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Background  Since the completion of the human genome project, the diversity of genome sequencing data produced for non-human primates has increased exponentially.  Papio  baboons are well-established biological models for studying human biology and evolution. Despite substantial interest in the evolution of  Papio , the systematics of these species has been widely debated, and the evolutionary history of  Papio  diversity is not fully understood.  Alu  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  Alu  insertion polymorphisms unique to the  Papio  lineage. To complete these analyses, we created a computational algorithm to identify novel  Alu  insertions in next-generation sequencing data.    Results  We identified 187,379  Alu  insertions present in the  Papio  lineage, yet absent from  M. mulatta  [Mmul8.0.1]. These elements were characterized using genomic data sequenced from a panel of twelve  Papio  baboons: two from each of the six extant  Papio  species. These data were used to construct a whole genome  Alu -based phylogeny of  Papio  baboons. The resulting cladogram fully-resolved relationships within  Papio .    Conclusions  These data represent the most comprehensive  Alu- based phylogenetic reconstruction reported to date. In addition, this study produces the first fully resolved  Alu- based phylogeny of  Papio  baboons.    Electronic supplementary material  The online version of this article (10.1186/s13100-018-0118-3) contains supplementary material, which is available to authorized users.

A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms