PT  - JOURNAL ARTICLE
AU  - Isaäc J. Nijman
AU  - Benjamin D. Rosen
AU  - Zhuqing Zheng
AU  - Yu Jiang
AU  - Tristan Cumer
AU  - Kevin G. Daly
AU  - Valentin A. Bâlteanu
AU  - Beate Berger
AU  - Thor Blichfeldt
AU  - Geert Boink
AU  - Sean Carolan
AU  - Vlatka Cubric-Curik
AU  - Juha Kantanen
AU  - Amparo Martínez
AU  - Raffaele Mazza
AU  - Negar Khayatzadeh
AU  - Namshin Kim
AU  - Nadjet-Amina Ouchene-Khelifi
AU  - Filipe Pereira
AU  - Anne da Silva
AU  - Mojca Simčič
AU  - Johann Sölkner
AU  - Alison Sutherland
AU  - Johannes Tigchelaar
AU  - Econogene Consortium
AU  - Paolo Ajmone-Marsan
AU  - Daniel G. Bradley
AU  - Licia Colli
AU  - François Pompanon
AU  - Johannes A. Lenstra
TI  - Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats
AID  - 10.1101/2020.02.17.952051
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.02.17.952051
4099  - http://biorxiv.org/content/early/2020/02/17/2020.02.17.952051.short
4100  - http://biorxiv.org/content/early/2020/02/17/2020.02.17.952051.full
AB  - The male-specific part of the Y-chromosome is in mammalian and many other species the longest haplotype that is inherited without recombination. By its paternal transmission it has a small effective population size in species with dominant males. In several species, Y-chromosomal haplotypes are sensitive markers of population history and introgression. Previous studies have identified in domestic goats four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic differentiation and several regional variants. In this study we used published whole-genome sequences of 70 male goats from 16 modern breeds, 11 ancient-DNA samples and 29 samples from seven wild goat species. We identified single-copy male-specific SNPs in four scaffolds, containing SRY, ZFY, DBY with SSX3Y and UTY, and USP9Y with UMN2001, respectively. Phylogenetic analyses indicated haplogroups corresponding to the haplotypes Y1B, Y2A and Y2B, respectively, but Y1A was split into Y1AA and Y1AB. All haplogroups were detected in ancient DNA samples from southeast Europe and, with the exception of Y1AB, in the bezoar goat, which is the wild ancestor of the domestic goats. Combining these data with those of previous studies and with genotypes obtained by Sanger sequencing or the KASP assay yielded haplogroup distributions for 132 domestic breeds or populations. The phylogeographic differentiation indicated paternal population bottlenecks on all three continents. This possibly occurred during the Neolithic introductions of domestic goats to those continents with a particularly strong influence in Europe along the Danubian route. This study illustrates the power of the Y-chromosomal haplotype for the reconstructing the history of mammalian species with a wide geographic range.