Data_Sheet_7_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，大部分的鰤鱼属物种广泛分布于东亚近海区域，具有多样化的形态特征及不同的生态习性。由于谱系排序不完整、广泛存在杂交及基因渗入，鰤鱼属物种的进化关系及种群结构复杂。因此，为系统地阐明鰤鱼属的进化关系，探索不同鰤鱼物种间的基因渗入及自然杂交现象，并检测适应性进化中多样化性状的选择性标记，本研究对来自10个物种的122个鰤鱼样本进行了全基因组重测序。系统发育分析显示，鰤鱼双斑（Takifugu bimaculatus）与鰤鱼黄斑（Takifugu flavidus）、鰤鱼长形（Takifugu oblongus）、鰤鱼短鼻（Takifugu niphobles）、鰤鱼红鳍（Takifugu rubripes）、鰤鱼暗斑（Takifugu obscurus）、鰤鱼黄斑马（Takifugu xanthoptreus）和鰤鱼眼斑（Takifugu ocellatus）之间存在稳固的姐妹群关系。进一步的混合分析表明，T. obscurus种群发生了分化，且T. bimaculatus与T. flavidus之间存在双向基因流动。利用物种特异性的纯合遗传变异位点，我们在中国东海和台湾海峡南部检测到T. bimaculatus与T. flavidus之间不对称的基因渗入。通过基因组规模的遗传多样性扫描，我们检测到涉及半规管生殖节律的syt1、zar1和tgfbr1等基因在T. niphobles中的两个副本，这些基因参与记忆形成、胚胎成熟及雌性繁殖。此外，我们还发现了大量与昼夜节律相关基因和内分泌激素基因的CDS区域相关的T. niphobles特异性突变。对于鰤鱼物种而言，本研究提供了可靠的遗传资源和结果，用于谱系、基因渗入、杂交及适应性进化研究，并可作为制定保护及增殖释放政策的指南。