A ddRAD-based population genetics and phylogenetics of an endangered freshwater fish from Japan
A ddRAD-based population genetics and phylogenetics of an endangered freshwater fish from Japan
复制标题
DOI：
10.1007/s10592-020-01275-5
复制
发表时间：
2020-04-19
影响因子：
2.2
通讯作者：
Kawamura, Kouichi
中科院分区：
文献类型：
--
作者：
Takahashi, Tetsumi;Nagano, Atsushi J.;Kawamura, Kouichi
古罗氏鱼是日本群岛特有的一种小型鲤科鱼。这条鱼经常与外来亚种红鳉杂交，非遗传的红鳉种群已经大大减少。先前基于线粒体和核DNA的研究确定了基因渗入群体并推断了系统发育关系，但由于使用的遗传标记数量较少，这些方法可能导致对基因渗入的低估或结果不明确。本研究应用双消化限制位点相关DNA （ddRAD）测序进行配位测试和系统发育推断。根据用于处理ddRAD序列的策略，数据矩阵的大小和内容可以有所不同；因此，我们用不同的处理策略准备了25个数据矩阵。基于25个数据矩阵的分配测试得出了类似的分配模式，并提供了在以前的研究中被确定为非渗入种群的一些种群中存在渗入的证据。最大似然（ML）系统发育树在鲁棒性和拓扑结构上存在差异；有趣的是，低统计支持度的ML树比高统计支持度的ML树更能反映鱼类的地理分布。这些结果表明，ddRAD测序可以比传统的DNA标记更敏感地检测渗入，ddRAD测序对亚种内密切相关群体的系统发育推断有用，并且统计上稳健的ML树不一定反映真实的系统发育。讨论了ddRAD数据在该亚种保护遗传学和进化历史中的应用。
Rhodeus ocellatus kurumeus is a small cyprinid fish endemic to the Japanese archipelago. This fish frequently hybridizes with an exotic subspecies Rhodeus ocellatus ocellatus, and non-introgressed populations of R. o. kurumeus have greatly decreased. Previous studies based on mitochondrial and nuclear DNA identified introgressed populations and inferred phylogenetic relationships, but these approaches may lead to underestimates of introgression or ambiguous results owing to the small number of genetic markers used. The present study applied double digest restriction site-associated DNA (ddRAD) sequencing to assignment tests and phylogenetic inferences. Data matrices can vary in size and content depending on the strategies used to process ddRAD sequences; therefore, we prepared 25 data matrices with various processing strategies. The assignment tests based on the 25 data matrices resulted in similar assignment patterns and provided evidence for introgression in some populations that had been identified as non-introgressed populations in previous studies. The maximum-likelihood (ML) phylogenetic trees differed in robustness and topology among the 25 matrices; interestingly, ML trees with low statistical support reflected geographical distributions of fish better than ML trees with high statistical support. These results indicate that ddRAD sequencing can detect introgression with greater sensitivity than conventional DNA markers, that ddRAD sequencing is useful for phylogenetic inference among closely related populations within a subspecies, and that statistically robust ML trees do not necessarily reflect the true phylogeny. Application of ddRAD data to conservation genetics and evolutionary history of this subspecies are also discussed.