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By its paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. We used whole-genome sequences (WGSs) of 386 domestic goats from 75 modern breeds and 7 wild goat species generated by the VarGoats goat genome project. Phylogenetic analyses indicated five domestic haplogroups Y1AA, Y1AB, Y1B, Y2A and Y2B. Haplogroup distributions for 180 domestic breeds indicate ancient paternal population bottlenecks during the migration into northern Europe, southern Asia and Africa. Sharing of haplogroups reveals male-mediated introgressions: from Asia into Madagascar and, more recently, into the South-African Boer goat; then from this breed into other southeastern African goats; and from Europe into native Korean and Ugandan goats. This study illustrates the power of the Y-chromosomal variation for the reconstructing the history of domestic species with a wide geographic range.

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.

By its paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. We used whole-genome sequences (WGSs) of 386 domestic goats from 75 modern breeds and 7 wild goat species generated by the VarGoats goat genome project. Phylogenetic analyses indicated five domestic haplogroups Y1AA, Y1AB, Y1B, Y2A and Y2B. Haplogroup distributions for 180 domestic breeds indicate ancient paternal population bottlenecks during the migration into northern Europe, southern Asia and Africa. Sharing of haplogroups reveals male-mediated introgressions: from Asia into Madagascar and, more recently, into the South-African Boer goat ; then from this breed into other southeastern African goats ; and from Europe into native Korean and Ugandan goats. This study illustrates the power of the Y-chromosomal variation for the reconstructing the history of domestic species with a wide geographic range.

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.

Genetic isolation of breeds may result in a significant loss of diversity and have consequences on health and performance. In this study, we examined the effect of geographic isolation on caprine genetic diversity patterns by genotyping 480 individuals from 25 European and African breeds with the Goat SNP50 BeadChip and comparing patterns of homozygosity of insular and nearby continental breeds. Results: Among the breeds analysed, number and total length of ROH varied considerably and depending on breeds, ROH could cover a substantial fraction of the genome (up to 1.6 Gb in Icelandic goats). When compared with their continental counterparts, goats from Iceland, Madagascar, La Palma and Ireland (Bilberry and Arran) displayed a significant increase in ROH coverage, ROH number and F ROH values (P value < 0.05). Goats from Mediterranean islands represent a more complex case because certain populations displayed a significantly increased level of homozygosity (e.g. Girgentana) and others did not (e.g. Corse and Sarda). Correlations of number and total length of ROH for insular goat populations with the distance between islands and the nearest continental locations revealed an effect of extremely long distances on the patterns of homozygosity. Conclusions: These results indicate that the effects of insularization on the patterns of homozygosity are variable. Goats raised in Madagascar, Iceland, Ireland (Bilberry and Arran) and La Palma, show high levels of homozygosity, whereas those bred in Mediterranean islands display patterns of homozygosity that are similar to those found in continental populations. These results indicate that the diversity of insular goat populations is modulated by multiple factors such as geographic distribution, population size, demographic history, trading and breed management. © 2018 The Author(s)., We acknowledge financial support from the Spanish Ministry of Economy and Competitiveness (Project AGL2016‑76108‑R), the “Severo Ochoa Programme for Centres of Excellence in R&D”2016‑2019 (SEV‑2015‑0533), the CERCA Programme/Generalitat de Catalunya and the Dutch Stichting Zeldzame Huisdierrassen. Funding for FB and MR were provided by the Ensminger endowment, Hatch and State of Iowa funds. Tainã F Cardoso was funded with a fellowship from the CAPES Foundation‑Coordination of Improvement of Higher Education, Ministry of Education (MEC) of the Federal Government of Brazil.