ddRAD-seq Reveals Cryptic Phylogeographic Structure and Adaptive Population Differentiation of Hyporhamphus Intermedius in Heterogeneous Environments from China Mainland

Abstract

BackgroundSpecies differentiation and local adaptation in heterogeneous environments have been getting a large focus but poor knowledge of the mechanism. With widespread in coastal areas and the hyperdiverse freshwater systems in China, Hyporhamphus intermedius is an excellent material for phylogeography and local adaptation research. Here, 156 individuals were sampled in 8 sites from heterogeneous aquatic habitats to comprehend environmental and genetic contributions to phenotypic divergence. Results32,744 SNPs among populations and obvious population differentiation was found by ddRAD-seq among groups from the different watersheds. Population genetic structure was partly geographic, successfully classifying all individuals into three genetic subgroups corresponding to the North, the South and the Plateau Lakes with more migrations within region. Due to the transplant event, the strikingly increasing divergence in a short time indicated the tendency of local differentiation for introduced populations in the Plateau Lakes. Dorsal and anal traits varied widely between the Southern and others, which highlighted previously unrecognized lineages. Furthermore, we inferred the whole population is in response to balancing selection from neutrality test with positive value (Tajima's D=2.773), and demographic history underlay two main split events from the northern ancestral population. Subgroup ranges appear to counterparts to geographic regions with heterogeneous hydrological factors, indicating these features are likely important drivers of diversification.ConclusionsAccordingly, our results revealed that genetic polymorphism and divergence of Hyporhamphus intermedius in heterogeneous environments might be ascribed to a consequence of balancing selection, gene flow at microscales, and the impact of abiotic factors, verifying potentially that genetic differences among populations are the result of both genetic canalization and plastic responses to environmental heterogeneity.