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

Frederick Delfin, Jazelyn M Salvador, Gayvelline C Calacal, Henry B Perdigon, Kristina A Tabbada, Lilian P Villamor, Saturnina C Halos, Ellen Gunnarsdóttir, Sean Myles, David A Hughes, Shuhua Xu, Li Jin, Oscar Lao, Manfred Kayser, Matthew E Hurles, Mark Stoneking, Maria Corazon A De Ungria

Research output: Contribution to journalArticle (Academic Journal)peer-review

60 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)224-30
Number of pages7
JournalEuropean Journal of Human Genetics
Issue number2
Publication statusPublished - Feb 2011


  • African Continental Ancestry Group/genetics
  • Asian Continental Ancestry Group/genetics
  • Chromosomes, Human, Y/genetics
  • Emigration and Immigration
  • Ethnic Groups/genetics
  • Genetic Variation
  • Genetics, Population
  • Haplotypes
  • Humans
  • Male
  • Philippines/ethnology
  • Population Groups/genetics
  • Software


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