Phylogeographical and Morphological Analyses of Triplophysa stenura (Cypriniformes: Nemacheilidae) from the Three Parallel Rivers Region, China

The complete mitochondrial genome of Triplophysa grahami Regan 1906 (Cypriniformes: Nemacheilidae) and phylogenetic analysis

Triplophysa grahami Regan 1906 is a member of the family Nemacheilidae, Cypriniformes, and native loach in Yunnan. In this study, the complete mitochondrial genome (mitogenome) of T. grahami Regan 1906 was firstly reported and analyzed. The mitogenome of T. grahami Regan 1906 is 16,566 bp in length, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (D-loop). The arrangement and orientation of protein coding genes and RNAs in T. grahami Regan 1906 are identical to other species of Nemacheilidae. The base composition of T. grahami Regan 1906 mitogenome was 29.25% A, 28.55% T, 25.03% C, and 17.17% G. The phylogenetic analysis based on the mitogenome showed that T. grahami Regan 1906 belongs to the clade of genus Triplophysa and the monophyly of Triplophysa is identified. This study contributed valuable genetic data for T. grahami Regan 1906 and explored the phylogenetic relationships in Nemacheilidae.

Genetic Diversity and Population Differentiation of Kashgarian Loach (Triplophysa yarkandensis) in Xinjiang Tarim River Basin

Simple Summary

The distribution of Kashgarian loach (Triplophysa yarkandensis) is limited to the Tarim River basin, which is the largest inland river in China. However, the population size of T. yarkandensis has been diminishing, and it is critically endangered in the Tarim River basin due to the gradual depletion of water resources, together with alien invasion and agricultural cultivation in Tarim River. In this study, we adopted the RAD-seq method to investigate the population genetics of T. yarkandensis, and a high degree of genetic variations and significant genetic differentiation was detected among T. yarkandensis populations in the Tarim River basin. The obtained data contribute to understanding the genetic status of T. yarkandensis, and help to provide the scientific management strategies and direct future monitoring and utilization of the genetic resource in Xinjiang region.

Abstract

The distribution of Triplophysa yarkandensis is restricted to Xinjiang’s Tarim River basin. We collected 119 T. yarkandensis samples from nine geographic populations in the Tarim River basin and utilized the RAD-seq method for SNP genotyping. In this study, a total of 164.81 Gb bases were generated with the Illumina platform, and 129,873 candidate SNPs were obtained with the Stacks pipeline for population genetic analyses. High levels of genetic diversity were detected among nine populations. The AMOVA results showed that the majority of genetic variations originated from among populations (F_ST = 0.67), and the pairwise F_ST values ranged from 0.4579 to 0.8736, indicating high levels of genetic differentiation among these populations. The discriminate analysis of principal components (DAPCs) and neighbor joining (NJ) tree revealed that the nine populations could be separated into two clusters (i.e., south and north populations), and modest genetic differentiation between south and north populations was observed, while the individuals from several populations were not clustered together by geographical location. The evidence of two genetic boundaries between south and north populations (except TTM) was supported by barrier analysis. The Bayesian skyline plotting indicated that T. yarkandensis populations in the Tarim River basin had not experienced genetic bottlenecks, and the effective population size remained stable. This study first clarified the genetic diversity and differentiation of T. yarkandensis populations in the Tarim River basin, and it provided valuable molecular data for conservation and management of natural populations.

Phylogeography of Triplophysa stenura (Nemacheilidae): Responded to the Mid-Pleistocene Climate Transition in the Qinghai-Tibetan Plateau

Pleistocene climatic oscillations have greatly influenced the evolutionary histories and distribution patterns of most extant species. In this study, the phylogeographic patterns and evolutionary history of Triplophysa stenura were investigated. A total of 359 individuals from 19 locations covering the species' distribution range were collected, and two mitochondrial genes (COI and Cyt b) and the recombination activating protein 1 gene (Rag1) were analyzed. Two deeply divergent lineages, corresponding geographically to the northern and southern Tanggula Mountain, were observed, and shallow divergences were found within the southern and central Qinghai-Tibetan plateau (QTP). The estimated divergence time between the northern and southern Tanggula lineages was around 1.07 Mya. Within the southern Tanggula Mountain lineages, the Nu and Subansiri rivers populations were split about 0.74 Mya, and the southwestern and central QTP populations were divided with the southeastern QTP ones approximately 0.67 Mya. The divergence times of the lineages were matched with two major glaciations in QTP (the Xixiabangma Glaciation, 1.17-0.80 Mya and Kunlun Glaciation, 0.72-0.62 Mya). Together with demographic history analyses, our results highlighted that major glacial cycles during the mid-Pleistocene played a major role in sculpting the distribution pattern of T. stenura, and led to the gene homogenization crossing the drainage populations in the southwestern and central QTP.