UC Santa Cruz

Marine populations were long expected to exhibit weak genetic structure because many species possess pelagic larvae, large population sizes, and few barriers to dispersal. However, strong population structure is shown to be widespread across marine taxa even among species with high dispersal potential. Understanding how population divergence arises and persists in such dynamic systems remains a central challenge in evolutionary biology. This dissertation examines how historical isolation, environmental gradients, and selection shape population structure in marine fishes using physiological and genomic approaches. In Chapter 1, I examine population-level variation in thermal physiology between Pacific and Sea of Cortez populations of the longjaw mudsucker (Gillichthys mirabilis). Although broad thermal performance curves were largely similar, Sea of Cortez individuals showed lower thermal sensitivity and higher acute thermal tolerance after warm pre-conditioning, patterns that mirror a more thermally variable environment, though adaptation cannot be confirmed from this comparison alone. In Chapter 2, I use low-coverage whole-genome resequencing to assess genomic divergence between Pacific and Sea of Cortez populations of G. mirabilis. I find exceptionally high genomic differentiation, extensive fixed differences, and reciprocal phylogenetic monophyly between lineages, consistent with long-term allopatric isolation. Genome scans identify outlier loci enriched for nonsynonymous substitutions, suggesting selection acted alongside drift to shape divergence between these lineages. In Chapter 3, I investigate population genomic patterns in the barred surfperch (Amphistichus argenteus), a nearshore species lacking a pelagic larval stage. Genomic data reveal three distinct coastal clades and a highly divergent Santa Rosa Island lineage, shaped by isolation by distance and geographic breaks near major habitat discontinuities. The largest coastal break is across the Palos Verdes Peninsula, where candidate genes under selection are enriched for functions related to spermatogenesis and sperm motility, suggesting this break is maintained by selection on reproductive compatibility. Together, these results show contemporary population structure reflects the cumulative effects of historical isolation, ecological context, and selection across spatial and temporal scales. This work provides a comparative framework for understanding how population divergence arises and persists in marine environments and informs predictions of responses to environmental change.