Geographic distances and ocean currents influence Caribbean Acropora palmata population connectivity in the Lesser Antilles

Cryptic coral community composition across environmental gradients

Cryptic genetic variation is increasingly being identified in numerous coral species, with prior research indicating that different cryptic genetic lineages can exhibit varied responses to environmental changes. This suggests a potential link between cryptic coral lineages and local environmental conditions. In this study, we investigate how communities of cryptic coral lineages vary along environmental gradients. We began by identifying cryptic genetic lineages within six coral species sampled around St. Croix, USVI based on 2b-RAD sequencing data. We then analyzed associations between the distributions of cryptic lineages across the six coral species (i.e., "cryptic coral community composition") and ecoregions, or geographically distinct environmental conditions. Our findings show that depth is a more significant predictor of community composition than ecoregions and is the most influential factor among the 40 abiotic variables that characterize ecoregions. These results imply that cryptic coral communities are influenced by both depth and local environmental conditions, although the exact environmental factors driving these patterns remain unknown. Understanding community turnover across a seascape is important to consider when outplanting corals to restore a reef, as locally-adapted lineages may have differential fitness in different environmental conditions.

Fertile Hybrids Could Aid Coral Adaptation

Fertile hybrids can enhance the adaptive capacity and resilience of species under stress by increasing genetic diversity within populations, masking the effects of deleterious recessive alleles, and facilitating the introgression of beneficial genetic variants into parental species. However, many hybrids are infertile. We compared the fertility of aquarium-reared F1 hybrid and purebred corals of the species Acropora loripes and Acropora kenti and examined the viability of early life stages of second-generation (F2) hybrid and back-crossed planula larvae and recruits. The F1 hybrids spawned viable gametes and the F2 hybrid and back-crossed embryos developed into planula larvae and settled to become sessile coral recruits. The F1 hybrids had greater reproductive fitness than the F1 A. loripes purebred stock in an aquarium environment based on their probability of spawning and their fertilization success in crosses using their gametes. Interspecific coral hybrids can therefore be fertile and have high reproductive fitness, which could benefit the persistence of threatened coral reefs.

Some reef-building corals only disperse metres per generation

Understanding the dispersal potential of different species is essential for predicting recovery trajectories following local disturbances and the potential for adaptive loci to spread to populations facing extreme environmental changes. However, dispersal distances have been notoriously difficult to estimate for scleractinian corals, where sexually (as gametes or larvae) or asexually (as fragments or larvae) derived propagules disperse through vast oceans. Here, we demonstrate that generational dispersal distances for sexually produced propagules can be indirectly inferred for corals using individual-based isolation-by-distance (IbD) analyses by combining reduced-representation genomic sequencing with photogrammetric spatial mapping. Colonies from the genus Agaricia were densely sampled across plots at four locations and three depths in Curaçao. Seven cryptic taxa were found among the three nominal species (Agaricia agaricites, Agaricia humilis and Agaricia lamarcki), with four taxa showing generational dispersal distances within metres (two taxa within A. agaricites and two within A. humilis). However, no signals of IbD were found in A. lamarcki taxa and thus these taxa probably disperse relatively longer distances. The short distances estimated here imply that A. agaricites and A. humilis populations are reliant on highly localized replenishment and demonstrate the need to estimate dispersal distances quantitatively for more coral species.

Rampant asexual reproduction and limited dispersal in a mangrove population of the coral Porites divaricata

Corals are critical to marine biodiversity. Reproduction and dispersal are key to their resilience, but rarely quantified in nature. Exploiting a unique system-a fully censused, longitudinally characterized, semi-isolated population inhabiting mangroves-we used 2bRAD sequencing to demonstrate that rampant asexual reproduction most likely via parthenogenesis and limited dispersal enable the persistence of a natural population of thin-finger coral (Porites divaricata). Unlike previous studies on coral dispersal, knowledge of colony age and location enabled us to identify plausible parent-offspring relationships within multiple clonal lineages and develop tightly constrained estimates of larval dispersal; the best-fitting model indicates dispersal is largely limited to a few metres from parent colonies. Our results explain why this species is adept at colonizing mangroves but suggest limited genetic diversity in mangrove populations and limited connectivity between mangroves and nearby reefs. As P. divaricata is gonochoristic, and parthenogenesis would be restricted to females (whereas fragmentation, which is presumably common in reef and seagrass habitats, is not), mangrove populations likely exhibit skewed sex ratios. These findings suggest that coral reproductive diversity can lead to distinctly different demographic outcomes in different habitats. Thus, coral conservation will require the protection of the entire coral habitat mosaic, and not just reefs.

Cross-Hemispheric Genetic Diversity and Spatial Genetic Structure of Callinectes sapidus Reovirus 1 (CsRV1)

The movement of viruses in aquatic systems is rarely studied over large geographic scales. Oceanic currents, host migration, latitude-based variation in climate, and resulting changes in host life history are all potential drivers of virus connectivity, adaptation, and genetic structure. To expand our understanding of the genetic diversity of Callinectes sapidus reovirus 1 (CsRV1) across a broad spatial and host life history range of its blue crab host (Callinectes sapidus), we obtained 22 complete and 96 partial genomic sequences for CsRV1 strains from the US Atlantic coast, Gulf of Mexico, Caribbean Sea, and the Atlantic coast of South America. Phylogenetic analyses of CsRV1 genomes revealed that virus genotypes were divided into four major genogroups consistent with their host geographic origins. However, some CsRV1 sequences from the US mid-Atlantic shared high genetic similarity with the Gulf of Mexico genotypes, suggesting potential human-mediated movement of CsRV1 between the US mid-Atlantic and Gulf coasts. This study advances our understanding of how climate, coastal geography, host life history, and human activity drive patterns of genetic structure and diversity of viruses in marine animals and contributes to the capacity to infer broadscale host population connectivity in marine ecosystems from virus population genetic data.

Fine scale population structure of Acropora palmata and Acropora cervicornis in the Colombian Caribbean

Using a standardized SNP array, we identified two populations of Acropora cervicornis and one population of A. palmata in the Caribbean coast of Colombia. San Andrés was the most genetically differentiated location for both species. An average pairwise F_ST value of 0.131 and 0.050 between San Andrés and neighboring collection sites was estimated, for A. cervicornis and A. palmata, respectively. Based on population patterns of both acroporid species, we inferred that Magdalena River is not a barrier of genetic connectivity among Colombian populations. Genetic comparisons between the Colombian coast of Caribbean with other Caribbean locations agree with previous studies for both species, where four populations were identified in A. cervicornis and three in A. palmata. Our results support published bio-physical model predictions and highlight the Panama-Colombia gyre as a possible isolating mechanism within the western Caribbean. However, the genetic diversity in both species was about half (mean HE per site = 0.321 in A. palmata and 0.369 in A. cervicornis) than previous estimates in acroporid populations in the Caribbean. The lower genetic diversity as well their relative isolation and high levels of reef degradation may be of particular conservation concern that may require species-specific management coupled with science-based restoration efforts.

STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts

Standardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral. We developed a high-resolution hybridization-based genotype array coupled with an analysis workflow and database for the most speciose genus of coral, Acropora, and their symbionts. We designed the array to co-analyze host and symbionts based on bi-allelic single nucleotide polymorphisms (SNP) markers identified from genomic data of the two Caribbean Acropora species as well as their dominant dinoflagellate symbiont, Symbiodinium ‘fitti’. SNPs were selected to resolve multi-locus genotypes of host (called genets) and symbionts (called strains), distinguish host populations and determine ancestry of coral hybrids between Caribbean acroporids. Pacific acroporids can also be genotyped using a subset of the SNP loci and additional markers enable the detection of symbionts belonging to the genera Breviolum, Cladocopium, and Durusdinium. Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers were combined in a workflow called the Standard Tools for Acroporid Genotyping (STAG). The STAG workflow and database are contained within a customized Galaxy environment (https://coralsnp.science.psu.edu/galaxy/), which allows for consistent identification of host genet and symbiont strains and serves as a template for the development of arrays for additional coral genera. STAG data can be used to track temporal and spatial changes of sampled genets necessary for restoration planning and can be applied to downstream genomic analyses. Using STAG, we uncover bi-directional hybridization between and population structure within Caribbean acroporids and detect a cryptic Acroporid species in the Pacific.

Oceanographic features and limited dispersal shape the population genetic structure of the vase sponge Ircinia campana in the Greater Caribbean

Understanding population genetic structure can help us to infer dispersal patterns, predict population resilience and design effective management strategies. For sessile species with limited dispersal, this is especially pertinent because genetic diversity and connectivity are key aspects of their resilience to environmental stressors. Here, we describe the population structure of Ircinia campana, a common Caribbean sponge subject to mass mortalities and disease. Microsatellites were used to genotype 440 individuals from 19 sites throughout the Greater Caribbean. We found strong genetic structure across the region, and significant isolation by distance across the Lesser Antilles, highlighting the influence of limited larval dispersal. We also observed spatial genetic structure patterns congruent with oceanography. This includes evidence of connectivity between sponges in the Florida Keys and the southeast coast of the United States (>700 km away) where the oceanographic environment is dominated by the strong Florida Current. Conversely, the population in southern Belize was strongly differentiated from all other sites, consistent with the presence of dispersal-limiting oceanographic features, including the Gulf of Honduras gyre. At smaller spatial scales (<100 km), sites showed heterogeneous patterns of low-level but significant genetic differentiation (chaotic genetic patchiness), indicative of temporal variability in recruitment or local selective pressures. Genetic diversity was similar across sites, but there was evidence of a genetic bottleneck at one site in Florida where past mass mortalities have occurred. These findings underscore the relationship between regional oceanography and weak larval dispersal in explaining population genetic patterns, and could inform conservation management of the species.