Population Genomics Reveals Genetic Divergence and Adaptive Differentiation of Chinese Sea Bass (Lateolabrax maculatus)

Abstract

The marine species usually show high dispersal capabilities accompanied by high levels of gene flow. On the other hand, many physical barriers distribute along the continental marginal seas and may prevent dispersals and increase population divergence. These complexities along the continental margin generate serious challenges to population genetic studies of marine species. Chinese sea bass Lateolabrax maculatus distributes broad latitudinal gradient spanning from the tropical to the mid-temperate zones in the continental margin seas of the Northwest Pacific Ocean. Using the double digest restriction-site-associated DNA tag sequencing (ddRAD) approach, we genotyped 10,297 SNPs for 219 Chinese seabass individuals of 12 populations along the Chinese coast in the Northwest Pacific region. Genetic divergence among these populations was evaluated, and population structure was established. The results suggested that geographically distant populations in the Bohai Gulf and the Beibu Gulf retain significant genetic divergence, which are connected by a series of intermediate populations in between. The results also suggested that Leizhou Peninsula, Hainan Island, and Shandong Peninsula are major physical barriers and substantially block gene flow and genetic admixture of L. maculatus. We also investigated the potential genetic basis of local adaptation correlating with population differentiation of L. maculatus. The sea surface temperature is a significantly differentiated environmental factor for the distribution of L. maculatus. The correlation of water temperature and genetic variations in extensively distributed populations was investigated with Bayesian-based approaches. The candidate genes underlying the local selection in geographically divergent populations were identified and annotated, providing clues to understand the potential mechanisms of adaptive evolution. Overall, our genome scale population genetic analysis provided insight into population divergence and local adaptation of Chinese sea bass in the continental marginal seas along Chinese coast.

Population Genomics in Rhamdia quelen (Heptapteridae, Siluriformes) Reveals Deep Divergence and Adaptation in the Neotropical Region

“…The two highly divergent clusters were detected in the Negro River (4-NR-RB) and in the Merin Lagoon (9-ML-QC) basins. Latitudinal differentiation associated with water temperature has also been reported in the Chinese Sea Bass (Lateolabrax maculatus (Cuvier, 1828)) by RAD-seq analysis on populations of the continental marginal seas along the Chinese coast [21]. Furthermore, a parallel pattern of genomic divergence along a latitudinal gradient was found in sunflower (Helianthus genus) studies [80].…”

“…In such an evolutionary context, it was hypothesized that genomic footprints of selection might be associated with local adaptation to different environments and could therefore be retrieved using genomic screening across populations [17].Restriction site-associated DNA sequencing (RAD-seq) is a high-throughput technique that enables the simultaneous identification and genotyping of thousands of SNPs (Single Nucleotide Polymorphisms), indels and microsatellite markers in non-model organisms [18][19][20]. Genome-wide SNP population screening allows assessing genetic diversity, demographic and population structure, adaptive variation and the genetic architecture associated with traits of interest [21]. Neutral and adaptive genetic variation accounts for the demographic history and adaptive evolution of populations [22,23].…”

Chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus

“…A recent study identified a genome-wide variation of 22,648 single-nucleotide polymorphisms (SNPs) and used these SNPs to infer population structure and local adaptation of the spotted sea bass [9]. Furthermore, 10,297 SNPs from 219 spotted sea bass individuals belonging to 12 populations along the Chinese coast were used for genetic structure analysis in geographically distant populations [10]. In addition, a comprehensive transcriptome analysis identified sequences of genes involved in salinity adaptation and osmoregulation in the liver of the spotted sea bass, providing insights into the molecular mechanisms behind salinity acclimation in euryhaline teleosts [4].…”

Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast

“…An earlier study using isozyme and RAPD analyses had revealed differences among L. maculatus Chines populations from north to south (Li et al 2005). In addition, preliminary phylogenetic analysis demonstrated that populations of L. maculatus clustered into different clades, and suggested low genetic diversity within populations (Zhao et al 2018). Genetic diversity and population structure were investigated based on a single mitochondrial gene (COI) in five geographical populations (Wang et al 2017).…”