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Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions
  • +66
  • Vargoats Consortium,
  • Isaäc Nijman,
  • Benjamin Rosen,
  • Philippe Bardou,
  • Thomas Faraut,
  • Tristan Cumer,
  • Kevin Daly,
  • Zhuqing Zheng,
  • Yudong Cai,
  • Hojjat Asadollahpour,
  • Bengi Cinar-Kul,
  • Wei-Yi Zhang,
  • guangxin e,
  • A Ayin,
  • Hayley Baird,
  • Meirat Bakhtin,
  • Valentin Balteanu,
  • Diana Barfield,
  • Beate Berger,
  • Thor Blichfeldt,
  • Geert Boink,
  • Sri Rachma Bugiwati,
  • Zexi Cai,
  • Sean Carolan,
  • Emily Clark,
  • Vladka Cubrić Curik,
  • Muhammad 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 Martinez,
  • Joseph Masangkay,
  • Maho Masaoka,
  • Raffaele Mazza,
  • John McEwan,
  • Marco Milanesi,
  • Md Omar Faruque,
  • Yuto Nomura,
  • Nadjet-Amina Ouchene-Khelifi,
  • Filipe Pereira,
  • Goutam Sahana,
  • Mazdak Salavati,
  • Shinji Sasazaki,
  • Anne DA SILVA,
  • Mojca Simčič,
  • Johann Soelkner,
  • Alison Sutherland,
  • Johannes Tigchelaar,
  • Hongping Zhang,
  • Econogene Consortium,
  • Paolo Ajmone Marsan,
  • Daniel Bradley,
  • Licia Colli,
  • Cord Drögemüller,
  • Yu Jiang,
  • chuzhao Lei,
  • H Mannen,
  • Francois Pompanon,
  • GWENOLA TOSSER-KLOPP,
  • Johannes A. Lenstra
Vargoats Consortium
INRA

Corresponding Author:vargoats@inrae.fr

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Isaäc Nijman
Utrecht University
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Benjamin Rosen
Agriculture Research Service
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Philippe Bardou
INRA
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Thomas Faraut
INRA
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Tristan Cumer
University of Lausanne
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Kevin Daly
Trinity College
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Zhuqing Zheng
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Yudong Cai
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Hojjat Asadollahpour
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Bengi Cinar-Kul
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Wei-Yi Zhang
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guangxin e
Southwest University
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Hayley Baird
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Meirat Bakhtin
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Valentin Balteanu
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Diana Barfield
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Beate Berger
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Thor Blichfeldt
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Geert Boink
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Sri Rachma Bugiwati
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Sean Carolan
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Emily Clark
University of Edinburgh
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Vladka Cubrić Curik
University of Zagreb
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Muhammad Dagong
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Tashi Dorji
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Louise Drew
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Jiazhong Guo
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Jón Hallsson
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Simon Horvat
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Juha Kantanen
Natural Resources Institute Finland Jokioinen
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Fuki Kawaguchi
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Polat Kazymbet
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Negar khayatzadeh
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Namshin Kim
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Manoj Kumar Shah
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Yuying Liao
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Amparo Martinez
University of Cordoba
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Joseph Masangkay
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Maho Masaoka
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Raffaele Mazza
Associazione Italiana Allevatori
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John McEwan
AgResearch Invermay Agricultural Centre
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Marco Milanesi
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Md Omar Faruque
Bangladesh Agricultural University
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Yuto Nomura
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Nadjet-Amina Ouchene-Khelifi
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Filipe Pereira
University of Porto - CIIMAR
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Goutam Sahana
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Mazdak Salavati
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Shinji Sasazaki
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Anne DA SILVA
University de Limoges
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Mojca Simčič
University of Ljubljana
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Johann Soelkner
University of Natural Resources and Life Sciences
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Alison Sutherland
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Johannes Tigchelaar
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Hongping Zhang
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province
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Econogene Consortium
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Paolo Ajmone Marsan
Universita Cattolica del Sacro Cuore
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Daniel Bradley
Trinity College Dublin
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Licia Colli
Universita' di Piacenza
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Cord Drögemüller
University of Bern
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Yu Jiang
Northwest A&F University
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chuzhao Lei
Northwest A&F University
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H Mannen
Kobe University
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Francois Pompanon
University of Grenoble
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GWENOLA TOSSER-KLOPP
Institut National de Recherche pour lAgriculture, l'Alimentation, et l'Environnement Occitanie-Toulouse
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Johannes A. Lenstra
Utrecht University
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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, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we analyze whole-genome sequences of 386 domestic goats from 75 modern breeds and 7 wild goat species that 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 180 domestic breeds indicate ancient paternal population bottlenecks and expansions during the 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 geographic range.
05 Mar 2022Submitted to Molecular Ecology
08 Mar 2022Submission Checks Completed
08 Mar 2022Assigned to Editor
16 Mar 2022Reviewer(s) Assigned
12 Apr 2022Review(s) Completed, Editorial Evaluation Pending
17 Apr 2022Editorial Decision: Revise Minor
12 Jun 2022Review(s) Completed, Editorial Evaluation Pending
12 Jun 20221st Revision Received
20 Jun 2022Editorial Decision: Accept
Aug 2022Published in Molecular Ecology volume 31 issue 16 on pages 4364-4380. 10.1111/mec.16579