Fine-scale partitioning of genomic variation among recruits in an exploited fishery: causes and consequences.

Jonathan B Puritz,John R Gold,David S Portnoy

doi:10.1038/srep36095

Abstract

Conservation and management of exploited species depends on accurate knowledge of how genetic variation is partitioned across a fishery, especially as it relates to recruitment. Using double-digest restriction-site associated DNA sequencing, we surveyed variation in 7,382 single nucleotide polymorphisms (SNPs) in red snapper (Lutjanus campechanus) young-of-the-year (YOY) sampled at six localities and in adults sampled at two localities in the northern Gulf of Mexico. Significant genetic heterogeneity was detected between the two adult samples, separated by ~600 km, and at spatial scales less than five kilometers among samples of YOY. Genetic differences between YOY samples and between YOY samples and adult samples were not associated with geographic distance, and a genome scan revealed no evidence of loci under selection. Estimates of the effective number of breeders, allelic richness, and relatedness within YOY samples were not consistent with sweepstakes recruitment. Instead, the data demonstrate, at least within one recruitment season, that multiple pulses of recruits originate from distinct groups of spawning adults, even at small spatial scales. For exploited species with this type of recruitment pattern, protection of spawning adults over wide geographic areas may be critical for ensuring productivity and stability of the fishery by maintaining larval supply and connectivity.

Highlights

Metadata for each individual is given in Supplementary Table 1. double-digest restriction-site associated DNA sequencing (ddRAD) libraries were prepared following Portnoy et al.[17]; details may be found in Supplementary Methods
Genomic analyses revealed small-scale, spatial genetic heterogeneity among YOY red snapper sampled at different localities, providing evidence of independent groups of breeding individuals
The observed significant differences between adult populations, large variances in number of breeders (Nb), and inconsistent genetic similarities between adult and YOY localities are indicative of groups of independent breeding adults whose contribution to the generation varies spatially, and likely temporally

Summary

Methods

Samples of YOY red snapper were collected during the late fall of 2012 and early spring of 2013 from six, near-shore reefs and represent a single recruiting cohort. The initial dataset consisted of 339,032 variant SNP loci across 38,122 fragments. SNPs were extensively filtered and the final dataset consisted of 7,382 SNPs in 205 individuals. The program was run with all default values, with the exception of 30 pilot runs and a thinning interval of 100; significance of outlier loci was determined using a q-value which directly corresponded to a false discovery rate of 0.05. Homogeneity of haplotype distributions was tested using single-level analysis of molecular variance (Amova), and pairwise FST values and Nei’s genetic distance[19] were calculated using GenoDive[20] using 10,000 permutations to test for significance. The effective number of breeders (Nb) was estimated for each YOY sample, using the linkage disequilibrium method[23] with a 0.05 frequency cutoff, as implemented in NeEstimator[24]. Probability estimates based on multiple comparisons were corrected using a false discovery rate (FDR) procedure[27]

Results

Discussion

Data Accessibility