Mid-Pleistocene Transitions Forced Himalayan ibex to Evolve Independently after Split into an Allopatric Refugium

Pleistocene glaciations had profound impact on the spatial distribution and genetic makeup of species in temperate ecosystems. While the glacial period trapped several species into glacial refugia and caused abrupt decline in large populations, the interglacial period facilitated population growth and range expansion leading to allopatric speciation. Here, we analyzed 40 genomes of four species of ibex and found that Himalayan ibex in the Pamir Mountains evolved independently after splitting from its main range about 0.1 mya following the Pleistocene species pump concept. Demographic trajectories showed Himalayan ibex experienced two historic bottlenecks, one each c. 0.8-0.5 mya and c. 50-30 kya, with an intermediate large population expansion c. 0.2-0.16 mya coinciding with Mid-Pleistocene Transitions. We substantiate with multi-dimensional evidence that Himalayan ibex is an evolutionary distinct phylogenetic species of Siberian ibex which need to be prioritized as Capra himalayensis for taxonomic revision and conservation planning at a regional and global scale.

Automated summary

Pleistocene glaciations had a significant impact on the distribution and genetic makeup of species in temperate ecosystems. Through the analysis of ibex genomes, it was discovered that the Himalayan ibex in the Pamir Mountains evolved independently from its main range around 0.1 million years ago according to the Pleistocene species pump concept. The demographic trajectories of the Himalayan ibex indicated two historic bottlenecks and an intermediate population expansion coinciding with the Mid-Pleistocene Transitions. This study provides evidence that the Himalayan ibex is an evolutionary distinct species from the Siberian ibex and highlights the need for taxonomic revision and conservation planning.