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*, Econogene Consortium, VarGoats Consortium

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)


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
Issue number16
Early online date25 Jun 2022
Publication statusPrint publication - Aug 2022
Externally publishedYes

Bibliographical note

© 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.


  • domestication
  • goat
  • haplogroup
  • introgression
  • migration
  • phylogeography
  • Y-chromosome
  • DNA, Mitochondrial/genetics
  • Goats/genetics
  • Phylogeny
  • Haplotypes/genetics
  • Genetic Variation
  • Animals
  • Y Chromosome/genetics


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