Red drum (Sciaenops ocellatus) is an economically important marine fish species that supports a large recreational fishery in the United States and is cultured for both restoration and commercial purposes. Characterizing patterns of genetic diversity in wild populations of red drum is essential for understanding how genetic variation in the species is partitioned across space and time and for informed decisions regarding management of the recreational fishery and culture of the species. Advances in DNA sequencing technology now have allowed cost-effective genotyping of thousands of genetic markers and strategies for mapping those markers to the genome. This has led to an unprecedented level of resolution in characterizing patterns of genetic variation in wild populations. The objectives of this research were to supplement the existing red drum linkage map with additional anonymous and gene-linked microsatellite loci, to use the framework provided by the microsatellite-based map to saturate the map with genetic markers (SNP haplotypes) derived from next-generation sequencing, and to use the saturated linkage map, combined with genotypes of wild red drum, to (i) identify potential changes in genetic effective population size over time, and (ii) conduct a population genomic assessment of red drum in U.S. waters. A dense linkage map, consisting of 2,275 genetic markers, was generated. In addition, a method was developed to utilize the linkage map, along with data from studies of linkage disequilibrium, to detect changes in effective population size over time. The method was used to show a recent, temporary decline in effective population size in a sample of red drum from Matagorda Bay, Texas. A population genomic assessment of red drum revealed three distinct populations of red drum, corresponding to regions in the western Gulf of Mexico, the eastern Gulf of Mexico, and along the southeast Atlantic coast of the U.S. Signatures of natural selection (adaptive variation) were detected among sampled populations, and a set of environmental variables correlated to allele frequencies of loci potentially under selection was identified. Using the linkage map, 15 clusters of loci potentially under the influence of selection were mapped to individual chromosomes, and a set of candidate genes were identified, using comparative genomics. The result of the project is a set of genetic tools and information that will greatly benefit future study of red drum in a variety of contexts.
