Population Structure of Atlantic Croakers from the Gulf of Mexico: Evaluating a Single‐Stock Hypothesis Using a Genomic Approach

Abstract

The geographic structure of marine fish populations is an important element used in defining stock units, and genetic data have historically been used for this purpose. Here, genetic data were used to elicit population genomic patterns for Atlantic Croakers Micropogonias undulatus collected at five locations in the Gulf of Mexico (hereafter, “Gulf”) and a single location in the southern U.S. Atlantic. Mitochondrial DNA (mtDNA) haplotypes were used as a baseline for historical lineage delineation and in a comparison with a previous Atlantic Croaker study that was centered on the Atlantic coast. A genomic data set consisting of 3,682 single‐nucleotide polymorphism (SNP)‐containing loci was used to assess contemporary gene flow throughout the sampled area. Both the mtDNA and SNP data sets showed significant between‐basin estimates of genetic divergence (ɸst = 0.049 and FST = 0.002, respectively), while pairwise FST implied a low magnitude of divergence (FST ≤ 0.002) at all geographic scales. Comparison of patterns obtained from putatively “neutral” versus “outlier” SNP loci suggested contrasting genetic patterns at the extremes of the sampling distribution in the Gulf. Putatively neutral SNPs implied a single stock in the Gulf, whereas a handful of outliers suggested distinct populations in the eastern and western Gulf. The pattern observed at outlier loci could imply either the presence of natural selection impacting a small number of loci or otherwise could be explained as a remnant pattern reflective of historical geographic isolation. In either case, the weak population structure observed at a small number of SNP loci may be indicative of a more significant demographic structure; for this reason, caution is urged when treating Atlantic Croakers as a single stock in the Gulf.

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

“…; Anderson et al. ), 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.…”

“…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.…”

Species delimitation by DNA barcoding reveals undescribed diversity in Stelliferinae (Sciaenidae)

“…the Gulf of Mexico, off the Yucatan Peninsula in Mexico. The Florida Peninsula is known to have a profound influence on the circulation patterns of the local marine currents and forms a barrier between the coastal region of the North Atlantic and the Gulf of Mexico, restricting dispersal between the populations of different species found on the two sides of the peninsula, which limits gene flow and supports the differentiation of many taxa [46][47][48], including those of the sciaenids [49][50][51]. Given these considerations, the two lineages are very likely distinct species, although further research is needed for the validation of the taxa.…”