In this study, the phylogeographical pattern of the Amur minnow (Rhynchocypris lagowskii) widely distributed in the cold freshwaters of the Qinling Mountains was examined. A total of 464 specimens from 48 localities were sequenced at a 540bp region of the mitochondrial cytochrome b (Cytb) gene, and 69 haplotypes were obtained. The mean ratio of the number of synonymous and nonsynonymous substitutions per site (dN/dS) was 0.028 and indicated purifying selection. Haplotype diversity (h) and nucleotide diversity (π) of natural populations of R. lagowskii varied widely between distinct localities. Phylogenetic trees based on Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) methods, and network analysis showed five well-differentiated lineages, but these did not completely correspond to localities and geographic distribution. Meanwhile, analysis of molecular variances (AMOVA) indicated the highest proportion of genetic variation was attributed to the differentiation between populations rather than by our defined lineages.In addition, there was no significant correlation between the pairwise Fst values and geographic distance (p > .05). Based on the molecular clock calibration, the time to the most recent common ancestor (TMRCA) was estimated to have emerged from the Late Miocene to the Early Pleistocene. Finally, the results of demographic history based on the neutrality test, mismatch distribution, and Bayesian skyline plot (BSP) analyses showed that collectively, the populations were stable during the Pleistocene while one lineage (lineage E) probably underwent a slight contraction during the Middle Pleistocene and a rapid expansion from the Middle to the Late Pleistocene.Therefore, the study suggests the current phylogeographical pattern of R. lagowskii was likely shaped by geological events that led to vicariance followed by dispersal and secondary contact, river capture, and climatic oscillation during the Late Miocene to the Early Pleistocene in the Qinling Mountains.
Brachymystax tsinlingensis Li, 1966 is an endangered freshwater fish with economic, ecological, and scientific values. Study of the genome of B. tsinlingensis might be particularly insightful given that this is the only Brachymystax species with genome. We present a high-quality chromosome-level genome assembly and protein-coding gene annotation for B. tsinlingensis with Illumina short reads, Nanopore long reads, Hi-C sequencing reads, RNA-seq reads from 5 tissues/organs. The final chromosome-level genome size is 2,031,709,341 bp with 40 chromosomes. We found that the salmonids have a unique GC content and codon usage, have a slower evolutionary rate, and possess specific positively selected genes. We also confirmed the salmonids have undergone a whole-genome duplication event and a burst of transposon-mediated repeat expansion, and lost HoxAbβ Hox cluster, highly expressed genes in muscle may partially explain the migratory habits of B. tsinlingensis. The high-quality B. tsinlingensis assembled genome could provide a valuable reference for the study of other salmonids as well as aid the conservation of this endangered species.
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