Sequential evolution drives range expansion of Chinese caterpillar fungus across the Qinghai-Tibet Plateau.

The Chinese caterpillar fungus Ophiocordyceps sinensis has colonized the extreme high-elevation environment of the Qinghai-Tibet Plateau despite severe cold, hypoxia and intense UV radiation. We analysed 305 whole genomes, including 69 newly sequenced genomes, and resolved nine phylogenetic clades with a mosaic geographic distribution, with the Hengduan Mountains acting as both a diversity centre and a corridor for gene flow. These clades represent three evolutionary regimes: early lineages (Clades 1-4) primarily shaped by incomplete lineage sorting (ILS), intermediate lineages (Clades 5-8) shaped by the combined effects of ILS and introgression, and the most recent lineage (Clade 9) associated with candidate signatures of selection. Functional analyses revealed that ILS retained pathogenicity-related genes, introgression introduced adaptations in RNA processing, mitochondrial transport and lipid metabolism and candidate regions under selection targeted UV-damage repair and DNA replication. Together, these results demonstrate how ILS, introgression and selection-associated genomic changes acted sequentially to maintain parasitic lifestyle, enable environmental adaptation and drive rapid radiation under extreme alpine conditions.