UC Santa Cruz

Understanding the genomic architecture of speciation remains a challenge in evolutionary biology. Among broadcast-spawning marine invertebrates, reproductive isolation is thought to be established and maintained by the divergence of gamete recognition proteins located on the surfaces of sperm and egg cells. However, it remains unclear whether gametic isolation has been an effective barrier to gene flow during and/or following speciation. In this dissertation, I characterized the history of introgression among the North Pacific sea urchin species of the family Strongylocentrotidae to deepen our understanding of their diversification and evaluate the importance of gametic isolation in speciation. Using whole-genome sequencing data from each strongylocentrotid species and cutting-edge phylogenomic approaches, I documented widespread introgression in both extant taxa and ancestral lineages, demonstrating that gametic isolation did not effectively limit introgression. I implemented a phylogenetic hidden Markov model to locate the specific regions of the genome affected by introgression, finding evidence of strong selection against introgression across much of the genome. Although introgressed variation has predominantly persisted in slowly evolving, low-divergence genomic regions, numerous protein-coding genes showed both introgression and historical positive selection, suggesting an adaptive role for introgression. Finally, I showed that the two gamete recognition proteins responsible for species-selectivity in sea urchin fertilization, sperm protein bindin and its egg receptor, EBR1, have experienced historical adaptive introgression, a pattern inconsistent with expectations for barrier loci. My findings contribute to the body of literature evaluating the biological consequences of introgression and question the importance of gamete recognition proteins in the evolution of reproductive isolation among incipient strongylocentrotid sea urchin species.