Adaptation and evolutionary potential in light of anthropogenic stressors in the ocean
Creators: name: Hoey, Jennifer A.
Publisher: name: No Publisher Supplied
Year: 2020

description: Human-induced evolutionary pressures are prevalent, from the increased harvest of natural populations to climate change, and such forces threaten biodiversity and alter the rate and outcome of evolution. Adapting to novel conditions depends partly on standing genetic variation, and how dispersal, selection, and genetic drift interact to structure spatial and temporal genetic diversity. My dissertation focuses on how microevolutionary forces shape patterns of genetic diversity across space and through time, and how the processes inferred from past and current genomic patterns might influence evolutionary potential in the future. I use an important fishery species, summer flounder (Paralichthys dentatus), as a model for understanding adaptation in the context of fishing and climate change, and I do so by taking advantage of archived biological collections, high-throughput sequencing and rich fisheries datasets.In Chapter 1, I studied the scale at which dispersal and natural selection structure spatial patterns of genetic diversity in the sea. I used population assignment tests, Approximate Bayesian Computation (ABC), and genome scans with SNP genotypes to evaluate population structure and locus–environment associations in adult summer flounder along the U.S. East coast. Based on 1,137 SNPs across 232 individuals spanning nearly 1,900 km, I found no indication of population structure across the putative biogeographic barrier of Cape Hatteras, North Carolina (FST = 0.0014) or of isolation by distance along the coast using individual relatedness. ABC estimated the probability of dispersal across Cape Hatteras to be high (95% credible interval: 7–50% migration). However, I found 15 loci whose allele frequencies were associated with at least one of four environmental variables. Of those, 11 were correlated with bottom temperature. My findings suggest that spatial balancing selection can manifest in adaptive divergence on regional scales in marine fish despite high dispersal.In Chapter 2, I used SNP genotypes and otolith microchemistry from fish ‘ear stones’ to reconstruct larval dispersal patterns along the U.S. East coast through time. Using archived collections of larval summer flounder (n = 411) captured between 1989-2012 at five ingress locations, I found that neither genotypes nor otolith microchemistry alone were sufficient to identify the source of larval fish because allele frequencies were weakly differentiated among source locations and elemental signatures of putative sources could not be validated. However, microchemistry identified clusters of larvae (n = 3-33 larvae/cluster) that originated in the same location, and assignment of larval clusters could be made with substantially more confidence. I found that most larvae likely originated near Cape Hatteras and that larvae were transported in both directions across Cape Hatteras. This novel approach demonstrates that summer flounder dispersal is widespread throughout their range, both on intra- and inter-generational timescales, and may be an important process for synchronizing population dynamics and maintaining genetic diversity during an era of rapid environmental change. In Chapter 3, I took advantage of summer flounder’s well know population history to test if SNP data were useful for detecting changes in demography. I genotyped archived collections of larval summer flounder (n = 285) from three cohorts to examine how contemporary effective population size and genetic diversity responded to changes in fishing intensity in a natural population. Despite little to no detectable change in genetic diversity, coalescent-based demographic modeling from site frequency spectra revealed that summer flounder population size declined dramatically. The timing and direction of change corresponded to the observed decline in spawning stock biomass from independent surveys of fish abundance. Despite subsequent increase in census abundance, I could not determine whether effective population size also increased over time. These results demonstrate that genetic sampling can be useful for detecting population trends, even in species with large effective sizes.My dissertation research broadly demonstrates how an understanding of genetic variation across space and time, and used in combination with other data types, can be useful for understanding the past, present, and future of marine organisms in a changing world.