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

<b>Abstract</b><br/><p>Lenoks, species within the genus <em>Brachymystax</em>, are freshwater salmonids with a scattered distribution in the rivers of Siberia, Northeast China, Xinjiang, Hebei, and the Qinling Mountains. Owing to long-term population declines, all species assigned to <em>Brachymystax</em> are protected by law in China. However, the evolutionary history and species-level systematics of this genus remain controversial, complicating taxonomic designations and conservation efforts. 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 <em>B. tsinlingensis</em> and re-sequenced the genomes of 103 individuals of Chinese <em>Brachymystax</em> 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 <em>B. lenok</em> and <em>B. tumensis</em> are not close relatives, but the former is more closely related to the new species <em>B</em>.<em> </em>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 <em>Brachymystax</em> caused by the strong gene flow between <em>B. lenok</em> and <em>B. tumensis</em>. 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.</p>