Genetic and epigenetic insight into morphospecies in a reef coral

Incongruence between conventional and molecular systematics has left the delineation of many species unresolved. Reef-building corals are no exception, with phenotypic plasticity among the most plausible explanations for alternative morphospecies. As potential molecular signatures of phenotypic plasticity, epigenetic processes may contribute to our understanding of morphospecies. We compared genetic and epigenetic variation in Caribbean branching Porites spp., testing the hypothesis that epigenetics— specifically, differential patterns of DNA methylation—play a role in alternative morphotypes of a group whose taxonomic status has been questioned. We used reduced representation genome sequencing to analyze over 1,000 single nucleotide polymorphisms and CpG sites in 27 Porites spp. exhibiting a range of morphotypes from a variety of habitats in Belize. We found stronger evidence for genetic rather than epigenetic structuring, identifying three well-defined genetic groups. One of these groups exhibited significantly thicker branches, and branch thickness was a better predictor of genetic groups than depth, habitat, or symbiont type. Epigenetic patterns were more subtle, with no clear groups. The more thickly branched individuals in one of the genetic groups exhibited some epigenetic similarity, suggesting potential covariation of genetics and epigenetics. This covariation was further supported by a positive association between pairwise genetic and epigenetic distance. We speculate that epigenetic patterns are a complex mosaic reflecting inheritance and diverse environmental histories. Given the role of genetics in branching Porites spp. morphospecies we were able to detect with genome-wide sequencing, use of such techniques throughout the geographic range may help settle their phylogeny.