1. Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats
- Author
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Benjamin D. Rosen, A Martinez, Filipe Pereira, François Pompanon, Johann Sölkner, Licia Colli, Sutherland A, Isaac J. Nijman, Kevin G. Daly, Simčič M, Raffaele Mazza, Blichfeldt T, Valentin Adrian Bâlteanu, Paolo Ajmone-Marsan, Daniel G. Bradley, Carolan S, Johannes A. Lenstra, Tristan Cumer, Yu Jiang, Berger B, Nadjet-Amina Ouchene-Khelifi, da Silva A, Juha Kantanen, Cubric-Curik, Namshin Kim, Boink G, Negar Khayatzadeh, Zhuqing Zheng, J Tigchelaar, Génomique AniMale, Amélioration, Adaptation (GAMAA), PEIRENE (PEIRENE), Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), and Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
- Subjects
0106 biological sciences ,0303 health sciences ,education.field_of_study ,Phylogenetic tree ,[SDV]Life Sciences [q-bio] ,Haplotype ,Population ,Introgression ,Biology ,010603 evolutionary biology ,01 natural sciences ,Haplogroup ,03 medical and health sciences ,Ancient DNA ,Population bottleneck ,Effective population size ,Evolutionary biology ,education ,030304 developmental biology - Abstract
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.
- Published
- 2021