Water Buffalo Genomic Diversity and Post-Domestication Migration Routes

The 90K Affymetrix Axiom^® Buffalo Genotyping Array has been used to genotype river buffalo samples from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil. Model-based clustering algorithms (Admixture and FastStructure software) and graph tools (Treemix and network analysis) have been applied to SNP data to evaluate the levels of molecular diversity and to highlight population structure and migration events. The best-fitting resolution devised by Bayesian clustering highlighted three distinct gene pools in pure river as well as in pure swamp buffalo populations, together with some genomic admixture occurring in the Philippines and in Brazil, in agreement with documented importations of animals for breed improvement purposes. The Mediterranean buffalo and the Carabao breed from Brazil represent the most differentiated gene pools within the river and swamp group, respectively, which is most likely due to genetic bottlenecks, isolation and selection. Gene flow events, evidenced by Treemix and Network analyses, highlighted a likely contribution from the river buffalo gene pool to the admixed swamp populations and, within river buffaloes, from the Mediterranean to the breeds from Colombia and Brazil. When evaluated in a geographical framework, the results of our analyses support archeozoological evidence for the domestication of river and swamp buffalo in the Indian subcontinent and in Southeast Asia, respectively, and furthermore revealed some unexpected patterns of migration, which suggest that the spread of domestic buffaloes out of the domestication center may have followed alternative migration routes.