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.
Highlights
Genetic variation within and among contemporaneous populations is the result of the interplay among historical events and evolution‐ ary‐genetic forces such as genetic drift, selection, and gene flow that change or maintain gene frequencies and act at the genomic, individual, and population levels (Garant, Forde, & Hendry, 2007)
A key tenet of population genetics is that differences in se‐ lectively “neutral” loci arise from the balance between genetic drift and gene flow and can be used to study demographic and historical processes; alternatively, loci under the influence of selection often exhibit “outlier” patterns of variation that can be used to infer the role of selection operating in local and/or regional environments (Luikart, England, Tallmon, Jordan, & Taberlet, 2003)
Geneti‐ cally distinct populations in these three regions are documented for 13 species of coastal or nearshore fishes (Supporting information Table S9), with separation occurring around the Florida Peninsula and the northeastern Gulf
Summary
Genetic variation within and among contemporaneous populations is the result of the interplay among historical events and evolution‐ ary‐genetic forces such as genetic drift, selection, and gene flow (migration) that change or maintain gene frequencies and act at the genomic, individual, and population levels (Garant, Forde, & Hendry, 2007). A key tenet of population genetics is that differences in se‐ lectively “neutral” loci arise from the balance between genetic drift and gene flow and can be used to study demographic and historical processes; alternatively, loci under the influence of selection often exhibit “outlier” patterns of variation that can be used to infer the role of selection operating in local and/or regional environments (Luikart, England, Tallmon, Jordan, & Taberlet, 2003). We used a linkage map developed for red drum (Hollenbeck et al, 2017) to identify chromosomal locations of outlier loci to assess chromosomal architecture of putatively adaptive variation
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