Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservation
Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservation
复制标题
利用环境 DNA 评估濒危鱼类 Gnathopogon caerulescens 的遗传多样性及其在鱼类保护中的潜在用途
DOI：
10.1002/edn3.408
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发表时间：
2023
影响因子：
--
通讯作者：
Kikko Takeshi
中科院分区：
文献类型：
--
作者：
Wakimura Kei;Uchii Kimiko;Kikko Takeshi
琵琶鱼是日本琵琶湖的特有鱼类，是湖泊渔业的重要鱼类之一。自20世纪90年代数量下降以来，它已被列为濒危物种，因此需要保护。最近越来越多的研究强调为保护目的纳入遗传多样性的重要性。在这项研究中，我们旨在评估线粒体DNA单倍型组成的g。利用环境DNA （eDNA）来确定该物种的遗传多样性。我们开发了一种基于eDNA的单倍型方法，使用高通量测序（HTS），可以准确地检测和消除错误的HTS读数，即使目标序列是由单个或几个错配区分的。利用该方法进行的野外调查成功地揭示了当地赤霉病菌的遗传结构。caerulescenspopulations。我们发现星形的单倍型网络由两个主要的单倍型和几个罕见的单倍型组成，除了一个。小毛羽种群经历了历史上的扩张，在20世纪90年代的种群衰退中，其种群规模并未缩小到罕见单倍型被消灭的程度。在单倍型数量和单倍型多样性(h)方面，北方种群的遗传多样性较低，表明北方种群的下降比南方更严重。我们展示了eDNA分析在濒危物种群体遗传学中的实际应用。使用这种方法进行持续监测将有助于养护和管理鱼类资源。
Gnathopogon caerulescens, an endemic fish of Lake Biwa, Japan, is one of the most important fishes for lake fisheries. It has been listed as an endangered species following its population decline in the 1990s and thus needs conservation. An increasing number of studies have recently stressed on the importance of incorporating genetic diversity for conservation purposes. In this study, we aimed to evaluate the mitochondrial DNA haplotype composition ofG. caerulescensusing environmental DNA (eDNA) to determine the genetic diversity of this species. We developed an eDNA‐based haplotyping approach using high‐throughput sequencing (HTS), which can accurately detect and eliminate erroneous HTS reads, even when the target sequences are differentiated by a single or a few mismatches. Field surveys using the developed method successfully revealed the genetic structure of localG. caerulescenspopulations. We found star‐shaped haplotype networks with two major haplotypes accompanied by several rare haplotypes for all local populations except one, which suggested that theG. caerulescenspopulation had undergone a historical expansion, and its population size did not shrink to the extent that rare haplotypes were eliminated during the population decline in the 1990s. We also observed that the genetic diversity was lower in the northern populations in terms of haplotype number and haplotype diversity (h), suggesting that the decline in population was more severe in the north than in the south. We demonstrated the practical use of eDNA analysis in population genetics of endangered species. Continuous monitoring using this approach would facilitate the conservation and management of fish resources.