AUTHOR=Liu Bo , Zhou Zhixiong , Bai Yulin , Yang Junyi , Shi Yue , Pu Fei , Xu Peng 

TITLE=Genome-Scale Phylogenetic and Population Genetic Studies Provide Insight Into Introgression and Adaptive Evolution of Takifugu Species in East Asia

JOURNAL=Frontiers in Genetics

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.625600

DOI=10.3389/fgene.2021.625600

ISSN=1664-8021

ABSTRACT=<p>As a typical marine adaptive radiation species, most <italic>Takifugu</italic> 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 <italic>Takifugu</italic> species was complicated because of incomplete lineage sorting, widespread hybridization and introgression. Therefore, to systematically clarify the phylogenetic relationships of <italic>Takifugu</italic> genus, explore the introgression and natural hybridization between different <italic>Takifugu</italic> species, and detect the selective signatures in the adaptive evolution of diversified traits, whole-genome resequencing was used in 122 <italic>Takifugu</italic> samples from 10 species. Phylogenetic analysis showed solid sister-group relationships between <italic>Takifugu bimaculatus</italic> and <italic>Takifugu flavidus</italic>, <italic>Takifugu oblongus</italic>, and <italic>Takifugu niphobles</italic>, <italic>Takifugu rubripes</italic>, and <italic>Takifugu obscurus</italic>, <italic>Takifugu xanthoptreus</italic>, and <italic>Takifugu ocellatus</italic>. Further admixture analysis indicated the divergence of <italic>T. obscurus</italic> population and the bidirectional gene flow between <italic>T. bimaculatus</italic> and <italic>T. flavidus</italic>. Using species-specific homozygous genetic variance sites, we detected the asymmetric introgression between <italic>T. bimaculatus</italic> and <italic>T. flavidus</italic> at China East sea and southern Taiwan Strait. By genome-scale genetic diversity scanning, we detected two copies of <italic>syt1</italic>, <italic>zar1</italic> and <italic>tgfbr1</italic> related to the semilunar reproduction rhythm in <italic>T. niphobles</italic>, involved in memory formation, embryo maturation and female reproduction. Furthermore, we also found lots of <italic>T. niphobles</italic> specific mutations in CDS region of circadian rhythm related genes and endocrine hormone genes. For <italic>Takifugu</italic> 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.</p>