A computational reconstruction of phylogeny using insertion polymorphisms.

Background: Since the completion of the human genome project, the diversity of genome sequencing data produced for non-human primates has increased exponentially. baboons are well-established biological models for studying human biology and evolution. Despite substantial interest in the evolution of , the systematics of these species has been widely debated, and the evolutionary history of diversity is not fully understood. elements are primate-specific transposable elements with a well-documented mutation/insertion mechanism and the capacity for resolving controversial phylogenetic relationships. In this study, we conducted a whole genome analysis of insertion polymorphisms unique to the lineage. To complete these analyses, we created a computational algorithm to identify novel insertions in next-generation sequencing data.

Results: We identified 187,379 insertions present in the lineage, yet absent from [Mmul8.0.1]. These elements were characterized using genomic data sequenced from a panel of twelve baboons: two from each of the six extant species. These data were used to construct a whole genome -based phylogeny of baboons. The resulting cladogram fully-resolved relationships within .

Conclusions: These data represent the most comprehensive based phylogenetic reconstruction reported to date. In addition, this study produces the first fully resolved based phylogeny of baboons.