Data_Sheet_6_Genome-Scale Phylogenetic and Population Genetic Studies Provide Insight Into Introgression and Adaptive Evolution of Takifugu Species in East Asia.PDF

As a typical marine adaptive radiation species, most Takifugu species are widely distributed in East Asian offshore, which have diversified morphological characteristics and different ecological habits. The phylogenetic relationship and population structure of the Takifugu species was complicated because of incomplete lineage sorting, widespread hybridization and introgression. Therefore, to systematically clarify the phylogenetic relationships of Takifugu genus, explore the introgression and natural hybridization between different Takifugu species, and detect the selective signatures in the adaptive evolution of diversified traits, whole-genome resequencing was used in 122 Takifugu samples from 10 species. Phylogenetic analysis showed solid sister-group relationships between Takifugu bimaculatus and Takifugu flavidus, Takifugu oblongus, and Takifugu niphobles, Takifugu rubripes, and Takifugu obscurus, Takifugu xanthoptreus, and Takifugu ocellatus. Further admixture analysis indicated the divergence of T. obscurus population and the bidirectional gene flow between T. bimaculatus and T. flavidus. Using species-specific homozygous genetic variance sites, we detected the asymmetric introgression between T. bimaculatus and T. flavidus at China East sea and southern Taiwan Strait. By genome-scale genetic diversity scanning, we detected two copies of syt1, zar1 and tgfbr1 related to the semilunar reproduction rhythm in T. niphobles, involved in memory formation, embryo maturation and female reproduction. Furthermore, we also found lots of T. niphobles specific mutations in CDS region of circadian rhythm related genes and endocrine hormone genes. For Takifugu species, our research provides reliable genetic resources and results for the phylogeny, introgression, hybridization and adaptive evolution, and could be used as a guide for the formulation of the protection and proliferation release policies.

作为一种典型的海洋适应性辐射物种，大多数河鲀属物种广泛分布于东亚近海区域，并展现出多样化的形态特征和独特的生态习性。由于谱系排序不完整、广泛杂交及基因渗入，河鲀属物种的进化关系和种群结构复杂。因此，为了系统地阐明河鲀属的进化关系，探讨不同河鲀物种间的基因渗入和自然杂交现象，以及检测多元化性状在适应性进化过程中的选择性标记，本研究对来自10个物种的122个河鲀样本进行了全基因组重测序。系统发育分析表明，河鲀双斑（Takifugu bimaculatus）与河鲀淡黄（Takifugu flavidus）、河鲀长形（Takifugu oblongus）、河鲀红鳍（Takifugu rubripes）、河鲀暗色（Takifugu obscurus）、河鲀黄斑（Takifugu xanthoptreus）和河鲀眼斑（Takifugu ocellatus）之间存在着稳固的姐妹群关系。进一步的混合分析揭示了河鲀暗色种群的分化和河鲀双斑与河鲀淡黄之间的双向基因流。通过利用物种特异性纯合遗传变异位点，我们在中国东海和台湾海峡南部检测到了河鲀双斑与河鲀淡黄之间的非对称基因渗入。通过基因组规模的遗传多样性扫描，我们发现了与河鲀长形半规管繁殖节律相关的syt1、zar1和tgfbr1基因的两个拷贝，这些基因参与记忆形成、胚胎成熟和雌性繁殖。此外，我们还发现了大量与河鲀长形相关的突变，这些突变位于与昼夜节律相关基因和内分泌激素基因的编码序列区域。本研究为河鲀物种的谱系、基因渗入、杂交和适应性进化提供了可靠的遗传资源和研究成果，可作为制定保护和增殖释放政策的指导。