UBC Theses and Dissertations
Population structure of yelloweye rockfish (Sebastes ruberrimus) driven by limited dispersal and selection Siegle, Matthew Ray
Natural selection and local adaptation influence fish abundances and distributions on both short and long-term time scales: first, by influencing recruitment dynamics and second, by affecting long-term population persistence in fluctuating environmental conditions. Little is known, however, about the significance of adaptive population divergence in the marine environment. In this study, I utilized an FST outlier approach to detect putatively selected loci from an Amplified Fragment Length Polymorphism (AFLP) marker dataset of yelloweye rockfish (Sebastes ruberrimus) collected from southeast Alaska south to Oregon. During the data analysis phase, a plate bias was detected and efforts to eliminate this effect were unsuccessful. Therefore, each PCR plate was analyzed separately, resulting in seven independent analyses. A total of 966-1580 AFLP loci were identified for the seven plates, and 0-10 loci (0-0.79%) per plate were identified as FST outliers by program, BAYESCAN. Based on results from the outlier analyses, datasets composed of neutral loci (those with no support for being under selection) and outlier loci (those exceeding a minimum posterior threshold of 0.7, corresponding to a moderate amount of support for being under selection) were established for each plate. Global FST values are approximately five times greater for the outlier datasets (mean FST=0.56) than for putatively neutral loci (mean FST=0.10). The genetic clustering program, STRUCTURE, identified similar patterns of population structure both for the neutral and outlier datasets. The outlier datasets, however, lead to overall higher assignment probabilities of individual fish to genetic groups than observed with the neutral datasets. In addition, several similar clustering patterns (e.g. southern vs. northern genetic clusters, presence of isolated clusters) were observed across several plates, providing independent evidence for regionally restricted gene flow. Overall, my results suggest that population structure driven by neutral processes may be reinforced by natural selection, which has implications for the management of yelloweye rockfish fishery stocks and the scale of connectivity within the Rockfish Conservation Area marine reserve network.
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