DNA methylation is an epigenetic mark that plays an inadequately understood role in gene regulation, particularly in non-model species. Because it can be influenced by the environment, DNA methylation may contribute to the ability of organisms to acclimatize and adapt to environmental change. We evaluated the distribution of gene body methylation in reef-building corals, a group of organisms facing significant environmental threats. Gene body methylation in six species of corals was inferred from in silico transcriptome analysis of CpG O/E, an estimate of germline DNA methylation that is highly correlated with patterns of methylation enrichment. Consistent with what has been documented in most other invertebrates, all corals exhibited bimodal distributions of germline methylation suggestive of distinct fractions of genes with high and low levels of methylation. The hypermethylated fractions were enriched with genes with housekeeping functions, while genes with inducible functions were highly represented in the hypomethylated fractions. High transcript abundance was associated with intermediate levels of methylation. In three of the coral species, we found that genes differentially expressed in response to thermal stress and ocean acidification exhibited significantly lower levels of methylation. These results support a link between gene body hypomethylation and transcriptional plasticity that may point to a role of DNA methylation in the response of corals to environmental change.

Seasonal variation in the algal symbiosis and growth of Astrangia poculata, a facultatively symbiotic temperate scleractinian, was explored in Rhode Island, USA. Coral pigmentation and growth were measured simultaneously and repeatedly in both zooxanthellate (corals with symbionts) and azooxanthellate (symbiont free) colonies at 2 sites (~10 km apart) over a 15 mo period using nondestructive digital image analysis methods. A chlorophyll density proxy based on coral pigmentation was derived from multivariate analysis of color data from coral images, and polyps were enumerated to measure colony growth. Among zooxanthellate corals, predicted chlorophyll density exhibited significant seasonal fluctuations that were positively related to temperature, with maxima occurring during late summer and early autumn. Pigmentation dynamics in azooxanthellate corals were more variable, although many of these corals displayed temporal fluctuations in pigmentation. Growth also exhibited seasonal fluctuations positively related to temperature, and ceased during the coldest 3 to 4 mo of the year. Corals lost live polyps during the winter as a result of tissue thinning and dormancy, which rendered the colony unable to fend off settling organisms. Although zooxanthellate colonies were able to grow faster than azooxanthellate colonies, coral pigmentation explained only 23% of the variation in growth rate, emphasizing the importance of heterotrophy as the primary source of nutrition for A. poculata at this northern margin of its range.

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 epigeneticsspecifically, 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 samples of 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. In contrast, no clear epigenetic patterns emerged with respect to phenotypic or habitat variables. While there was a weak positive correlation between pairwise genetic and epigenetic distance, two pairs of putative clones exhibited substantial epigenetic differences, suggesting a strong environmental effect. We speculate that epigenetic patterns are a complex mosaic reflecting diverse environmental histories superimposed over a relatively small heritable component. 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 of these corals may help settle their phylogeny.

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