Seven snow carp genomes reveal a shared autopolyploid origin and dynamic rediploidization during plateau uplift
The uplift of the Qinghai-Tibetan Plateau (QTP) profoundly reshaped the evolutionary landscape of its endemic fauna. Snow carps (Schizothoracinae), a lineage of autopolyploid cyprinid fishes, have undergone extensive diversification and polyploidization in response to the extreme environments, but the lack of genomic analyses hindered the understanding of their origin and diversification. Here, we present high-quality genome assemblies for seven snow carp species representing both basal and highly specialized lineages. Comparative genomic analyses reveal that all snow carps are autotetraploids with extensive chromosomal fusions, which increase progressively from basal to specialized lineages. Phylogenomic reconstruction based on whole-genome data uncovers pervasive conflicts in gene tree topologies, primarily driven by incomplete lineage sorting and historical introgression. By integrating paralog phylogenies and Hi-C contact maps, we demonstrate that the apparent heterogeneity in WGD histories reflects delayed rediploidization following a single ancestral autopolyploidization event, rather than multiple independent WGDs. Our findings redefine the evolutionary trajectory of snow carps, highlighting how genome duplication, chromosomal fusion, and population dynamics collectively facilitated their species diversification across the QTP.