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Abstract The establishment of reproductive isolation between species via gametic incompatibility initially requires within-species variation in reproductive compatibility. We investigate how within-species variation in sperm and egg recognition proteins, potentially generated via sexual conflict, influences reproductive isolation between two partially sympatric sea urchin species; the North American west coast Mesocentrotus franciscanus and the circumpolar Strongylocentrotus droebachiensis. Barriers to hybridization are stronger when eggs are given a choice of conspecific versus heterospecific sperm and the variation in hybridization among crosses can be explained by whether the sperm or egg protein variant is ancestral or derived. Derived proteins can be recognized as different and prevent hybridization. Examination of the allele frequencies of these proteins in M. franciscanus in and out of sympatry with S. droebachiensis along the west coast of North America reveals evidence of reinforcement selection and reproductive character displacement in eggs but not sperm, which likely reflects the differential cost of hybridization for males and females. 

Abstract The abundance of many Caribbean corals has declined over the past few decades, yet nowPorites astreoidesis more common on many shallow reefs than in the 1980s and shows evidence of local adaptation. We compare the small‐scale (1–8000 m) genetic structure of this brooding species and the broadcasting coralOrbicella annularison reefs (<14 m depth) in St. John, US Virgin Islands, to examine how larval dispersal and asexual propagation contribute to the retention of genotypes within reefs. Populations ofP. astreoideshave genetic structure across reefs separated by a few 100 m, increased relatedness within reefs, and parthenogenetic larval propagation confirmed by parent–offspring genotyping. Within reefs,P. astreoidescolonies <1 m apart are more related, independent of clonal reproduction, than corals at greater distances. In contrast,O. annularislacks across‐reef genetic structure, has low relatedness within and among reefs, and does not produce asexual larvae. Small‐scale genetic structure and high relatedness inP. astreoidesare evident even without considering asexual propagation, but asexual reproduction enhances these differences. Neither species shows the genetic signature of inbreeding or reduced genotypic diversity despite the high within‐site relatedness ofP. astreoides. Monitoring on these reefs from 1987 indicates thatPoriteshas increased in abundance whileOrbicellahas decreased in abundance. The success ofPoritesis due to greatly increased settlement and recruitment compared withOrbicella. Together these results indicate that high numbers of locally retained and successful genotypes might explain the relative success ofPoriteson shallow, present‐day reefs in the Caribbean.