Data_Sheet_4_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.

作为典型的海洋适应性辐射类群，多数东方鲀属（Takifugu）物种广泛分布于东亚近岸海域，其形态特征多样，生态习性各异。由于不完全谱系分选、广泛存在的杂交与基因渐渗现象，东方鲀属物种的系统发育关系与种群结构极为复杂。为此，为系统厘清东方鲀属的系统发育关系、解析不同物种间的基因渐渗与自然杂交现象，并探究适应性演化中多样性状的选择印记，本研究对10个物种共122份东方鲀样本开展了全基因组重测序。系统发育分析结果显示，双斑东方鲀（Takifugu bimaculatus）与黄鳍东方鲀（Takifugu flavidus）、长鳍东方鲀（Takifugu oblongus）与星点东方鲀（Takifugu niphobles）、红鳍东方鲀（Takifugu rubripes）与暗纹东方鲀（Takifugu obscurus）、黄褶东方鲀（Takifugu xanthoptreus）与眼斑东方鲀（Takifugu ocellatus）之间存在稳健的姐妹群关系。进一步的群体结构分析显示，暗纹东方鲀种群存在明显分化，且双斑东方鲀与黄鳍东方鲀之间存在双向基因流。利用物种特异性纯合遗传变异位点，本研究在东海与台湾海峡南部海域检测到双斑东方鲀与黄鳍东方鲀之间存在不对称基因渐渗现象。通过全基因组尺度的遗传多样性扫描，本研究在星点东方鲀（Takifugu niphobles）中检测到与半月繁殖节律相关的syt1、zar1及tgfbr1基因的两个拷贝，这些基因分别参与记忆形成、胚胎成熟与雌性生殖过程。此外，本研究还在星点东方鲀的节律相关基因与内分泌激素基因的编码区（CDS）中发现了大量物种特异性突变位点。本研究为东方鲀属物种的系统发育、基因渐渗、自然杂交与适应性演化研究提供了可靠的遗传资源与分析结果，同时可为该类群的保护与增殖放流政策制定提供参考依据。