Data from: Population genomics of endangered lenoks (<em>Brachymystax</em> spp.) in China reveals the presence of cryptic species

In particular, the geographical separation of populations may have resulted in the formation of phenotypically similar cryptic species. We built a chromosome-level genome assembly of B. tsinlingensis and re-sequenced the genomes of 103 individuals of Chinese Brachymystax spp. from five geographically isolated locations. Population genomic and phylogenomic analyses based on nuclear SNPs and mitochondrial genomes revealed six different genetic lineages, of which at least one, the Hebei lineage, represents a cryptic species.

Notably, the results suggest that the sympatric species B. lenok and B. tumensis are not close relatives, but the former is more closely related to the new species B. sp. Xinjiang with an estimated divergence time of c. 630 Ka, indicating that closely-related sympatric species may not have evolved via sympatric speciation in areas influenced by Pleistocene climate changes. We observed mito-nuclear phylogenomic discordance in Brachymystax caused by the strong gene flow between B. lenok and B. tumensis.

Phylogenetic and demographic analyses emphasize the important role of interglacial refugia in promoting speciation and underscore the impact of historical gene flow. Compared to other lenoks, the Gansu population had the lowest genetic diversity, suggesting that particular attention to protect its genetic resources may be required. Finally, we suggest that cross-regional proliferation and release of lenoks should be banned in the future to protect the genetic integrity of these divergent groups.