Genetic Diversity and Structure Analysis of Percocypris pingi (Cypriniformes: Cyprinidae): Implications for Conservation and Hatchery Release in the Yalong River

RESEARCH ARTICLE Genetic Diversity and Structure Analysis of Percocypris pingi (Cypriniformes: Cyprinidae): Implications for Conservation and Hatchery Release in the Yalong River Xiaoyan Li1☯, Yuanping Deng1☯, Kun Yang1, Weixiong Gan2, Rukui Zeng2, Longjun Deng2, Zhaobin Song1,3* a11111 1 Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China, 2 Yalong River Hydropower Development Company, Ltd., Chengdu, China, 3 Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China ☯ These authors contributed equally to this work. * OPEN ACCESS Citation: Li X, Deng Y, Yang K, Gan W, Zeng R, Deng L, et al. (2016) Genetic Diversity and Structure Analysis of Percocypris pingi (Cypriniformes: Cyprinidae): Implications for Conservation and Hatchery Release in the Yalong River. PLoS ONE 11(12): e0166769. doi:10.1371/ journal.pone.0166769 Editor: Samuel Rezende Paiva, Embrapa, BRAZIL Received: April 12, 2016 Accepted: November 3, 2016 Published: December 2, 2016 Copyright: © 2016 Li et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the paper and its Supporting Information files. Funding: Yalong River Hydropower Development Company, Ltd. (No. 12H0856) and Program for New Century Excellent Talents in University (No. NCET-11-0347). Yalong River Hydropower Development Company, Ltd. provided financial support for field studies and relevant expenditure (e.g., field sampling and purchasing artificial propagated samples); Program for New Century Excellent Talents in University provided financial Abstract Percocypris pingi is a near threatened cyprinid species, which has suffered a dramatic decline due to anthropogenic factors. As one response to this decline, hatchery release for P. pingi has been conducted in the lower reaches of the Yalong River since 2012. To understand the conservation status of this species and the potential impact of the release of hatchery-reared fish, we studied the genetic diversity and population structure of wild and hatchery populations of P. pingi. Two hatchery populations (Jinping [JPH] and Ya’an [YAH]) and two wild populations (Muli [MLW] and Woluo [WLW]) of P. pingi were analyzed based on microsatellite markers and the mitochondrial DNA control region. The results showed that P. pingi possesses moderate levels of genetic diversity, with observed heterozygosities ranging from 0.657 to 0.770 and nucleotide diversities ranging from 0.00212 to 0.00491. Our results also suggested WLW harbors considerable proportions of genetic diversity in this species and serves as a refuge for P. pingi during anthropogenic disturbance, thus playing an important role for the conservation of P. pingi populations. Microsatellite and mitochondrial markers both indicated close genetic relationships between YAH and MLW, JPH and WLW, respectively. The results to some extent reflected the geographical provenances for original broodstocks of the two hatchery populations, which provide some practical guidance for hatchery release of P. pingi. The existence of remarkable genetic divergence distributed along limited geographical range (approximately 10 kilometers) suggests the two wild populations should be regarded at least as two distinct evolutionary significant units (ESUs) and management units (MUs). Considering reduced intra-population genetic variation in hatchery population for release and significant genetic compositions of the two hatchery populations, some appropriate breeding strategies were proposed to benefit conservation of P. pingi. PLOS ONE | DOI:10.1371/journal.pone.0166769 December 2, 2016 1 / 18 Genetic Diversity and Structure Analysis of Percocypris pingi support for laboratory experiments and relevant expenditure (e.g., DNA extraction, genotyping and sequencing). Weixiong Gan, Rukui Zeng and Longjun Deng are employed by Yalong River Hydropower Development Company, Ltd. Yalong River Hydropower Development Company, Ltd. provided support in the form of salaries for authors WG, RZ and LD and played a role in data collection, contributed reagents and analysis tools. The specific roles of these authors are articulated in the ‘author contributions’ section. Competing Interests: This study was funded in part by Yalong River Hydropower Development Company, Ltd (http://www.ehdc.com.cn/faces/en/ overview2.html). This company is an enterprise engaged in development of hydropower projects and generation of hydroelectric energy. At the same time, it has been doing environment protection work associated with the hydropower development. Weixiong Gan, Rukui Zeng and Longjun Deng are employed by Yalong River Hydropower Development Company, Ltd. There are no patents, products in development or marketed products to declare. This does not alter our adherence to all the PLOS ONE policies on sharing data and materials. Introduction Percocypris pingi (Tchang) (Cypriniformes: Cyprinidae) is an important commercial fish [1] distributed in the upper reaches of the Yangtze River and its tributaries [2,3,4], mainly in the Qingyi, Dadu, Yalong and Jinsha rivers. Percocypris pingi prefers lotic habitats and spawns several thousand eggs in these lotic habitats once each spring [1]. Because of large size and delicious taste, the fish has been strongly targeted and overexploited by commercial fishermen. In addition, other anthropogenic interferences, such as habitat deterioration and water pollution, have led to further decline of P. pingi populations [3,5]. Percocypris pingi was once widely distributed in the main channel and tributaries of the Yalong River, the largest branch of the Jinsha River, which runs through the provinces of Qinghai and Sichuan in western China. Due to the construction of a number of series of hydropower stations and overexploitation, P. pingi populations in this river have decreased dramatically in recent years, and its distribution range has been drastically reduced [6,7]. It now occurs mainly in the lower reaches of the Yalong River, the Muli River (a tributary of the Yalong) and the Woluo River (a tributary of the Muli). Also, Wild resources of P. pingi in the Qingyi and Dadu rivers were very limited based on our visiting investigation. The continuously deteriorating conservation status of P. pingi has led to its classification as a near threatened species for conservation in the IUCN Red List [8], and its listing as a protected wild animal in Sichuan Province. In May 2015, P. pingi was classified as Endangered (EN) in the Red List of China’s Vertebrates [9]. Specific conservation strategies, and additional studies on population genetics of P. pingi that could pr (...truncated)