Phylogenetic signals from point mutations and polymorphic Alu insertions

Allelic frequency data derived from five polymorphic Alu insertion loci and five point mutation polymorphic loci were compared to determine their abil ity to infer phylogenetic relationships among human populations. While poin t mutation polymorphisms inferred a monophyletic Caucasian clade that is co rroborated by other studies, these data failed to support the generally acc epted monophyly of Orientals with native Americans. In addition, there is l ess statistical bootstrap support for the maximum-likelihood tree derived f rom the point mutation polymorphisms as compared to those generated from ei ther the Alu insertion data or the combined Alu insertion + point mutation data. The Alu data and the combined Alu insertion + point mutation data inf erred a monophyletic relationship among the Oriental and native American po pulations. The Alu insertion data and the combined Alu insertion + point mu tation data also displayed two separate, well defined, tight clusters of th e Caucasian and the Oriental + native American populations which was not in ferred from the point mutation data. These findings indicate greater phylog enetic information contained in Alu insertion frequencies than in allelic f requencies derived from point-mutations.