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

SIMPLE SUMMARY: The Siberian ibex has a wide distribution, spanning various mountainous regions and cold deserts in countries like India, China, Pakistan, Kazakhstan, Tajikistan, Russia, and Mongolia. Our study specifically examined the Himalayan ibex, which is an edge population of Siberian ibex found in India. Through genomic analysis, we discovered that the Himalayan ibex evolved as a distinct lineage after separating from the main population around 100,000 years ago, due to geographical isolation. By studying the region’s past geography using paleo-climatic models and deep sequencing data, we observed significant transformations, including high mountains and deep valleys, particularly in the Pamir range, likely played a significant role in the divergence and independent evolution of the Himalayan ibex, after experiencing two historic genetic bottlenecks. Based on our findings, we propose prioritizing the Himalayan ibex as a unique phylogenetic species and advocate for its conservation attention and taxonomic revision. Furthermore, we hope that our research will inspire collaborative efforts and discussions among different countries to address the conservation and management of ibex populations worldwide. ABSTRACT: 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.