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

The distribution of <i>Triplophysa yarkandensis</i> is restricted to Xinjiang’s Tarim River basin. We collected 119 <i>T. yarkandensis</i> samples from nine geographic populations in the Tarim River basin and utilized the RAD-seq method for SNP genotyping. In this study, a to...

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Main Authors: Xiaoyun Zhou, Shaokui Yi, Wenhao Zhao, Qiong Zhou, Jianzhong Shen, Dapeng Li, Bin Huo, Rong Tang
Format: Article
Language:English
Published: MDPI AG 2021-08-01
Series:Biology
Subjects:
Online Access:https://www.mdpi.com/2079-7737/10/8/734
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spelling doaj-234c396ae1174ef5a3e3797f477007bb2021-08-26T13:32:08ZengMDPI AGBiology2079-77372021-08-011073473410.3390/biology10080734Genetic Diversity and Population Differentiation of Kashgarian Loach (<i>Triplophysa yarkandensis</i>) in Xinjiang Tarim River BasinXiaoyun Zhou0Shaokui Yi1Wenhao Zhao2Qiong Zhou3Jianzhong Shen4Dapeng Li5Bin Huo6Rong Tang7College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, ChinaCollege of Life Sciences, Huzhou University, Huzhou 313000, ChinaCollege of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, ChinaCollege of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, ChinaCollege of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, ChinaCollege of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, ChinaCollege of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, ChinaCollege of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, ChinaThe distribution of <i>Triplophysa yarkandensis</i> is restricted to Xinjiang’s Tarim River basin. We collected 119 <i>T. yarkandensis</i> 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 (<i>F</i><sub>ST</sub> = 0.67), and the pairwise <i>F</i><sub>ST</sub> 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 <i>T. yarkandensis</i> 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 <i>T. yarkandensis</i> populations in the Tarim River basin, and it provided valuable molecular data for conservation and management of natural populations.https://www.mdpi.com/2079-7737/10/8/734Tarim Rivergene flowbarrierBayesian skyline plotting
collection DOAJ
language English
format Article
sources DOAJ
author Xiaoyun Zhou
Shaokui Yi
Wenhao Zhao
Qiong Zhou
Jianzhong Shen
Dapeng Li
Bin Huo
Rong Tang
spellingShingle Xiaoyun Zhou
Shaokui Yi
Wenhao Zhao
Qiong Zhou
Jianzhong Shen
Dapeng Li
Bin Huo
Rong Tang
Genetic Diversity and Population Differentiation of Kashgarian Loach (<i>Triplophysa yarkandensis</i>) in Xinjiang Tarim River Basin
Biology
Tarim River
gene flow
barrier
Bayesian skyline plotting
author_facet Xiaoyun Zhou
Shaokui Yi
Wenhao Zhao
Qiong Zhou
Jianzhong Shen
Dapeng Li
Bin Huo
Rong Tang
author_sort Xiaoyun Zhou
title Genetic Diversity and Population Differentiation of Kashgarian Loach (<i>Triplophysa yarkandensis</i>) in Xinjiang Tarim River Basin
title_short Genetic Diversity and Population Differentiation of Kashgarian Loach (<i>Triplophysa yarkandensis</i>) in Xinjiang Tarim River Basin
title_full Genetic Diversity and Population Differentiation of Kashgarian Loach (<i>Triplophysa yarkandensis</i>) in Xinjiang Tarim River Basin
title_fullStr Genetic Diversity and Population Differentiation of Kashgarian Loach (<i>Triplophysa yarkandensis</i>) in Xinjiang Tarim River Basin
title_full_unstemmed Genetic Diversity and Population Differentiation of Kashgarian Loach (<i>Triplophysa yarkandensis</i>) in Xinjiang Tarim River Basin
title_sort genetic diversity and population differentiation of kashgarian loach (<i>triplophysa yarkandensis</i>) in xinjiang tarim river basin
publisher MDPI AG
series Biology
issn 2079-7737
publishDate 2021-08-01
description The distribution of <i>Triplophysa yarkandensis</i> is restricted to Xinjiang’s Tarim River basin. We collected 119 <i>T. yarkandensis</i> 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 (<i>F</i><sub>ST</sub> = 0.67), and the pairwise <i>F</i><sub>ST</sub> 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 <i>T. yarkandensis</i> 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 <i>T. yarkandensis</i> populations in the Tarim River basin, and it provided valuable molecular data for conservation and management of natural populations.
topic Tarim River
gene flow
barrier
Bayesian skyline plotting
url https://www.mdpi.com/2079-7737/10/8/734
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