Evaluation of the population structure and phylogeography of the Japanese Genji firefly, Luciola cruciata, at the nuclear DNA level using RAD-Seq analysis
Evaluation of the population structure and phylogeography of the Japanese Genji firefly, Luciola cruciata, at the nuclear DNA level using RAD-Seq analysis
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DOI：
10.1038/s41598-020-58324-9
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发表时间：
2020-01-30
影响因子：
4.6
通讯作者：
Nagano, Yukio
中科院分区：
文献类型：
--
作者：
Kato, Dai-ichiro;Suzuki, Hirobumi;Nagano, Yukio
源氏萤火虫Luciola cruciata广泛分布于日本的主要岛屿（本州岛、四国岛和九州岛），根据雄性求偶的闪光间隔（慢闪4秒或快闪2秒）将其分为两种生态类型。生态类型的边界对应于分隔日本东部和西部的大破裂带——大凹。虽然这两种类型的遗传分化程度已经使用等位酶和线粒体DNA序列数据进行了评估，但尚未使用全基因组数据进行评估。基于单端限制性位点相关DNA （RAD-Seq）、主成分分析、基因水平系统发育树分析、混合分析和Wright's固定指数分析获得的全基因组数据，我们确定了十字L. crucata的3个系统发育类群：东本州、西本州和九州。这个分组对应于生态类型：东本州为慢闪型，西本州和九州为快闪型。虽然在相邻区域或人工移植区域有例外的基因渗入现象，但在自然群体中几乎没有群体间的基因流动。在聚结模型下的系统发育树也评估了东本州、西本州和九州群之间的分化。此外，由于这三个类群的分布格局与日本列岛的地质历史相一致，因此可以推断出十字花科植物的替代物种形成情景。此外，我们还鉴定了可用于区分三个遗传群的遗传标记，用于自然保护和再生中萤火虫移植的遗传管理。
The Genji firefly, Luciola cruciata, is widely distributed throughout the major Japanese islands (Honshu, Shikoku, and Kyushu) and distinguished into two ecological types on the basis of the flash interval of the mate-seeking males (4-sec slow-flash or 2-sec fast-flash intervals). The boundary of the ecological types corresponds to the Fossa Magna, a great rupture zone that separates eastern and western Japan. Although the degree of genetic differentiation of the two types has been evaluated using allozyme and mitochondrial DNA sequence data, it has not been evaluated using genome-wide data. Based on the genome-wide data obtained using single-end restriction-site-associated DNA (RAD-Seq), principal component, gene-level phylogenetic tree, admixture, and Wright's fixation index analyses, we identified three phylogenetic groups in L. cruciata: East-Honshu, West-Honshu, and Kyushu. This grouping corresponds to the ecological types: East-Honshu to the slow-flash type and West-Honshu and Kyushu to the fast-flash type. Although introgression was exceptionally observed around adjacent or artificially transplanted areas, gene flow among the groups was almost absent in the natural populations. The phylogenetic tree under the coalescent model also evaluated differentiation among the East-Honshu, West-Honshu and Kyushu groups. Furthermore, because the distribution patterns of the three groups are consistent with the geological history of Japanese islands, a vicariant speciation scenario of L. cruciata is concluded. In addition, we identified genetic markers that can be used to distinguish the three genetic groups for genetic management of firefly transplantation in nature conservation and regeneration.