Abstract
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 , DDX3Ygenes, which in domestic goats identified four major Y-chromosomal
haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning.
Here, we analyze whole-genome sequences of 386 domestic goats from 75
modern breeds and 7 wild goat species that 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
180 domestic breeds indicate ancient paternal population bottlenecks and
expansions during the 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 geographic range.