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ABSTRACT Coral reefs are increasingly threatened by disease outbreaks, yet little is known about the genetic mechanisms underlying disease resistance. Since the 1970s, White Band Disease (WBD) has decimated the Caribbean staghorn coralAcropora cervicornis. However, 15% or more of individuals are highly disease‐resistant, and the genes controlling the production of Argonaut proteins, involved in microRNA (miRNA) post‐transcriptional gene silencing, are up‐regulated in WBD‐resistant corals. This suggests that miRNAs may be key regulators of coral immunity. In this study, we conducted an in situ disease transmission experiment with five healthy‐exposed control tanks and five WBD‐exposed tanks, each containing 50A. cervicornisgenotypes, sampled over 7 days and then sequenced miRNAs from 12 replicate genotypes, including 12 WBD‐exposed and 12 healthy‐exposed control fragments from two time points. We identified 67bona fidemiRNAs inA. cervicornis, 3 of which are differentially expressed in disease‐resistant corals. We performed a phylogenetic comparison of miRNAs across cnidarians and found greater conservation of miRNAs in more closely related taxa, including all three differentially expressed miRNAs being conserved in more than oneAcroporacoral. One of the three miRNAs has putative genomic targets involved in the cnidarian innate immunity. In addition, community detection coupled with over‐representation analysis of our miRNA–messenger RNA (mRNA) target network found two key uniqueA. cervicornismiRNAs regulating multiple important immune‐related pathways such as Toll‐like receptor pathway, endocytosis, and apoptosis. These findings highlight how multiple miRNAs may help the coral host maintain immune homeostasis in the presence of environmental stress including disease. 

Diseases have caused unprecedent mortality in Caribbean coral communities. White band disease (WBD) has killed up to 95% of all endangered Caribbean Acroporids since it was first observed in 1979. Despite the devastating impacts of WBD, its etiology is currently unknown although recent research identified two bacterial strains – ASVs classified as aCysteiniphilum litoraleand aVibriosp., as the most likely pathogens. To better understand the disease etiology of WBD, we pretreated corals with antibiotics to determine how prophylactic use of antibiotics impacts the transmission of WBD in a replicated tank-based experiment. We found the prophylactic use of antibiotics led to significantly reduced infection rates in disease exposed corals with a 30-percentage point decrease in the infection rate. Analyses of 16S rRNA amplicon gene sequencing data in the disease exposed corals demonstrated that antibiotic pretreatment resulted in coral microbiomes which were less speciose and contained relatively fewerVibriospp. than untreated corals, indicating that the benefit of the antibiotic pretreatment was its ability to reduce the relative abundance of intrinsic secondary opportunists and/or opportunistic pathogens suggesting their likely importance to the etiology of WBD. We propose two distinct etiologies involving either an extrinsic keystone pathogen (Cysteiniphilum litorale) or overgrowth of intrinsic opportunistic pathogens (Vibriospp.). Future research should isolate these strains to confirm the etiology of white band disease. 

Abstract Coral species in the genus Acropora are key ecological components of coral reefs worldwide and represent the most diverse genus of scleractinian corals. While key species of Indo-Pacific Acropora have annotated genomes, no annotated genome has been published for either of the two species of Caribbean Acropora. Here we present the first fully annotated genome of the endangered Caribbean staghorn coral, Acropora cervicornis. We assembled and annotated this genome using high-fidelity nanopore long-read sequencing with gene annotations validated with mRNA sequencing. The assembled genome size is 318 Mb, with 28,059 validated genes. Comparative genomic analyses with other Acropora revealed unique features in A. cervicornis, including contractions in immune pathways and expansions in signaling pathways. Phylogenetic analysis confirms previous findings showing that A. cervicornis diverged from Indo-Pacific relatives around 41 million years ago, with the closure of the western Tethys Sea, prior to the primary radiation of Indo-Pacific Acropora. This new A. cervicornis genome enriches our understanding of the speciose Acropora and addresses evolutionary inquiries concerning speciation and hybridization in this diverse clade. 

White band disease (WBD) has caused unprecedented declines in the CaribbeanAcroporacorals, which are now listed as critically endangered species. Highly disease-resistantAcropora cervicornisgenotypes exist, but the genetic underpinnings of disease resistance are not understood. Using transmission experiments, a newly assembled genome, and whole-genome resequencing of 76A. cervicornisgenotypes from Florida and Panama, we identified 10 genomic regions and 73 single-nucleotide polymorphisms that are associated with disease resistance and that include functional protein-coding changes in four genes involved in coral immunity and pathogen detection. Polygenic scores calculated from 10 genomic loci indicate that genetic screens can detect disease resistance in wild and nursery stocks ofA. cervicornisacross the Caribbean. 

Abstract AimHumans are unintentionally affecting the evolution of fishery species directly through exploitation and indirectly by altering climate. We aim to test for a relationship between biogeographic patterns in the shell phenotypes of an over‐exploited shellfish and the presence of humans to identify human‐mediated adaptive trade‐offs. The implications of these trade‐offs are discussed with respect to the sustainability of the fishery. TaxonThe endemic Hawaiian intertidal limpet, ‘opihi makaiauli (Patellagastropoda, Nacellidae, Cellana exarata) MethodsWe surveyed phenotypic characters associated with temperature and predation avoidance across the entire species range and tested for differences in the relationship between these characters and latitude, on islands with and without humans. ResultsAmong all limpets surveyed, there was a bimodal distribution in shell colour (light, dark) and a parapatric pattern of shell coloration across the archipelago with lighter shells being prevalent on the uninhabited islands and darker, more camouflaged shells being prevalent on the inhabited islands. On the cooler, uninhabited islands, all morphometric characters associated with thermal avoidance (surface area, height and doming) increased with decreasing latitude. On the hotter, inhabited islands, however, shells were flatter, less variable and less adapted for avoiding thermal stress than predation. Main ConclusionsThe biogeographic patterns in shell phenotype and previous genetic studies suggest that the population is beginning to bifurcate in response to disruptive and directional selection as well as geographic isolation between the islands with and without humans. Decreased phenotypic and genetic diversity on the inhabited islands despite much larger populations of ‘opihi suggests a prominent historical bottleneck. The prevalence of maladaptive dark, flat phenotypes for thermal avoidance on the inhabited islands suggests that predation is a stronger selective force, driving adaptive trade‐offs in shape and colour. We propose that this is likely a case of fisheries‐induced evolution and a millennium of harvesting is the most likely selective pressure driving the observed biogeographic patterns in shell morphology. The flatter, darker shells will allow body temperatures to rise higher in direct sunlight, therefore we hypothesize that the thermal niche of ‘opihi is narrower on inhabited islands and will continue to narrow as Earth warms.