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The plastic ability for a range of phenotypes to be exhibited by the same genotype allows organisms to respond to environmental variation and may modulate fitness in novel environments. Differing capacities for phenotypic plasticity within a population, apparent as genotype by environment interactions (GxE), can therefore have both ecological and evolutionary implications. Epigenetic gene regulation alters gene function in response to environmental cues without changes to the underlying genetic sequence and likely mediates phenotypic variation. DNA methylation is currently the most well described epigenetic mechanism and is related to transcriptional homeostasis in invertebrates. However, evidence quantitatively linking variation in DNA methylation with that of phenotype is lacking in some taxa, including reef‐building corals. In this study, spatial and seasonal environmental variation in Bonaire, Caribbean Netherlands was utilized to assess relationships between physiology and DNA methylation profiles within genetic clones across different genotypes ofAcropora cervicornisandA. palmatacorals. The physiology of both species was highly influenced by environmental variation compared to the effect of genotype. GxE effects on phenotype were only apparent inA. cervicornis. DNA methylation in both species differed between genotypes and seasons and epigenetic variation was significantly related to coral physiological metrics. Furthermore, plastic shifts in physiology across seasons were significantly positively correlated with shifts in DNA methylation profiles in both species. These results highlight the dynamic influence of environmental conditions and genetic constraints on the physiology of two important Caribbean coral species. Additionally, this study provides quantitative support for the role of epigenetic DNA methylation in mediating phenotypic plasticity in invertebrates.

 

Algal symbiont shuffling in favour of more thermotolerant species has been shown to enhance coral resistance to heat‐stress. Yet, the mechanistic underpinnings and long‐term implications of these changes are poorly understood. This work studied the modifications in coral DNA methylation, an epigenetic mechanism involved in coral acclimatization, in response to symbiont manipulation and subsequent heat stress exposure. Symbiont composition was manipulated in the great star coralMontastraea cavernosathrough controlled thermal bleaching and recovery, producing paired ramets of three genets dominated by either their native symbionts (genusCladocopium) or the thermotolerant species (Durusdinium trenchi). Single‐base genome‐wide analyses showed significant modifications in DNA methylation concentrated in intergenic regions, introns and transposable elements. Remarkably, DNA methylation changes in response to heat stress were dependent on the dominant symbiont, with twice as many differentially methylated regions found in heat‐stressed corals hosting different symbionts (Cladocopiumvs.D.trenchii) compared to all other comparisons. Interestingly, while differential gene body methylation was not correlated with gene expression, an enrichment in differentially methylated regions was evident in repetitive genome regions. Overall, these results suggest that changes in algal symbionts favouring heat tolerant associations are accompanied by changes in DNA methylation in the coral host. The implications of these results for coral adaptation, along with future avenues of research based on current knowledge gaps, are discussed in the present work.

 

Phenotypic plasticity is defined as a property of individual genotypes to produce different phenotypes when exposed to different environmental conditions. This ability may be expressed at behavioral, biochemical, physiological, and/or developmental levels, exerting direct influence over species' demographic performance. In reef-building corals, a group critically threatened by global change in the Anthropocene, non-genetic mechanisms (i.e., epigenetic and microbiome variation) have been shown to participate in plastic physiological responses to environmental change. Yet, the precise way in which these mechanisms interact, contribute to such responses, and their adaptive potential is still obscure. The present work aims to fill this gap by using a multi-omics approach to elucidate the contribution and interconnection of the mechanisms modulating phenotypic plasticity in staghorn coral (Acropora cervicornis) clones subject to different depth conditions. Results show changes in lipidome, epigenome and transcriptome, but not in symbiotic and microbial communities. In addition, a potential shift toward a more heterotrophic feeding behavior was evidenced in corals at the deeper site. These observations are consistent with a multi-mechanism modulation of rapid acclimation in corals, underscoring the complexity of this process and the importance of a multifactorial approach to inform potential intervention to enhance coral adaptive capacity. 

Scientists continue to study the red tide and fish-kill events happening in Florida. Machine learning applications using remote sensing data on coastal waters to monitor water quality parameters and detect harmful algal blooms are also being studied. Unmanned Surface Vehicles (USVs) and Autonomous Underwater Vehicles (AUVs) are often deployed on data collection and disaster response missions. To enhance study and mitigation efforts, robots must be able to use available data to navigate these underwater environments. In this study, we compute a satellite-derived underwater environment (SDUE) model by implementing a supervised machine learning model where remote sensing reflectance (Rrs) indices are labeled with in-situ data they correlate with. The models predict bathymetry and water quality parameters given a recent remote sensing image. In our experiment, we use Sentine1-2 (S2) images and in-situ data of the Biscayne Bay to create an SDUE that can be used as a Chlorophyll-a map. The SDUE is then used in an Extended Kalman Filter (EKF) application that solves an underwater vehicle localization and navigation problem. 

Abstract Farfantepenaeus duorarum (Burkenroad, 1939) is a commercially harvested decapod shrimp that ranges from the eastern coast of the United States, through the Gulf of Mexico, and as far south as Isla Mujeres, Mexico. We report for the first time the complete mitochondrial genome of F. duorarum. The mitochondrial genome is 15,971 base pairs in length and is comprised of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, and 22 transfer RNA genes. An intergenic space 982 bp in length located between the rrnS (12S) and trnI (Isoleucine) genes is presumed to be the D-loop. The mitochondrial gene order in F. duorarum is identical to that reported for congeners. To assess selection pressures within the mitochondrial genome, KA/KS ratios were calculated for all PCGs, and show values < 1, indicating that all genes are evolving under purifying selection. This work contributes one more mitochondrial genome to the penaeid shrimps, an economically targeted group.