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The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups

Frederick Delfin1,2, Jazelyn M Salvador1, Gayvelline C Calacal1, Henry B Perdigon1, Kristina A Tabbada1, Lilian P Villamor1, Saturnina C Halos1, Ellen Gunnarsdóttir2, Sean Myles1,6, David A Hughes2, Shuhua Xu3, Li Jin3, Oscar Lao4, Manfred Kayser4, Matthew E Hurles5, Mark Stoneking2 and Maria Corazon A De Ungria1

European Journal of Human Genetics (2011) 19, 224–230; doi:10.1038/ejhg.2010.162; published online 29 September 2010

Abstract

The Philippines exhibits a rich diversity of people, languages, and culture, including so-called ‘Negrito’ groups that have for long fascinated anthropologists, yet little is known about their genetic diversity. We report here, a survey of Y-chromosome variation in 390 individuals from 16 Filipino ethnolinguistic groups, including six Negrito groups, from across the archipelago. We find extreme diversity in the Y-chromosome lineages of Filipino groups with heterogeneity seen in both Negrito and non-Negrito groups, which does not support a simple dichotomy of Filipino groups as Negrito vs non-Negrito. Filipino non-recombining region of the human Y chromosome lineages reflect a chronology that extends from after the initial colonization of the Asia-Pacific region, to the time frame of the Austronesian expansion. Filipino groups appear to have diverse genetic affinities with different populations in the Asia-Pacific region. In particular, some Negrito groups are associated with indigenous Australians, with a potential time for the association ranging from the initial colonization of the region to more recent (after colonization) times. Overall, our results indicate extensive heterogeneity contributing to a complex genetic history for Filipino groups, with varying roles for migrations from outside the Philippines, genetic drift, and admixture among neighboring groups.