East Timor is a country which harbors multiple ethnolinguistic groups generally
assigned to an Austronesian or Papuan ancestry. The present study aimed to characterize
Y-chromosome haplotype diversity in East Timor, and to test possible population structures
based on linguistic and/or geographical information. Using a set of 12 Y-chromosome-specific
STRs (DYS19, DYS389I and II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437,
DYS438, and DYS439), haplotypes were established in 342 individuals from 12 linguistic groups
(Tetum, Kwaimina, Galoli, Wetarese, Dawan, Mambai, Kemak, Tokodede, Bunak, Makasai,
Makalero, and Fataluku) belonging to the three major ethnolinguistic groups in East Timor:
two from the Timorese-Austronesian branch (Fabronic and Ramelaic), and a third including
languages related to a Trans-New Guinea phylum (Papuan). High values of haplotype diversity,
average gene diversity, and mean number of pairwise differences per locus were found in all 12
linguistic groups, except for the Wetarese from the island of Atau´ ro. Analysis of genetic variance
(AMOVA) and pairwise genetic distance analysis showed that the East Timor population is genetically
structured, and if the Bunak and Wetarese are excluded, samples group well with
respect to their language affinities, and furthermore, the most genetically homogeneous groups
are those following the broad ethnolinguistic classifications. Bunak and Wetarese behave as
outsider groups, and are genetically more closely related to populations classified in a different
linguistic group.