Genome-Wide Diversity of Goats From Indonesia and the Philippines Reveals Local Ancestry With Different Levels of Cosmopolitan Admixture.

In order to investigate the genetic diversity, differentiation, gene flows, and propagation routes of Island Southeast Asian (ISEA) goats, we genotyped 50K genome-wide SNPs in 57 Philippine and 30 Indonesian Katjang goats. Correlations of the distance from the domestication center and the genetic diversities of 21 Asian populations were significantly negative. A relatively high diversity of the Philippine population (He = 0.363) against the distance from the domestication center suggests a history of admixture, notably without large effects on their Katjang phenotype. This was confirmed by supervised PCA (Principal Component Analysis), f3 coancestry and f4 admixture analyses, Treemix-inferred migrations and model-based clustering (Admixture program). The inferred differential admixture of ISEA goats agreed with previously reported fixation of mtDNA haplogroup B in Indonesia, but not in the Philippines, and with high frequencies of African or European Y-chromosomal haplogroups that were not observed in Mainland Southeast Asia. We propose that admixture of cosmopolitan European and African goats into ISEA was mediated by a unique feature of the domestic goat, the maritime transport of goats during the colonial period as a source of provisions. This was followed by more recent imports of popular breeds such as Boer, and other cosmopolitan breeds.