Changes in Genome-wide Methylation in Response to Ocean Acidification in the Pteropod Limacina helicina antarctica and Evolutionary Differences in DNA Methylation Across Pteropoda

Epigenetic processes such as variation in DNA methylation can contribute to phenotypic plasticity and the rapid acclimatization of species to changing environments. Determining (i) the extent to which organisms may mount epigenetic responses to current and future climate extremes and (ii) how these processes vary across biodiversity will enrich our understanding of species’ capacities to acclimatize to global change over ecological timescales. The thecosome pteropod Limacina helicina antarctica is one of the most abundant species of macrozooplankton endemic to the Southern Ocean and, like many thecosomes, is considered a sentinel of ocean acidification (OA). Here, we assessed changes in DNA methylation in L. helicina antarctica under different OA conditions. We exposed L. helicina antarctica to low, medium, and high pCO₂ levels representing present day pCO₂ norms in the coastal Southern Ocean (255 μatm), present day extremes (530 μatm), and projected extremes (918 μatm) for up to 7 days. We then measured global DNA methylation and sequenced transcriptomes in each treatment across time. L. helicina antarctica significantly reduced genomic methylation in response to future pCO₂ extremes after 1 day of exposure followed by a return to control levels over time. L. helicina antarctica exposed to future pCO₂ extremes also exhibited substantially more differential expression than under current pCO₂ extremes, mainly by downregulating transcripts enriched with signatures of gene body methylation. Thus, transcriptomic responses by L. helicina antarctica to future pCO₂ extremes were likely regulated in part by DNA methylation. By studying genomic signatures of gene body methylation across transcriptome assemblies for six pteropod species and one outgroup, we have also uncovered distinct phylogenetic differences in DNA methylation (i) between thecosome and gymnosome pteropods and (ii) within the thecosome lineage. We are exploring how this variation shapes transcriptomic responses to OA across Pteropoda.