfeldt T. Boink G. Bugiwati S.R.A. Cai Z. Carolan S. Clark E. Cubric-Curik V. Dagong M.I.A. Dorji T. Drew L. Guo J. Hallsson J. Horvat S. Kantanen J. Kawaguchi F. Kazymbet P. Khayatzadeh N. Kim N. Shah M.K. Liao Y. Martínez A. Masangkay J. Masaoka M. Mazza R. McEwan J. Milanesi M. Omar F.M. Nomura Y. Ouchene-Khelifi N.-A. Pereira F. Sahana G. Salavati M. Sasazaki S. Da Silva A. Simčič M. Sölkner J. Sutherland A. Tigchelaar J. Zhang H. Ajmone-Marsan P. Bradley D.G. Colli L. Drögemüller C. Jiang Y. Lei C. Mannen H. Pompanon F. Tosser-Klopp G. Lenstra J.A. Kijas J. Guldbrandtsen B. Denoyelle L. Sarry J. le Talouarn E. Alberti A. Orvain C. Engelen S. Duby D. Martin P. Danchin C. Duclos D. Allain D. Arquet R. Mandonnet N. Naves M. Palhiere I. Rupp R. Pompanon F. Rezaei H.R. Foran M. Stella A. Del Corvo M. Crisa A. Marletta D. Crepaldi P. Ottino M. Randi E. Mujibi D.F. Gondwe T. Benjelloun B. Taela M.D.G. Nash O. Moaeen-ud-Din M. Visser C. Goyache F. Alvarez I. Amills M. Sànchez A. Capote J. Jordana J. Pons A. Balears I. Molina A. Mruttu H.A. Masiga C.W. Van Tassell C.P. Reecy J. Luikart G. Sikosana J. Anila H. Petrit D. Roswitha B. Philippe B. Aziz F. Christos P. El-Barody M.A.A. Pierre T. Phillip E. Gordon L. Albano B.-P. Stéphanie Z. Michel T. Georg E. Horst B. Eveline I.-A. Lühken G. Krugmann D. Eva-Maria P. Shirin L. Katja G. Christina P. Jutta R. Marco B. Andreas G. Al Tarrayrah J. Georgios K. Olga K. Katerina K. Christina L. Anton I. Lazlo F. Gabriele C. Elisabetta M. Marco P. Antonello C. Tiziana S. Mario C. Francesca F. Stefano G. Marta M. Bordonaro S. Giuseppe D.U. Fabio P. Mariasilvia D.A. Alessio V. Irene C. Lorraine P. Mahamoud A.-S. Van Cann L.M. Roman N. Popielarczyk D. Ewa S. Augustin V. Susana D. Javier C. Oscar C. David G. Régis C. Gabriela O.-R. Glowatzki M.-L. Okan E. Inci T. Evren K. Mike B. Trinidad P. Gabriela J. Godfrey H. Stella D. Louise W. Martin T. Sam J. Riccardo S.
August 2022John Wiley and Sons Inc
Molecular Ecology
2022#31Issue 164364 - 4380 pp.
By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographical range.
domestication , goat , haplogroup , introgression , migration , phylogeography , Y-chromosome
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Utrecht Univ., Utrecht, Netherlands
Univ. Medical Center Utrecht, Utrecht Univ., Utrecht, Netherlands
Agriculture Research Service, Beltsville, MD, United States
GenPhySE, Univ. Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
Trinity College Dublin, Dublin, Ireland
College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
Faculty of Veterinary Medicine, Ankara Univ., Ankara, Turkey
Southwest Univ., Chongqing, China
Kobe Univ., Kobe, Japan
AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
Astana Medical Univ., Astana, Kazakhstan
Inst. of Life Sciences, Univ. Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
Pleystole, Qld, Australia
Univ. Natural Resources and Life Sciences Vienna (BOKU), Vienna, Austria
Norwegian Association of Sheep and Goat Breeders, Aas, Norway
Stichting Zeldzame Huisdierrassen, Wageningen, Netherlands
Hasanuddin Univ., Makassar, Indonesia
Aarhus Univ., Tjele, Denmark
Old Irish Goat Society, Mulranny, Ireland
Univ. Edinburgh, Edinburgh, United Kingdom
Univ. Zagreb, Zagreb, Croatia
International Centre for Integrated Mountain Development, Kathmandu, Nepal
Finch Hatton, Qld, Australia
Sichuan Agricultural Univ., Chengdu, China
Agricultural Univ. Iceland, Reykjavik, Iceland
Univ. Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
Natural Resources Institute Finland (Luke), Jokioinen, Finland
Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
National Animal Nutrition Research Centre, Lalitpur, Nepal
Guangxi Key Laboratory of Livestock Genetic Improvement, Guangxi, China
Universidad de Córdoba, Córdoba, Spain
Univ. of the Philippines, Los Banos, Philippines
Laboratorio Genetica e Servizi, Agrotis srl, Cremona, Italy
Univ. degli studi della Tuscia, Viterbo, Italy
Bangladesh Agricultural Univ., Mymensingh, Bangladesh
Science Veterinary Inst., University of Blida, Blida, Algeria
IDENTIFICA Genetic Testing Maia & Centre for Functional Ecology, Porto, Portugal
E2LIM, Univ. Limoges, Limoges, France
New Zealand Arapawa Goat Association, Masterton, New Zealand
Univ. Cattolica del S. Cuore di Piacenza and BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy
UCSC PRONUTRIGEN Nutrigenomics Res. Centre, Piacenza, Italy
UCSC BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy
Univ. Bern, Bern, Switzerland
Utrecht Univ.
Univ. Medical Center Utrecht
Agriculture Research Service
GenPhySE
Université Grenoble Alpes
Trinity College Dublin
College of Animal Science & Technology
Faculty of Veterinary Medicine
Southwest Univ.
Kobe Univ.
AgResearch
Astana Medical Univ.
Inst. of Life Sciences
Pleystole
Univ. Natural Resources and Life Sciences Vienna (BOKU)
Norwegian Association of Sheep and Goat Breeders
Stichting Zeldzame Huisdierrassen
Hasanuddin Univ.
Aarhus Univ.
Old Irish Goat Society
Univ. Edinburgh
Univ. Zagreb
International Centre for Integrated Mountain Development
Finch Hatton
Sichuan Agricultural Univ.
Agricultural Univ. Iceland
Univ. Ljubljana
Natural Resources Institute Finland (Luke)
Korea Research Institute of Bioscience and Biotechnology (KRIBB)
National Animal Nutrition Research Centre
Guangxi Key Laboratory of Livestock Genetic Improvement
Universidad de Córdoba
Univ. of the Philippines
Laboratorio Genetica e Servizi
Univ. degli studi della Tuscia
Bangladesh Agricultural Univ.
Science Veterinary Inst.
IDENTIFICA Genetic Testing Maia & Centre for Functional Ecology
E2LIM
New Zealand Arapawa Goat Association
Univ. Cattolica del S. Cuore di Piacenza and BioDNA Biodiversity and Ancient DNA Res. Centre
UCSC PRONUTRIGEN Nutrigenomics Res. Centre
UCSC BioDNA Biodiversity and Ancient DNA Res. Centre
Univ. Bern
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