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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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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