Diversity and Origins of Domestic Buffalo

River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil have been genotyped with the 90K Affymetrix Axiom® Buffalo Genotyping Array. Geographic patterns of SNP diversity in pure river and pure swamp buffaloes confirm archeozoological data on the domestication of river buffalo in the Indian subcontinent and of swamp buffalo in Southeast Asia and provide hints on buffalo migrations and history. In pure river buffalo three main gene pools are identified. One includes breeds from the Indian subcontinent (Pakistan) and those recently exported from there to Bulgaria, Brazil and Colombia; the second includes breeds that moved from the domestication center westwards (Iran, Egypt and Turkey); the third is formed by the Italian Mediterranea, recently exported to Mozambique. Mediterranea represents a highly differentiated gene pool due to bottlenecks, isolation, selection and possibly to genetic contributions from breeds not included in our sampling. Four gene pools are identified in pure swamp buffalo. The first is in China; the second in Indonesian islands other than Sumatra; the third in the Philippines and the fourth in Thailand and Sumatra. Some level of admixture between river and swamp is observed in the Philippines and in Brazil