Effects of spawning success and rearing-environment on genome-wide variation of red drum in a large stock-enhancement program

Abstract

Stock enhancement is an increasingly popular fisheries management strategy in which high mortality of early life history stages is circumvented by rearing juveniles in controlled or semi-controlled conditions. While the success of such programs is generally measured by the number of stocked individuals or individuals recruiting to the wild populations, an important consideration is minimizing impacts to the genetic diversity of wild populations by maximizing the number of breeders contributing to stocked progeny. The contribution of individual breeders is impacted both by variance in spawning success among adults and variance in mortality among families during grow-out. To disentangle the effects that these sources of variance have on parental contribution, red drum broodfish participating in three spawning events at the TWPD Marine Development Center were genotyped at several thousand SNP-containing loci along with their progeny. Progeny were sampled at three time points; shortly after introduction to grow-out ponds (T1), approximately midway through grow-out (T2), and as fingerlings during harvesting to be stocked in bays (T3). Using composite genotypes, progeny were assigned to parents to determine the reproductive success of individual broodfish at T1, T2, and T3 and to identify changes in the effective number of breeders (Nb) during rearing in grow-out ponds. Relationships between reproductive success and broodfish-specific parameters, including age and condition when introduced to the hatchery, time spent in the hatchery, and estimated age at spawning were assessed. Finally, associations between components of genomic variation in progeny from each sampling period and environmental parameters including salinity, pH, temperature, and dissolved oxygen present in the grow-out ponds, were identified. The results indicate that initial variance in reproductive success, including the failure of some individuals to spawn successfully, has the greatest impact on Nb. Mortality during growth had a relatively small impact on Nb and, in some cases, led to increases in Nb. Further, both family and environmental conditions in the outdoor rearing ponds significantly shaped the genetic diversity of stocked yearlings. Overall, these findings indicate that outdoor rearing in a semi-controlled environment exposes progeny to a range of environmental conditions across the season, which appears to play a role in maintaining and sometimes increasing Nb.