Abstract
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.
Highlights
Adaptive radiation leadsP to the evolution of different species with diverse ecological features and phenotypes within a rapidly multiplying lineage
We re-sequenced the genome of 70 wild Takifugu individuals and downloaded the re-sequencing data of an additional 52 individuals from NCBI, who belonged to 10 different Takifugu species, to estimate sites of genetic variation, phylogenetic relationships, potential hybridization and introgression, and the presence of selective signatures of adaptive evolution in the different species
Using a 50 kb sliding window on a genome-wide scale, we found that T. flavidus (Tf) and T. bimaculatus (Tb) had the highest number of polymorphisms, which may be related to frequent introgressions between them (Figure 1D)
Summary
Adaptive radiation leadsP to the evolution of different species with diverse ecological features and phenotypes within a rapidly multiplying lineage. The widespread incomplete lineage sorting (ILS), hybridization, gene introgression, and the complicated lineage relationships among cichlids were studied and elucidated on a genomewide scale (Brawand et al, 2014; Meier et al, 2017; Malinsky et al, 2018). Species that have arisen from adaptive radiation have high genetic similarity, exhibit diverse phenotypes, and are excellent specimens for the study of evolutionary developmental biology and evolutionary genomics (Macfadden and Hulbert, 1988). Using comparative genomics and population genetics, many studies have identified candidate genes underlying phenotypic differentiation among species are a product of adaptive radiation, such as dog (Akey et al, 2010), cichlid fishes (Torres-Dowdall et al, 2017) and finch (Tebbich et al, 2010)
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