Genomic Studies of Red Snapper (Lutjanus campechanus) in U.S .Waters of the Gulf of Mexico and Atlantic Ocean

Red snapper (Lutjanus campechanus) historically has supported extremely important commercial and recreational fisheries in U.S. waters, but has been overfished for at least the last 25 years.  Successful rebuilding efforts and future management of these fisheries depend on accurate knowledge of genetic structure and connectivity among subpopulations or stocks.  Failure to recognize existing genetic structure may lead to localized stock depletion, while defining patterns of connectivity is critical to understanding metapopulation dynamics and recruitment potential.  The advent of next-generation sequencing technology has transcended fishery genetics from a simple approach (survey of a handful of genetic markers) to a complex genomics approach where thousands of loci across the genome can be assayed.  Using restriction-site associated DNA tags (RAD tags), we surveyed variation in >3,000 single nucleotide polymorphisms (SNPs) from red snapper sampled at five geographic localities: three from the northern Gulf of Mexico and two from the U.S. southeast Atlantic coast.  Here, we present estimates of genetic structure, population connectivity, and effective population size, based on presumed, selectively neutral loci, and discuss the role of these traditional metrics and the role of putative loci under selection (identified by F_ST outliers) in delineating the stock structure of an exploited fishery.