Coral micro-fragmentation assays for optimizing active reef restoration efforts.

The global decline of coral reefs has driven considerable interest in active coral restoration. Despite their importance and dominance on mature reefs, relatively few coral restoration projects use slower growth forms like massive and encrusting coral species. Micro-fragmentation can increase coral cover by orders of magnitude faster than natural growth, which now allows cultivation of slow growing massive forms and shows promise and flexibility for active reef restoration. However, the major causes of variation in growth and survival of outplanted colonies remain poorly understood. Here, we report simple outplanting assays to aid in active reef restoration of slower growing species and increase the likelihood of restoration success. We used two different micro-fragmentation assays. Pyramid assays were used to examine variation associated with fragment size (ranging from ≈1-9 cm2), nursery residence time (for both in-situ and ex-situ nurseries), and 2D vs. 3D measurements of growth. Block assays were used to examine spatial variation among individual performance at outplanting sites in the field. We found 2D and 3D measurements correlated well, so measured survivorship and growth using top-down planar images for two of the main Hawaiian reef building corals, the plating Montipora capitata and the massive Porites compressa. Pyramid assays housed and outplanted from the in-situ nursery showed no effect of residence time or size on overall survivorship or growth for either species. Results from the ex-situ nursery, however, varied by species, with P. compressa again showing no effect of nursery residence time or size on survivorship or growth. In contrast, nursery culture resulted in improved survivorship of small M. capitata fragments, but net growth showed a weak positive effect of nursery time for medium fragments. Small fragments still suffered higher mortality than either medium or large fragments. Due to their lower mortality, medium fragments (≈3 cm2) appear to be the best compromise between growth and survivorship for outplanting. Likewise, given weak positive gains relative to the investment, our results suggest that it could be more cost-effective to simply outplant medium fragments as soon as possible, without intermediate culture in a nursery. Furthermore, the block assay revealed significant differences in survivorship and growth among sites for individuals of both species, emphasizing the importance of considering spatial variation in coral survival and growth following outplanting. These results highlight the value of using short-term micro-fragmentation assays prior to outplanting to assess size, and location specific performance, optimizing the efficiency of active reef restoration activities and maximizing the probability of success for active coral restoration projects.

Evolutionary genomics of endangered Hawaiian tree snails (Achatinellidae: Achatinellinae) for conservation of adaptive capacity.

Phylogenomic studies can provide insights into speciation, adaptation, and extinction, while providing a roadmap for conservation. Hawaiian tree snails are a model system for an adaptive radiation facing an extinction crisis. In the last 5 years, nearly all populations of Hawaiian tree snails across the 30 remaining species in the subfamily Achatinellinae (Achatinellidae) have declined from hundreds or thousands in the wild down to undetectable levels. Nearly 100 species historically occurred across dramatic environmental gradients on five of the Hawaiian Islands, but habitat loss, overcollection, and predation by invasive species have decimated populations. As such, this system offers the opportunity to integrate efforts to conserve evolutionary potential into conservation planning for a rapidly declining subfamily. Here, we used genome-wide, restriction-site associated DNA sequencing (RADseq), along with mitochondrial genome reconstruction, to resolve evolutionary relationships to inform conservation efforts. Phylogenetic analysis of nearly 400k genome-wide SNPs from 59 populations and 25 species across six genera in the family Achatinellidae, was generally concordant with taxonomy, geography, and mtDNA with several notable exceptions; mtDNA was unable to resolve some deeper nodes (e.g., the monophyly of Achatinella), while SNP data did not resolve as many shallow nodes. Both phylogenetic and coalescent analysis revealed deep divergences between populations within Achatinella mustelina that were consistent with species-level differences. Given cryptic species-level divergence within populations that are geographically proximate, they are at higher risk of extirpation from invasive predators and climate change than previously assumed. This study clarifies evolutionary relationships within this model system for adaptive radiation, forming the basis for conservation strategies such as translocation, captive rearing, and hybridization trials to prevent the loss of capacity to adapt to rapidly changing environmental conditions.

Atlantia, a new genus of Dendrophylliidae (Cnidaria, Anthozoa, Scleractinia) from the eastern Atlantic.

Atlantia is described as a new genus pertaining to the family Dendrophylliidae (Anthozoa, Scleractinia) based on specimens from Cape Verde, eastern Atlantic. This taxon was first recognized as Enallopsammia micranthus and later described as a new species, Tubastraea caboverdiana, which then changed the status of the genus Tubastraea as native to the Atlantic Ocean. Here, based on morphological and molecular analyses, we compare fresh material of T. caboverdiana to other dendrophylliid genera and describe it as a new genus named Atlantia in order to better accommodate this species. Evolutionary reconstruction based on two mitochondrial and one nuclear marker for 67 dendrophylliids and one poritid species recovered A. caboverdiana as an isolated clade not related to Tubastraea and more closely related to Dendrophyllia cornigera and Leptopsammia pruvoti. Atlantia differs from Tubastraea by having a phaceloid to dendroid growth form with new corallites budding at an acute angle from the theca of a parent corallite. The genus also has normally arranged septa (not Portualès Plan), poorly developed columella, and a shallow-water distribution all supporting the classification as a new genus. Our results corroborate the monophyly of the genus Tubastraea and reiterate the Atlantic non-indigenous status for the genus. In the light of the results presented herein, we recommend an extensive review of shallow-water dendrophylliids from the Eastern Atlantic.

Unexpectedly high genetic diversity in a rare and endangered seabird in the Hawaiian Archipelago.

Seabirds in the order of Procellariiformes have one of the highest proportions of threatened species of any avian order. Species undergoing recovery may be predicted to have a genetic signature of a bottleneck, low genetic diversity, or higher rates of inbreeding. The Hawaiian Band-rumped Storm Petrel ('Ake'ake; Hydrobates castro), a long-lived philopatric seabird, suffered massive population declines resulting in its listing under the Endangered Species Act in 2016 as federally Endangered. We used high-throughput sequencing to assess patterns of genetic diversity and potential for inbreeding in remaining populations in the Hawaiian Islands. We compared a total of 24 individuals, including both historical and modern samples, collected from breeding colonies or downed individuals found on the islands of Kaua'i, O'ahu, Maui, and the Big Island of Hawai'i. Genetic analyses revealed little differentiation between breeding colonies on Kaua'i and the Big Island colonies. Although small sample sizes limit inferences regarding other island colonies, downed individuals from O'ahu and Maui did not assign to known breeding colonies, suggesting the existence of an additional distinct breeding population. The maintenance of genetic diversity in future generations is an important consideration for conservation management. This study provides a baseline of population structure for the remaining nesting colonies that could inform potential translocations of the Endangered H. castro.

RADseq population genomics confirms divergence across closely related species in blue coral (Heliopora coerulea).

BACKGROUND: Heliopora coerulea, the blue coral, is the octocoral characterized by its blue skeleton. Recently, two Heliopora species were delimited by DNA markers: HC-A and HC-B. To clarify the genomic divergence of these Heliopora species (HC-A and HC-B) from sympatric and allopatric populations in Okinawa, Japan, we used a high throughput reduced representation genomic DNA sequencing approach (ezRAD). RESULTS: We found 6742 biallelic SNPs shared among all target populations, which successfully distinguished the HC-A and HC-B species in both the sympatric and allopatric populations, with no evidence of hybridization between the two. In addition, we detected 410 fixed SNPs linking functional gene differences, including heat resilience and reproductive timing, between HC-A and HC-B. CONCLUSIONS: We confirmed clear genomic divergence between Heliopora species and found possible genes related to stress-responses and reproduction, which may shed light on the speciation process and ecological divergence of coral species.

Rare coral under the genomic microscope: timing and relationships among Hawaiian Montipora.

BACKGROUND: Evolutionary patterns of scleractinian (stony) corals are difficult to infer given the existence of few diagnostic characters and pervasive phenotypic plasticity. A previous study of Hawaiian Montipora (Scleractinia: Acroporidae) based on five partial mitochondrial and two nuclear genes revealed the existence of a species complex, grouping one of the rarest known species (M. dilatata, which is listed as Endangered by the International Union for Conservation of Nature - IUCN) with widespread corals of very different colony growth forms (M. flabellata and M. cf. turgescens). These previous results could result from a lack of resolution due to a limited number of markers, compositional heterogeneity or reflect biological processes such as incomplete lineage sorting (ILS) or introgression. RESULTS: All 13 mitochondrial protein-coding genes from 55 scleractinians (14 lineages from this study) were used to evaluate if a recent origin of the M. dilatata species complex or rate heterogeneity could be compromising phylogenetic inference. Rate heterogeneity detected in the mitochondrial data set seems to have no significant impacts on the phylogenies but clearly affects age estimates. Dating analyses show different estimations for the speciation of M. dilatata species complex depending on whether taking compositional heterogeneity into account (0.8 [0.05-2.6] Myr) or assuming rate homogeneity (0.4 [0.14-0.75] Myr). Genomic data also provided evidence of introgression among all analysed samples of the complex. RADseq data indicated that M. capitata colour morphs may have a genetic basis. CONCLUSIONS: Despite the volume of data (over 60,000 SNPs), phylogenetic relationships within the M. dilatata species complex remain unresolved most likely due to a recent origin and ongoing introgression. Species delimitation with genomic data is not concordant with the current taxonomy, which does not reflect the true diversity of this group. Nominal species within the complex are either undergoing a speciation process or represent ecomorphs exhibiting phenotypic polymorphisms.

Complex signatures of genomic variation of two non-model marine species in a homogeneous environment.

BACKGROUND: Genomic tools are increasingly being used on non-model organisms to provide insights into population structure and variability, including signals of selection. However, most studies are carried out in regions with distinct environmental gradients or across large geographical areas, in which local adaptation is expected to occur. Therefore, the focus of this study is to characterize genomic variation and selective signals over short geographic areas within a largely homogeneous region. To assess adaptive signals between microhabitats within the rocky shore, we compared genomic variation between the Cape urchin (Parechinus angulosus), which is a low to mid-shore species, and the Granular limpet (Scutellastra granularis), a high shore specialist. RESULTS: Using pooled restriction site associated DNA (RAD) sequencing, we described patterns of genomic variation and identified outlier loci in both species. We found relatively low numbers of outlier SNPs within each species, and identified outlier genes associated with different selective pressures than those previously identified in studies conducted over larger environmental gradients. The number of population-specific outlier loci differed between species, likely owing to differential selective pressures within the intertidal environment. Interestingly, the outlier loci were highly differentiated within the two northernmost populations for both species, suggesting that unique evolutionary forces are acting on marine invertebrates within this region. CONCLUSIONS: Our study provides a background for comparative genomic studies focused on non-model species, as well as a baseline for the adaptive potential of marine invertebrates along the South African west coast. We also discuss the caveats associated with Pool-seq and potential biases of sequencing coverage on downstream genomic metrics. The findings provide evidence of species-specific selective pressures within a homogeneous environment, and suggest that selective forces acting on small scales are just as crucial to acknowledge as those acting on larger scales. As a whole, our findings imply that future population genomic studies should expand from focusing on model organisms and/or studying heterogeneous regions to better understand the evolutionary processes shaping current and future biodiversity patterns, particularly when used in a comparative phylogeographic context.

A genomic glance through the fog of plasticity and diversification in Pocillopora.

Scleractinian corals of the genus Pocillopora (Lamarck, 1816) are notoriously difficult to identify morphologically with considerable debate on the degree to which phenotypic plasticity, introgressive hybridization and incomplete lineage sorting obscure well-defined taxonomic lineages. Here, we used RAD-seq to resolve the phylogenetic relationships among seven species of Pocillopora represented by 15 coral holobiont metagenomic libraries. We found strong concordance between the coral holobiont datasets, reads that mapped to the Pocillopora damicornis (Linnaeus, 1758) transcriptome, nearly complete mitochondrial genomes, 430 unlinked high-quality SNPs shared across all Pocillopora taxa, and a conspecificity matrix of the holobiont dataset. These datasets also show strong concordance with previously published clustering of the mitochondrial clades based on the mtDNA open reading frame (ORF). We resolve seven clear monophyletic groups, with no evidence for introgressive hybridization among any but the most recently derived sister species. In contrast, ribosomal and histone datasets, which are most commonly used in coral phylogenies to date, were less informative and contradictory to these other datasets. These data indicate that extant Pocillopora species diversified from a common ancestral lineage within the last ~3 million years. Key to this evolutionary success story may be the high phenotypic plasticity exhibited by Pocillopora species.

Restriction of sponges to an atoll lagoon as a result of reduced environmental quality.

The lagoon at Palmyra Atoll in the central Pacific was subject to major military modifications during WWII and now the dominant fauna on the lagoon's hard substrate are sponges, not corals. In this study, we quantified the physical and biological factors explaining the variation in sponge distribution patterns across 11 sites to determine the potential for the sponges in the lagoon at Palmyra to invade the surrounding reef systems. Significant differences in sponge assemblages were found among all but three sites. For all the models we examined the strongest environmental relationships were found for variables related to sedimentation/turbidity and food/habitat availability. Our findings suggest that the sponges in Palmyra's lagoon are likely to be restricted to this habitat type where they are associated with conditions resulting from the earlier heavy disturbance and are unlikely to spread to the outer reef environments unless there is a dramatic decline in environmental quality.