Genome-Wide Patterns of Linkage Disequilibrium in Red Drum (Sciaenops ocellatus)

Patterns of linkage disequilibrium (LD) in wild populations provide information about the role of natural selection and past demography in shaping contemporary genetic variation. As a result of the development of genotyping-by-sequencing techniques, genome-wide distributions of single-nucleotide polymorphisms (SNPs) are increasingly available for wild populations of non-model species. Using double-digest, restriction-site associated DNA (ddRAD) sequencing, we obtained genotypes at 5,945 SNP loci for wild red drum (Sciaenops ocellatus) at three localities in the northern Gulf of Mexico and three localities along the southeast U.S. Atlantic coast. Using the same approach, we obtained 1,551 polymorphic SNP loci from parents and F₁ progeny from an outbred, single-pair experimental cross. Combining estimates of recombination rates from the experimental cross and estimates of LD from wild populations, we investigated genome-wide patterns of LD on a spatial scale. Significant differences in patterns of LD among sampled localities were observed.  The implications of our findings for management of the species are considered.