Revisiting conservation units for the endangered mountain yellow-legged frog species complex (Rana muscosa, Rana sierrae) using multiple genomic methods
Revisiting conservation units for the endangered mountain yellow-legged frog species complex (Rana muscosa, Rana sierrae) using multiple genomic methods
复制标题
DOI：
10.1007/s10592-023-01568-5
复制
发表时间：
2023-09
影响因子：
2.2
通讯作者：
Allison Q. Byrne;Andrew P. Rothstein;Lydia L. Smith;Hannah Kania;Roland A. Knapp;Daniel M. Boiano;
中科院分区：
文献类型：
--
作者：
Allison Q. Byrne;Andrew P. Rothstein;Lydia L. Smith;Hannah Kania;Roland A. Knapp;Daniel M. Boiano;
保护基因组学的见解极大地改善了许多濒危物种的恢复计划。然而，大多数分类群尚未从基因组技术的全面应用中受益。山黄腿蛙（Rana muscosaandRana sierrae）是一种复杂的山黄腿蛙，它们生活在加州和内华达州的内华达山脉和横向/半岛山脉。这两个物种在它们的历史分布中都急剧下降。保护管理计划概述了广泛的正在进行的恢复工作，但仍然基于主要使用单个线粒体序列确定的遗传结构。我们的研究使用了两种不同的测序策略——扩增子测序和外显子捕获——来完善我们对这些濒危两栖动物种群遗传学的理解。我们使用口腔拭子、博物馆组织样本和存档的皮肤拭子对其分布范围内的青蛙种群进行基因分型。利用扩增子测序和外显子组捕获数据集分别和组合，我们记录了五个主要的遗传集群。值得注意的是，我们在国王峡谷国家公园发现了支持以前物种边界的证据，在个别地点有一些例外。尽管我们看到了遗传聚类的证据，特别是在那里。muscosaclade，我们也发现了一些跨簇边界的混合物的证据。Sierraeclade提出了一个人口结构的垫脚石模型。我们还发现南部的nr。Muscosacluster具有大量的纯合性和最低的总体杂合性，这与先前在该地区显著下降的报告一致。总的来说，我们的研究结果明确了濒危物种范围内的管理单位名称，并强调了采样整个物种范围的重要性，即使在收集基因组规模数据时也是如此。
Insights from conservation genomics have dramatically improved recovery plans for numerous endangered species. However, most taxa have yet to benefit from the full application of genomic technologies. The mountain yellow-legged frog species complex,Rana muscosaandRana sierrae,inhabits the Sierra Nevada mountains and Transverse/Peninsular Ranges of California and Nevada. Both species have declined precipitously throughout their historical distributions. Conservation management plans outline extensive ongoing recovery efforts but are still based on the genetic structure determined primarily using a single mitochondrial sequence. Our study used two different sequencing strategies – amplicon sequencing and exome capture – to refine our understanding of the population genetics of these imperiled amphibians. We used buccal swabs, museum tissue samples, and archived skin swabs to genotype frog populations across their range. Using the amplicon sequencing and exome capture datasets separately and combined, we document five major genetic clusters. Notably, we found evidence supporting previous species boundaries within Kings Canyon National Park with some exceptions at individual sites. Though we see evidence of genetic clustering, especially in theR. muscosaclade, we also found evidence of some admixture across cluster boundaries in theR. sierraeclade, suggesting a stepping-stone model of population structure. We also find that the southernR. muscosacluster had large runs of homozygosity and the lowest overall heterozygosity of any of the clusters, consistent with previous reports of marked declines in this area. Overall, our results clarify management unit designations across the range of an endangered species and highlight the importance of sampling the entire range of a species, even when collecting genome-scale data.