Title: An Alu-based phylogeny of gibbons (Hylobatidae)

Abstract Gibbons (Hylobatidae) are small arboreal apes indigenous to Southeast Asia that diverged from other apes ~15-18 mya. Extant lineages radiated rapidly 6-10 mya and are organized into four genera ( Hylobates , Hoolock , Symphalangus , and Nomascus ) consisting of 12-19 species. The use of SINEs (Short INterspersed Elements) as phylogenetic markers has seen recent popularity due to several desirable characteristics: the ancestral state of a locus is known to be the absence of an element, rare potentially homoplasious events are relatively easy to resolve, and samples can be quickly and inexpensively genotyped. During the radiation of primates, one particular family of SINEs, the Alu family, has proliferated in primate genomes. Nomascus leucogenys (Northern white-cheeked gibbon) sequences were analyzed for repetitive content with RepeatMasker using a custom library. Sequences containing Alu elements identified as members of a gibbon-specific subfamily were then compared to orthologous positions in other primate genomes. A primate phylogenetic panel consisting of 18 primate species, including 13 gibbon species representing all four extant genera, was assayed for all loci and a total of 125 gibbon-specific