Independent and adaptive evolution of phenotypic novelties driven by coral symbiosis in barnacle larvae

Systematics and character evolution of capitate hydrozoans

Capitate hydrozoans are a morphologically and ecologically diverse hydrozoan suborder, currently including about 200 species. Being grouped in two clades, Corynida and Zancleida, these hydrozoans still show a number of taxonomic uncertainties at the species, genus and family levels. Many Capitata species established symbiotic relationships with other benthic organisms, including bryozoans, other cnidarians, molluscs and poriferans, as well as with planktonic dinoflagellates for mixotrophic relationships and with bacteria for thiotrophic ectosymbioses. Our study aimed at providing an updated and comprehensive phylogeny reconstruction of the suborder, at modelling the evolution of selected morphological and ecological characters, and at testing evolutionary relationships between the symbiotic lifestyle and the other characters, by integrating taxonomic, ecological and evolutionary data. The phylogenetic hypotheses here presented shed light on the evolutionary relationships within Capitata, with most families and genera being recovered as monophyletic. The genus Zanclea and family Zancleidae, however, were divided into four divergent clades, requiring the establishment of the new genus Apatizanclea and the new combinations for species in Zanclea and Halocoryne genera. The ancestral state reconstructions revealed that symbiosis arose multiple times in the evolutionary history of the Capitata, and that homoplasy is a common phenomenon in the group. Correlations were found between the evolution of symbiosis and morphological characters, such as the perisarc. Overall, our results highlighted that the use of genetic data and a complete knowledge of the life cycles are strongly needed to disentangle taxonomic and systematic issues in capitate hydrozoans. Finally, the colonization of tropical habitat appears to have influenced the evolution of a symbiotic lifestyle, playing important roles in the evolution of the group.

Gene co-option, duplication and divergence of cement proteins underpin the evolution of bioadhesives across barnacle life histories

Acquisition of new genes often results in the emergence of novel functions and is a key step in lineage-specific adaptation. As a group of sessile crustaceans, barnacles establish permanent attachment through initial cement secretion at the larval phase followed by continuous cement secretion in juveniles and adults. However, the origins and evolution of barnacle larval and adult cement proteins remain poorly understood. By performing microdissection of larval cement glands, transcriptome and shotgun proteomics and immunohistochemistry validation, we identified 30 larval and 27 adult cement proteins of the epibiotic turtle barnacle Chelonibia testudinaria, of which the majority are stage- and barnacle-specific. While only two proteins, SIPC and CP100K, were expressed in both larvae and adults, detection of protease inhibitors and the cross-linking enzyme lysyl oxidase paralogs in larvae and adult cement. Other barnacle-specific cement proteins such as CP100k and CP52k likely share a common origin dating back at least to the divergence of Rhizocephala and Thoracica. Different CP52k paralogues could be detected in larval and adult cement, suggesting stage-specific cement proteins may arise from duplication followed by changes in expression timing of the duplicates. Interestingly, the biochemical properties of larval- and adult-specific CP52k paralogues exhibited remarkable differences. We conclude that barnacle larval and adult cement systems evolved independently, and both emerged from co-option of existing genes and de novo formation, duplication and functional divergence of lineage-specific cement protein genes. Our findings provide important insights into the evolutionary mechanisms of bioadhesives in sessile marine invertebrates.

Host specificity and adaptive evolution in settlement behaviour of coral-associated barnacle larvae (Cirripedia: Pyrgomatidae)

Coral-associated organisms often exhibit a continuum of host specificities. We do not know whether the variation in host specificity is related to the settlement organs or preferential settlement behaviours of the larvae. We examined the morphology of attachment discs, the settlement and metamorphosis of coral barnacles-Pyrgoma cancellatum (lives in a single coral species), Nobia grandis (two families of corals), and Armatobalanus allium (six families of corals). Our results revealed that the attachment organ of all three species are spear-shaped with sparse villi, indicating that the morphology of the attachment organs does not vary among species with different host specificities. Larvae of P. cancellatum and N. grandis only settle on their specific hosts, suggesting that chemical cues are involved in the settlement. Cyprids of N. grandis display close searching behaviour before settlement. Cyprids of P. cancellatum settle immediately on their specific host corals, without any exploratory behaviour. The host specificity and exploratory behaviours of coral barnacle cyprids are results of adaptive evolution. We argue that there is a trade-off between exploration and energy conservation for metamorphosis processes. Coral barnacle metamorphosis is longer when compared to free-living species, likely because it involves the development of a tube-shaped base on the coral surface.

Single-specimen systematics resolves the phylogeny and diversity conundrum of enigmatic crustacean y-larvae

Resolving the evolutionary history of organisms is a major goal in biology. Yet for some taxa the diversity, phylogeny, and even adult stages remain unknown. The enigmatic crustacean "y-larvae" (Facetotecta) is one particularly striking example. Here we use extensive video-imaging and single-specimen molecular sequencing of >200 y-larval specimens to comprehensively explore for the first time their evolutionary history and diversity. This integrative approach revealed five major clades of Facetotecta, four of which encompass a considerable larval diversity. Whereas morphological analyses recognized 35 y-naupliar "morphospecies", molecular species delimitation analyses suggested the existence of between 88 and 127 species. The phenotypic and genetic diversity between the morphospecies suggests that a more elaborate classification than the current one-genus approach is needed. Morphology and molecular data were highly congruent at shallower phylogenetic levels, but no morphological synapomorphies could be unambiguously identified for major clades, which mostly comprise both planktotrophic and lecithotrophic y-nauplii. We argue that lecithotrophy arose several times independently whereas planktotrophic y-nauplii, which are structurally more similar across clades, most likely display the ancestral feeding mode of Facetotecta. We document a remarkably complex and highly diverse phylogenetic backbone for a taxon of marine crustaceans, the full life cycle of which remains a mystery.

Living on fire: Deactivating fire coral polyps for larval settlement and symbiosis in the fire coral-associated barnacle Wanella milleporae (Thoracicalcarea: Wanellinae)

Symbiosis is increasingly recognized as being an important component in marine systems, and many such relationships are initiated when free-swimming larvae of one partner settle and become sedentary on a host partner. Therefore, several crucial questions emerge such as the larva's mechanism of locating a host, selection of substratum and finally settlement on the surface of its future partner. Here, we investigated these mechanisms by studying how larvae of the fire coral-associated barnacle Wanella milleporae move, settle and establish symbiosis with their host, Millepora tenera. Cyprids of W. milleporae possess a pair of specialized antennules with bell-shaped attachment discs that enable them to explore and settle superficially on the hostile surface of the fire coral. Intriguingly, the stinging polyps of the fire coral remain in their respective pores when the cyprids explore the fire coral surface. Even when cyprids come into contact with the nematocysts on the extended stinging polyps during the exploratory phase, no immobilization effects against the cyprids were observed. The exploratory phase of Wanella cyprids can be divided into a sequence of wide searching (large step length and high walking speed), close searching (small step length and low speed) and inspection behavior, eventually resulting in permanent settlement and metamorphosis. After settlement, xenogeneic interactions occur between the fire coral and the newly metamorphosed juvenile barnacle. This involved tissue necrosis and regeneration in the fire coral host, leading to a callus ring structure around the juvenile barnacle, enhancing survival rate after settlement. The complex exploratory and settlement patterns and interactions documented here represent a breakthrough in coral reef symbiosis studies to show how invertebrates start symbiosis with fire corals.

Black Mantle Tissue of Endolithic Mussels (Leiosolenus spp.) Is Cloaking Borehole Orifices in Caribbean Reef Corals

Bioerosion caused by boring mussels (Mytilidae: Lithophaginae) can negatively impact coral reef health. During biodiversity surveys of coral-associated fauna in Curaçao (southern Caribbean), morphological variation in mussel boreholes was studied. Borings were found in 22 coral species, 12 of which represented new host records. Dead corals usually showed twin siphon openings, for each mussel shaped like a figure of eight, which were lined with a calcareous sheath and protruded as tubes from the substrate surface. Most openings surrounded by live coral tissue were deeper and funnel-shaped, with outlines resembling dumbbells, keyholes, ovals or irregular ink blotches. The boreholes appeared to contain black siphon and mantle tissue of the mussel. Because of the black color and the hidden borehole opening in live host corals, the mantle tissue appeared to mimic dark, empty holes, while they were actually cloaking live coral tissue around the hole, which is a new discovery. By illustrating the morphological range of borehole orifices, we aim to facilitate the easy detection of boring mussels for future research.

Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes

BACKGROUND

The barnacles are a group of >2,000 species that have fascinated biologists, including Darwin, for centuries. Their lifestyles are extremely diverse, from free-swimming larvae to sessile adults, and even root-like endoparasites. Barnacles also cause hundreds of millions of dollars of losses annually due to biofouling. However, genomic resources for crustaceans, and barnacles in particular, are lacking.

RESULTS

Using 62× Pacific Biosciences coverage, 189× Illumina whole-genome sequencing coverage, 203× HiC coverage, and 69× CHi-C coverage, we produced a chromosome-level genome assembly of the gooseneck barnacle Pollicipes pollicipes. The P. pollicipes genome is 770 Mb long and its assembly is one of the most contiguous and complete crustacean genomes available, with a scaffold N50 of 47 Mb and 90.5% of the BUSCO Arthropoda gene set. Using the genome annotation produced here along with transcriptomes of 13 other barnacle species, we completed phylogenomic analyses on a nearly 2 million amino acid alignment. Contrary to previous studies, our phylogenies suggest that the Pollicipedomorpha is monophyletic and sister to the Balanomorpha, which alters our understanding of barnacle larval evolution and suggests homoplasy in a number of naupliar characters. We also compared transcriptomes of P. pollicipes nauplius larvae and adults and found that nearly one-half of the genes in the genome are differentially expressed, highlighting the vastly different transcriptomes of larvae and adult gooseneck barnacles. Annotation of the genes with KEGG and GO terms reveals that these stages exhibit many differences including cuticle binding, chitin binding, microtubule motor activity, and membrane adhesion.

CONCLUSION

This study provides high-quality genomic resources for a key group of crustaceans. This is especially valuable given the roles P. pollicipes plays in European fisheries, as a sentinel species for coastal ecosystems, and as a model for studying barnacle adhesion as well as its key position in the barnacle tree of life. A combination of genomic, phylogenetic, and transcriptomic analyses here provides valuable insights into the evolution and development of barnacles.

Phylogeny and shell form evolution of the hydrothermal vent asymmetrical barnacles (Cirripedia, Thoracicalcarea, Neoverrucidae)

Imbricaverruca and Neoverruca are two genera of hydrothermal vent asymmetrical barnacles in Neoverrucidae, but found in vents of the Southwest Pacific and Northwest Pacific Oceans, respectively. Imbricaverruca has a flattened operculum and the shell base with multiple whorls of imbricating plates, while Neoverruca has an inclined operculum and the shell base with fewer developed imbricating plates. It has been hypothesized that Imbricaverruca has apomorphic shell characters in Neoverrucidae. Although the monophyletic relationship of the vent barnacle members in the superfamily Neolepadoidea were confirmed based on molecular phylogeny, the relationships between Neobrachylepadidae and Neoverrucidae, and between Neoverruca and Imbricaverruca have not been determined because there are no molecular data on Imbricaverruca. In this study, we sequenced three nuclear (18S rDNA, 28S rDNA, histone 3) and one mitochondrial (CO1) genes of I. yamaguchii from the Southwest Pacific. Our phylogenetic results showed that Neobrahchylepadidae is the sister taxon to Neoverrucidae (Imbricaverruca + Neoverruca), and Imbricaverruca and Neoverruca are monophyletic sister taxa each other, which not supporting the previous hypothesis that Neoverruca is sister to the clade containing Neobrahchylepadidae and Neolepadidae. These were implied that the differences in shell forms between Neoverruca and Imbricaverruca are a result of independent divergent evolution in different deep-sea basins.