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

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