Whole Genome Analysis Reveals Evolutionary History and Introgression Events in Bale Monkeys

<b>Background/Objective:</b> The Bale monkey (<i>Chlorocebus djamdjamensis</i>) is a threatened primate species endemic to Ethiopia and, in contrast to other members of the genus <i>Chlorocebus</i>, lives at high altitudes and feeds mainly on bamboo. Two populations of the species are present, one in continuous bamboo forest (CF) in the eastern part of the species' range, and the other in fragmented forest (FF) in the western part. Based on mitochondrial DNA and phenotypic characteristics, previous studies have suggested introgression by parapatric congeners into the FF population but not into the CF population. The objective of this study was to gain insights into the evolutionary history of Bale monkeys and their potential genetic adaptations to high altitudes and for bamboo consumption. <b>Methods:</b> We sequenced the whole genomes of individuals from both populations and compared their genomes with those of the other five <i>Chlorocebus</i> species. We applied phylogenetic methods and conducted population demographic simulations to elucidate their evolutionary history. A genome-wide analysis was conducted to assess gene flow and identify mutations potentially associated with adaptations to high altitudes and for bamboo metabolism. <b>Results:</b> Our analyses revealed Bale monkeys as the sister clade to <i>Chlorocebus aethiops</i> and showed that gene flow occurred between <i>C. aethiops</i> and FF but not between <i>C. aethiops</i> and CF. In addition, we detected non-synonymous mutations in genes potentially associated with the adaptation to high altitudes (<i>EPAS1</i>) in both populations and with the adaptation for bamboo metabolism (<i>TAS2R16</i>, <i>MPST</i>, and <i>TST</i>) mainly in the CF population. <b>Conclusions:</b> Our study provides insights into the evolutionary history of a threatened primate species and reveals the genetic basis for its adaptions to unique environments and for diet specialization.