Population genetic structure and demographic history of Rhodeus atremius suigensis, an endangered bitterling in Japan
Population genetic structure and demographic history of Rhodeus atremius suigensis, an endangered bitterling in Japan
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DOI：
10.1007/s10592-022-01461-7
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发表时间：
2022-07-09
影响因子：
2.2
通讯作者：
Smith，Carl
中科院分区：
文献类型：
--
作者：
Kawamura，Kouichi;Miyake，Takuya;Smith，Carl
人口统计事件可以通过遗传漂变塑造遗传多样性，通常在物种的遗传特征中留下持久的信号。日本冈山平原特有的一种濒临灭绝的苦鱼。在本研究中，我们通过对mtDNA ND1基因、微卫星标记（microsatellite markers， MS）和MHC类IIB基因的综合分析，推断其人口统计学历史和遗传结构。基于mtDNA，R。A. suigensis包括两个亚系；A和b，前者分布广泛，后者仅局限于东部MHC单态种群。系统发育分析显示r。水杉属，与水杉属一起；a. atremius，在更新世中期经历了一个实质性的瓶颈期。在MS和MHC中，所有人群的遗传多样性都很低；在痛苦的物种中排名最低。贝叶斯聚类分析表明，MS的两个聚类在其分布中心已经广泛渗入。这些群落似乎是在更新世末期由于分布的破坏而形成的，后来由于16世纪以来冈山平原的大规模开垦而混合在一起，导致许多种群的有效种群规模（Ne）下降。根据聚结分析，所有种群数量在20世纪中叶左右达到最低点。因此,R。a.suigensis在过去似乎经历了两大瓶颈。第一个瓶颈可能是由于更新世中期的气候变化，而第二个瓶颈则是由于近年来人类活动导致的生境退化和破碎化。
Demographic events can shape genetic diversity through genetic drift, often leaving a persistent signal in the genetic characteristics of species.Rhodeus atremius suigensisis an endangered bitterling fish endemic to the Okayama Plain, Japan. In this study, we inferred its demographic history and genetic structure using a comprehensive analysis of the mtDNA ND1 gene, microsatellite markers (MS) and MHC class IIB gene. Based on mtDNA,R. a. suigensisincluded two sublineages; A and B. While the former was widely distributed, the latter was restricted to eastern populations that were monomorphic in MHC. Phylogenetic analysis revealed thatR. a. suigensis, together withR. a. atremius, experienced a substantial bottleneck in the middle Pleistocene. In MS and MHC, genetic diversity was low in all populations; ranked as the lowest among bitterling species. Bayesian clustering suggested that two clusters of MS had been widely introgressed in the centre of its distribution. These clusters seem to have been formed by the disruption of the distribution in the last Pleistocene, and later admixed by a large-scale reclamation in the Okayama Plain since the sixteenth century, which triggered a decline in effective population size (Ne) in many populations. Based on coalescence analysis, all populations reached their lowestNearound the middle of the twentieth century. Accordingly,R. a.suigensisseems to have experienced two large bottlenecks in the past. While the first bottleneck was probably due to climatic changes in the middle Pleistocene, the second is due to anthropogenic degradation and fragmentation of habitats in recent years.