Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

Isaäc J. Nijman, Benjamin D. Rosen, Philippe Bardou, Thomas Faraut, Tristan Cumer, Kevin G. Daly, Zhuqing Zheng, Yudong Cai, Hojjat Asadollahpour, Bengi Çınar Kul, Wei-Yi Zhang, E. Guangxin, A. Ayin, Hayley Baird, Meirat Bakhtin, Valentin A. Bâlteanu, Diana Barfield, Beate Berger, Thor Blichfeldt, Geert BoinkSri R. A. Bugiwati, Zexi Cai, Sean Carolan, Emily Clark, Vlatka Cubric-Curik, Muhammad I. A. Dagong, Tashi Dorji, Louise Drew, Jiazhong Guo, Jón Hallsson, Simon Horvat, Juha Kantanen, Fuki Kawaguchi, Polat Kazymbet, Negar Khayatzadeh, Namshin Kim, Manoj Kumar Shah, Yuying Liao, Amparo Martínez, Joseph S. Masangkay, Maho Masaoka, Raffaele Mazza, John Mcewan, Marco Milanesi, Faruque Md. Omar, Yuto Nomura, Nadjet-Amina Ouchene-Khelifi, Filipe Pereira, Goutam Sahana, Mazdak Salavati, Shinji Sasazaki, Anne Da Silva, Mojca Simčič, Johann Sölkner, Alison Sutherland, Johannes Tigchelaar, Hongpin Zhang, Paolo Ajmone Marsan, Daniel G. Bradley, Licia Colli, Cord Drögemüller, Yu Jiang, Chuzhao Lei, Hideyuki Mannen, François Pompanon, Gwenola Tosser-Klopp, Johannes A. Lenstra, James Kijas, Bernt Guldbrandtsen, Laure Denoyelle, Julien Sarry, Estel Le Talouarn, Adriana Alberti, Céline Orvain, Stefan Engelen, Dylan Duby, Pierre Martin, Coralie Danchin, Delphine Duclos, Daniel Allain, Remy Arquet, Nathalie Mandonnet, Michel Naves, Isabelle Palhiere, Rachel Rupp, Francois Pompanon, Hamid R. Rezaei, Maeve Foran, Alessandra Stella, Marcello Del Corvo, Alessandra Crisa, Donata Marletta, Paola Crepaldi, Michele Ottino, Ettore Randi, Denis Fidalis Mujibi, Timothy Gondwe, Badr Benjelloun, Maria Da Gloria Taela, Oyekan Nash, Muhammad Moaeen-Ud-Din, Carina Visser, Felix Goyache, Isabel Alvarez, Marcel Amills, Armand Sànchez, Juan Capote, Jordi Jordana, Agueda Pons, Illes Balears, Antonio Molina, Hassan Ally Mruttu, Clet Wandui Masiga, Curtis P. Van Tassell, Jim Reecy, Gordon Luikart, Joseph Sikosana, Hoda Anila, Dobi Petrit, Baumung Roswitha, Baret Philippe, Fadlaoui Aziz, Papachristoforou Christos, M. A.A. El-Barody, Taberlet Pierre, England Phillip, Luikart Gordon, Beja-Pereira Albano, Zundel Stéphanie, Trommetter Michel, Erhardt Georg, Brandt Horst, Ibeagha-Awemu Eveline, Gesine Lühken, Daniela Krugmann, Prinzenberg Eva-Maria, Lipsky Shirin, Gutscher Katja, Peter Christina, Roosen Jutta, Bertaglia Marco, Georgoudis Andreas, Jamil Al Tarrayrah, Kliambas Georgios, Kutita Olga, Karetsou Katerina, Ligda Christina, Istvan Anton, Fesus Lazlo, Canali Gabriele, Milanesi Elisabetta, Pellecchia Marco, Carta Antonello, Sechi Tiziana, Cicogna Mario, Fornarelli Francesca, Giovenzana Stefano, Marilli Marta, S. Bordonaro, D’ Urso Giuseppe, Pilla Fabio, D’ Andrea Mariasilvia, Valentini Alessio, Cappuccio Irene, Pariset Lorraine, Abo-Shehada Mahamoud, Lisette M. Van Cann, Niznikowski Roman, Dominik Popielarczyk, Strzelec Ewa, Vlaic Augustin, Dunner Susana, Canon Javier, Cortes Oscar, Garcia David, Caloz Régis, Obexer-Ruff Gabriela, Marie-Louise Glowatzki, Ertugrul Okan, Togan Inci, Koban Evren, Bruford Mike, Perez Trinidad, Juma Gabriela, Hewitt Godfrey, Dalamitra Stella, Wiskin Louise, Taylor Martin, Jones Sam, Scarpa Riccardo

Research output: Contribution to journalArticle

Abstract

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.
Original languageEnglish
Pages (from-to)4364-4380
Number of pages17
JournalMolecular Ecology
Volume31
DOIs
Publication statusPublished - 2022

Keywords

  • domestication
  • goat
  • haplogroup
  • Y-chromosome
  • migration
  • phylogeography
  • introgression

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