Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats

Abstract

49The male-specific part of the Y-chromosome is in mammalian and many other species the 50 longest haplotype that is inherited without recombination. By its paternal transmission it has a 51 small effective population size in species with dominant males. In several species, Y-52 chromosomal haplotypes are sensitive markers of population history and introgression. 53Previous studies have identified in domestic goats four major Y-chromosomal haplotypes 54 Y1A, Y1B, Y2A and Y2B with a marked geographic differentiation and several regional 55 variants. In this study we used published whole-genome sequences of 70 male goats from 16 56 modern breeds, 11 ancient-DNA samples and 29 samples from seven wild goat species. We 57 identified single-copy male-specific SNPs in four scaffolds, containing SRY, ZFY, DBY with 58 SSX3Y and UTY, and USP9Y with UMN2001, respectively. Phylogenetic analyses indicated 59 haplogroups corresponding to the haplotypes Y1B, Y2A and Y2B, respectively, but Y1A was 60 split into Y1AA and Y1AB. All haplogroups were detected in ancient DNA samples from 61 southeast Europe and, with the exception of Y1AB, in the bezoar goat, which is the wild 62 ancestor of the domestic goats. Combining these data with those of previous studies and with 63 genotypes obtained by Sanger sequencing or the KASP assay yielded haplogroup distributions 64 for 132 domestic breeds or populations. The phylogeographic differentiation indicated 65 paternal population bottlenecks on all three continents. This possibly occurred during the 66 Neolithic introductions of domestic goats to those continents with a particularly strong 67 influence in Europe along the Danubian route. This study illustrates the power of the Y-68 chromosomal haplotype for the reconstructing the history of mammalian species with a wide 69 geographic range. 70 71 223 2018-01-8708 "Application of NGS in assessment of genomic variability in ruminants" and 224 by the European Union (projects ECONOGENE QLK5-CT2001-02461. We are grateful to 225 Dr E. Cuppen (Utrecht Medical Centre) for access to the dideoxy sequencing facilities. 226 227Acknowldegements. 228This study has benefited from an interaction with Vargoats consortium 229

A Hu sheep genome with the first ovine Y chromosome reveal introgression history after sheep domestication

“…In addition, a clear geographical distribution of most of the haplotypes was observed in contrast with previous conclusion that Y haplotypes displayed a weak phylogeographical structure (Meadows et al, 2006). This clear phylogeographic structure is probably a result of paternal bottlenecks during migration of males as has been found in goats (Nijman et al, 2020).…”

Herded and hunted goat genomes from the dawn of domestication in the Zagros Mountains

“…7B and SI Appendix, Supplementary Text and Table S17). All sequences from the AN Zagros fall within a single lineage, Y1AA, now at a low frequency in wild and domestic Iranian goats and absent from sampled Zagros wild males (55). In comparison, sampling of small numbers in predomestic goats from the Taurus Mountains show distinct haplotypes, while males from CN Serbia and CN East Iran display two different lineages (Fig.…”

The assembly of caprine Y chromosome sequence reveals a unique paternal phylogenetic pattern and improves our understanding of the origin of domestic goat

“…Previous studies also used Y chromosome data to study the evolutionary history of paternal lineage, but due to scarcity of data, they only targeted a few specific SNPs, genes ( SRY, ZFY, AMELY , and DDX3YY ‐linked loci), or parts of the male‐specific region in the Y chromosome, to define the two major haplogroups (Cinar Kul et al., 2015; Nijman et al., 2020; Pidancier et al., 2006; Tabata et al., 2018; Vidal et al., 2017; Waki et al., 2015). The assembly of an almost complete Y chromosome allowed us to explore the Y‐linked genetic structure in much higher detail, improve our understanding of its internal structure, and helped us better understand the evolutionary history of goat domestication.…”

“…Most goat phylogeographic studies focused on mtDNA data (Kamalakkannan et al, 2018;Naderi et al, 2008) and autosomal data (Bertolini et al, 2018;Kumar, Song et al, 2018;Zheng et al, 2020), whereas phylogeographic studies on the Y chromosome are relatively few. Most of these studies only focused on sequences of a few Y-linked genes (SRY, AMELY, and ZFY) or parts of the male-specific region on the Y chromosome (Cinar Kul et al, 2015;Nijman et al, 2020;Pidancier et al, 2006;Tabata et al, 2018;Vidal et al, 2017;Waki et al, 2015).…”

“…Most goat phylogeographic studies focused on mtDNA data (Kamalakkannan et al., 2018; Naderi et al., 2008) and autosomal data (Bertolini et al., 2018; Kumar, Song et al., 2018; Zheng et al., 2020), whereas phylogeographic studies on the Y chromosome are relatively few. Most of these studies only focused on sequences of a few Y‐linked genes ( SRY , AMELY , and ZFY ) or parts of the male‐specific region on the Y chromosome (Cinar Kul et al., 2015; Nijman et al., 2020; Pidancier et al., 2006; Tabata et al., 2018; Vidal et al., 2017; Waki et al., 2015). The limited phylogenetic signal carried by the Y chromosome fragments may not be powerful enough to give sufficient independent and complementary information for closely related breeds in paternal dispersal analysis (Boissinot & Boursot, 1997).…”