Disentangling complex genomic signals to understand population structure of an exploited, estuarine‐dependent flatfish

• Published in: Ecology and evolution 2021-10, Vol.11 (19), p.13415-13429
• Main Authors: O'Leary, Shannon J., Hollenbeck, Christopher M., Vega, Robert R., Portnoy, David S.
• Format: Article
• Language: English
• Subjects: Adaptation; Adults; Demographics; Divergence; Estuaries; Flounder; genetic‐environmental association; Genomes; Genomics; Habitats; Heterogeneity; local adaptation; Mitochondrial DNA; Mutation; Ocean basins; Original Research; Paralichthys lethostigma; Population; population genomics; Population structure; Salinity; Single-nucleotide polymorphism; Task forces
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.8064

Interpreting contemporary patterns of population structure requires an understanding of the interactions among microevolutionary forces and past demographic events. Here, 4,122 SNP‐containing loci were used to assess structure in southern flounder (Paralichthys lethostigma) sampled across its range in the US Atlantic Ocean (Atlantic) and Gulf of Mexico (Gulf) and relationships among components of genomic variation and spatial and environmental variables were assessed across estuarine population samples in the Gulf. While hierarchical Amova revealed significant heterogeneity within and between the Atlantic and Gulf, pairwise comparisons between samples within ocean basins demonstrated that all significant heterogeneity occurred within the Gulf. The distribution of Tajima's D estimated at a genome‐wide scale differed significantly from equilibrium in all estuaries, with more negative values occurring in the Gulf. Components of genomic variation were significantly associated with environmental variables describing individual estuaries, and environment explained a larger component of variation than spatial proximity. Overall, results suggest that there is genetic spatial autocorrelation caused by shared larval sources for proximal nurseries (migration/drift), but that it is modified by environmentally driven differentiation (selection). This leads to conflicting signals in different parts of the genome and creates patterns of divergence that do not correspond to paradigms of strong local directional selection. 4,122 SNP‐containing loci were used to assess structure in southern flounder (Paralichthys lethostigma) sampled across its range in the U.S. Atlantic Ocean (Atlantic) and Gulf of Mexico (Gulf). Components of genomic variation were significantly associated with environmental variables describing individual estuaries, and environment explained a larger component of variation than spatial proximity. In sum, results suggest that there is genetic spatial autocorrelation caused by shared larval sources for proximal nurseries (migration/drift), but that it is modified by environmentally driven differentiation (selection).