Alu Insertion Polymorphisms as Evidence for Population Structure in Baboons

Abstract

Male dispersal from the natal group at or near maturity is a feature of most baboon (Papio) species. It potentially has profound effects upon population structure and evolutionary processes, but dispersal, especially for unusually long distances, is not readily documented by direct field observation. In this pilot study, we investigate the possibility of retrieving baboon population structure in yellow (Papio cynocephalus) and kinda (Papio kindae) baboons from the distribution of variation in a genome-wide set of 494 Alu insertion polymorphisms, made available via the recently completed Baboon Genome Analysis Consortium. Alu insertion variation in a mixed population derived from yellow and olive (Papio anubis) baboons identified each individual’s proportion of heritage from either parental species. In an unmixed yellow baboon population, our analysis showed greater similarity between neighboring than between more distantly situated groups, suggesting structuring of the population by male dispersal distance. Finally (and very provisionally), an unexpectedly sharp difference in Alu insertion frequencies between members of neighboring social groups of kinda baboons suggests that intergroup migration may be more rare than predicted in this little known species.

Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis

“…In Preparation). Recent work also supports that the expansion of Alu elements is not unique to the olive baboon, but rather the Papio lineage as a whole [ 33 , 35 ].…”

“…The rapid radiation/expansion of genus Papio , which occurred only ~ 2.5 mya, likely contributes to this lack of allele fixation, along with gene flow from troop migration and hybridization occurring along active hybrid zones (Rogers et al: The comparative genomics, epigenomics and complex population history of Papio baboons. In Preparation) [ 33 ].…”

“…The recent findings of the Baboon Genome Analysis Consortium, along with other recent studies of mobile elements in the baboon genome have provided a great deal of new information (Rogers et al: The comparative genomics, epigenomics and complex population history of Papio baboons. In Preparation) [ 33 , 35 ]. This study found 127 novel Alu element subfamilies, supporting the high Alu mobilization rate reported by the Baboon Genome Analysis Consortium (Rogers et al: The comparative genomics, epigenomics and complex population history of Papio baboons.…”

“…In Preparation). Previous work on Alu elements in baboons has already been informative for population structure, species identification, and as a polymorphic marker for hybrid individuals in the field [ 33 – 35 ].…”

A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms

“…The disagreement is in essence philosophical, centered on the question of what constitutes a species . However, recent studies employ a phylogenetic species concept [ 26 – 29 ], positing that consistent differences in physical appearance, ecology and social behavior justify the recognition of six extant species: P. anubis , P. hamadryas , P. papio , P. cynocephalus , P. ursinus and P. kindae . In this study, we recognize all six as species.…”