Variable Patterns of Genomic Diversity in Young-of-the-Year Red Snapper Lutjanus campechanus in the Northern Gulf of Mexico

Red snapper (Lutjanus campechanus) has historically supported important commercial and recreational fisheries in U.S. waters, but has been overfished for at least the last 25 years.  Successful rebuilding efforts of these fisheries depend on accurate knowledge of how genetic variation is partitioned among subpopulations and among age classes.  In particular, understanding how variance in reproduction of adults and variance in recruitment success of larvae affects the genetic makeup of juvenile populations is critical for future management.  Using double-digest restriction-site associated DNA tags (ddRAD), we surveyed variation in ~4,000 single nucleotide polymorphisms (SNPs) from red snapper young-of-the-year (YOY) sampled at five geographic localities and adults from two localities in the northern Gulf of Mexico. Genetic diversity at putatively neutral SNPs showed a large variance among localities; three YOY samples were substantially less diverse than other YOY and adult samples, indicating that some YOY recruitment classes likely originate from a limited number of breeders.  While a lot of emphasis has been placed on utilizing outlier loci for delineating subpopulations or stocks in marine fisheries, our results demonstrate that putatively neutral loci contain information on demography that is critical for successful management.