Evolution of population structure in an estuarine‐dependent marine fish

Abstract

Restriction site‐associated DNA (RAD) sequencing was used to characterize neutral and adaptive genetic variation among geographic samples of red drum, Sciaenops ocellatus, an estuarine‐dependent fish found in coastal waters along the southeastern coast of the United States (Atlantic) and the northern Gulf of Mexico (Gulf). Analyses of neutral and outlier loci revealed three genetically distinct regional clusters: one in the Atlantic and two in the northern Gulf. Divergence in neutral loci indicated gradual genetic change and followed a linear pattern of isolation by distance. Divergence in outlier loci was at least an order of magnitude greater than divergence in neutral loci, and divergence between the regions in the Gulf was twice that of divergence between other regions. Discordance in patterns of genetic divergence between outlier and neutral loci is consistent with the hypothesis that the former reflects adaptive responses to environmental factors that vary on regional scales, while the latter largely reflects drift processes. Differences in basic habitat, initiated by glacial retreat and perpetuated by contemporary oceanic and atmospheric forces interacting with the geomorphology of the northern Gulf, followed by selection, appear to have led to reduced gene flow among red drum across the northern Gulf, reinforcing differences accrued during isolation and resulting in continued divergence across the genome. This same dynamic also may pertain to other coastal or nearshore fishes (18 species in 14 families) where genetically or morphologically defined sister taxa occur in the three regions.

Demographic, Taxonomic, and Genetic Characterization of the Snook Species Complex (Centropomus spp.) along the Leading Edge of Its Range in the Northwestern Gulf of Mexico

“…; Hollenbeck et al. ; Anderson et al. ), a finding that underscores the risk of overinterpreting smaller genetic data sets.…”

“…New genomic-based methods (e.g., Peterson et al 2012) allow for simultaneous locus discovery and genotyping of potentially thousands of genetic markers for a reduced per-sample cost. These "genomic" methods have frequently demonstrated a pattern whereby small numbers of loci (presumably under directional selection) show elevated divergence relative to the genomic mean in marine fishes (Portnoy et al 2015;Hollenbeck et al 2018;Anderson et al 2019), a finding that underscores the risk of overinterpreting smaller genetic data sets. Nevertheless, in the absence of such genomic data, the present data suggest a tentative single-stock management unit for each of the predominant snook species in Texas.…”

Population Genomics of an Anadromous Hilsa Shad Tenualosa ilisha Species across Its Diverse Migratory Habitats: Discrimination by Fine-Scale Local Adaptation

“…Our isolation by distance (IBD) results also suggested that the genetic structure demonstrates the effect of dispersion and selection for the outlier dataset, and these factors should be considered when delineating conservation and management units [50]. The outlier loci suggest adaptive responses to potential environmental factors, such as salinity, which vary on regional scales, while neutral loci are influenced by genetic drift [52]. Given that the divergences revealed by the outlier dataset are discordant with the neutral loci, these loci should be driven by the effects of selection and not by the isolation alone [53].…”

“…Genetic differentiation, under selective force, is not unprecedented, given that analysis based on markers under selection provides more structuring, compared to neutral markers [29,51]. This type of analysis is more promising for populations with a large effective size and minimal genetic drift effect [52], where a high level of gene flow may not be efficient to dilute the differentiation effects driven by adaptive markers [30]. The higher level of assignment success of NextRAD sequencing is likely due to larger number of loci and also outlier loci with a high discriminatory power.…”

Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region

“…Although similar genetic discriminations were observed, putatively adaptive SNP loci most powerfully detected the genetic discrimination, as revealed by demographic interpretations and inferred clustering analyses. Compared to conventional molecular markers used for population genetic studies, our SkimSeq approach uses unbiased whole genome sequences to accurately identify the traces of selection that cause genetic differentiation using a lower coverage area with combination of small population size [ 77 , 78 ]. We noted that the impact of random genetic drift is larger in smaller sample size [ 79 ].…”