Ancient rivers shaped the current genetic diversity of the wood mouse (Apodemus speciosus) on the islands of the Seto Inland Sea, Japan.
Ancient rivers shaped the current genetic diversity of the wood mouse (Apodemus speciosus) on the islands of the Seto Inland Sea, Japan.
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DOI：
10.1186/s40851-022-00193-3
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发表时间：
2022-06-21
影响因子：
2.7
通讯作者：
Yasuda, Kouki
中科院分区：
文献类型：
--
作者：
Sato, Jun J.;Yasuda, Kouki
关键词：
目前的生物分布受到当前和过去地理障碍的影响。然而，过去的地理因素（目前在海底是神秘的）是如何影响陆地动物目前的分布的，这一点仍然不清楚。在这里，我们研究了目前神秘的古代河流对目前的遗传分化的大日本林鼠，Apodemus speciosus，居住在日本濑户内海的岛屿。通过随机扩增子测序的基因分型（Genotyping by Random Amplicon Sequencing，Direct）分析92个A. speciosus个体。最大似然分析与94,142单核苷酸多态性（SNPs）确定的GRAS-Di分析。利用地理信息系统（GIS）进行河道分析，实现了古河道的可视化。最大似然分析表明，在濑户内海的岛屿中的每个人口的单系性的强有力的支持，它也显示了因之岛，Ikuchijima，Ohmishima-Hakatajima-大岛，Ohsakikamimojima-Ohsakishimojima，Kamikamagarijima-Shimokamagarijima，和Kurahashijima-Etajima岛屿之间的密切关系。SNPs的主成分分析也支持这些关系。此外，位于古河道干流东西两侧岛屿的个体，也在各自的支持下聚集在一起。这些系统发育关系与从古河流推断的古地理关系完全一致。总之，研究结果表明，目前分布的遗传不同的岛屿血统是由古代河流，目前淹没在濑户内海，日本。在线版本包含补充材料，可通过10.1186/s40851-022-00193-3获得。
The current distributions of organisms have been shaped by both current and past geographical barriers. However, it remains unclear how past geographical factors—currently cryptic on the sea floor—affected the current distributions of terrestrial animals. Here, we examined the effects of currently cryptic ancient rivers on current genetic differentiation of the large Japanese wood mouse, Apodemus speciosus, which inhabits islands in the Seto Inland Sea, Japan. Genome-wide polymorphisms were identified by GRAS-Di (Genotyping by Random Amplicon Sequencing, Direct) analysis of 92 A. speciosus individuals. Maximum-likelihood analysis was performed with 94,142 single nucleotide polymorphisms (SNPs) identified by GRAS-Di analyses. Ancient rivers were visualized by Geographic Information System (GIS) channel analysis. Maximum-likelihood analysis showed strong support for the monophyly of each population in the islands in the Seto Inland Sea; it also showed close relationships between Innoshima-Ikuchijima, Ohmishima-Hakatajima-Oshima, Ohmishima-Hakatajima, Ohsakikamijima-Ohsakishimojima, Kamikamagarijima-Shimokamagarijima, and Kurahashijima-Etajima islands. The principal component analyses of the SNPs also supported these relationships. Furthermore, individuals from islands located on the east and west sides of the main stream of the ancient river were clustered on each side with strong support. These phylogenetic relationships were completely congruent with the paleogeographic relationships inferred from ancient rivers. In conclusion, the findings demonstrated that the current distribution of genetically distinct island lineages was shaped by ancient rivers that are currently submerged beneath the Seto Inland Sea, Japan. The online version contains supplementary material available at 10.1186/s40851-022-00193-3.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
9.2
作者：
Chang CC;Chow CC;Tellier LC;Vattikuti S;Purcell SM;Lee JJ
通讯作者：
Lee JJ
影响因子：
5.1
作者：
Conrad, O.;Bechtel, B.;Boehner, J.
通讯作者：
Boehner, J.
影响因子：
4
作者：
Clark, PU;Mix, AC
通讯作者：
Mix, AC
影响因子：
10.7
作者：
Nguyen LT;Schmidt HA;von Haeseler A;Minh BQ
通讯作者：
Minh BQ