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

• Published in: Molecular ecology Vol. 31; no. 16; pp. 4364 - 4380
• Main Authors: Nijman, Isaäc J, Rosen, Benjamin D, Bardou, Philippe, Faraut, Thomas, Cumer, Tristan, Daly, Kevin G, Zheng, Zhuqing, Cai, Yudong, Asadollahpour, Hojjat, Kul, Bengi Çınar, Zhang, Wei‐yi, E, Guangxin, Ayin, A, Baird, Hayley, Bakhtin, Meirat, Bâlteanu, Valentin A, Barfield, Diana, Berger, Beate, Blichfeldt, Thor, Boink, Geert, Bugiwati, Sri R A, Cai, Zexi, Carolan, Sean, Clark, Emily, Cubric‐curik, Vlatka, Dagong, Muhammad I A, Dorji, Tashi, Drew, Louise, Guo, Jiazhong, Hallsson, Jón, Horvat, Simon, Kantanen, Juha, Kawaguchi, Fuki, Kazymbet, Polat, Khayatzadeh, Negar, Kim, Namshin, Shah, Manoj Kumar, Liao, Yuying, Martínez, Amparo, Masangkay, Joseph S, Masaoka, Maho, Mazza, Raffaele, Mcewan, John, Milanesi, Marco, Omar, Faruque Md, Nomura, Yuto, Ouchene‐khelifi, Nadjet‐amina, Pereira, Filipe, Sahana, Goutam, Salavati, Mazdak, Sasazaki, Shinji, da Silva, Anne, Simčič, Mojca, Sölkner, Johann, Sutherland, Alison, Tigchelaar, Johannes, Zhang, Hongpin, Ajmone‐marsan, Paolo, Bradley, Daniel G, Colli, Licia, Drögemüller, Cord, Jiang, Yu, Lei, Chuzhao, Mannen, Hideyuki, Pompanon, François, Tosser‐klopp, Gwenola, Lenstra, Johannes A
• Format: Journal Article
• Language: English
• Published: Wiley 2022
• Subjects: Animal genetics; Biodiversity; Genetics; Life Sciences; Populations and Evolution; haplogroup; domestication; migration; Y- chromosome; goat; introgression; phylogeography
• ISSN: 0962-1083; 1365-294X
• DOI: 10.1111/mec.16579

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 presentday 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 et al. (2021); see PRJEB37507 for the fastq files; vcf files are available upon reasonable request.