Phyllidiidae (Nudibranchia, Heterobranchia, Gastropoda): an integrative taxonomic approach including chemical analyses

Members of the widely distributed and common nudibranch family Phyllidiidae are often easily spotted in the marine environment because of their conspicuous colours and obvious presence on the reef. They are interesting with regard to their defensive chemical compounds that may lead to new drug discoveries. Despite their abundance, the family is also well known for its taxonomic problems and the difficulties in species identification due to very similarly coloured species and lack of morphological characters. In this study, phyllidiid species were analysed using an integrative approach. Molecular analysis of the mitochondrial genes 16S and CO1 was utilised, running phylogenetic analyses, species delimitation tests, and haplotype network analyses. Additionally, for the first time, external morphological characters were analysed, museum material was re-analysed, and chemical profiles were applied for characterising species. The analyses are based on sequences of 598 specimens collected in Indonesia by the team, with the addition of published sequences available on GenBank. This study comprises 11 species of Phyllidia, seven species of Phyllidiopsis, and at least 14 species of Phyllidiella. Moreover, 11 species belonging to these three genera are probably new to science, Phyllidiopsis pipeki is synonymised with P. krempfi, and Phyllidiella albonigra is resurrected. Some of the external colouration previously used for species identification is shown to not be valid, but alternative characters are provided for most species. Chemical analyses led to species characterisation in a few examples, indicating that these species use particular sponge species as food; however, many species show a broad array of compounds and are therefore characterised more by their composition or profile than by distinct or unique compounds.

Transcriptomics provides a robust framework for the relationships of the major clades of cladobranch sea slugs (Mollusca, Gastropoda, Heterobranchia), but fails to resolve the position of the enigmatic genus Embletonia

Background

The soft-bodied cladobranch sea slugs represent roughly half of the biodiversity of marine nudibranch molluscs on the planet. Despite their global distribution from shallow waters to the deep sea, from tropical into polar seas, and their important role in marine ecosystems and for humans (as targets for drug discovery), the evolutionary history of cladobranch sea slugs is not yet fully understood.

Results

To enlarge the current knowledge on the phylogenetic relationships, we generated new transcriptome data for 19 species of cladobranch sea slugs and two additional outgroup taxa (Berthella plumula and Polycera quadrilineata). We complemented our taxon sampling with previously published transcriptome data, resulting in a final data set covering 56 species from all but one accepted cladobranch superfamilies. We assembled all transcriptomes using six different assemblers, selecting those assemblies that provided the largest amount of potentially phylogenetically informative sites. Quality-driven compilation of data sets resulted in four different supermatrices: two with full coverage of genes per species (446 and 335 single-copy protein-coding genes, respectively) and two with a less stringent coverage (667 genes with 98.9% partition coverage and 1767 genes with 86% partition coverage, respectively). We used these supermatrices to infer statistically robust maximum-likelihood trees. All analyses, irrespective of the data set, indicate maximal statistical support for all major splits and phylogenetic relationships at the family level. Besides the questionable position of Noumeaella rubrofasciata, rendering the Facelinidae as polyphyletic, the only notable discordance between the inferred trees is the position of Embletonia pulchra. Extensive testing using Four-cluster Likelihood Mapping, Approximately Unbiased tests, and Quartet Scores revealed that its position is not due to any informative phylogenetic signal, but caused by confounding signal.

Conclusions

Our data matrices and the inferred trees can serve as a solid foundation for future work on the taxonomy and evolutionary history of Cladobranchia. The placement of E. pulchra, however, proves challenging, even with large data sets and various optimization strategies. Moreover, quartet mapping results show that confounding signal present in the data is sufficient to explain the inferred position of E. pulchra, again leaving its phylogenetic position as an enigma.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01944-0.

A molecular phylogeny of Thuridilla Bergh, 1872 sea slugs (Gastropoda, Sacoglossa) reveals a case of flamboyant and cryptic radiation in the marine realm

The genus Thuridilla Bergh, 1872 comprises mostly tropical sap-sucking sea slugs species with flamboyantly coloured forms. However, the potential for cryptic or pseudocryptic species masked by convergent or polymorphic colour patterns has not been tested using molecular characters. In this study, we sampled 20 of the 23 recognized worldwide species and performed the most comprehensive molecular phylogenetic analysis of the genus to date using a multi-locus approach combining two mitochondrial (cytochrome c oxidase subunit I, 16S rRNA) and two nuclear (Histone H3, 28S rRNA) genes using maximum likelihood, maximum-parsimony and Bayesian criteria. Three molecular species delimitation methods (ABGD, GMYC, bPTP) and the morphology of radular teeth were additionally used to aid in species delimitation. Our analyses supported 35 species within Thuridilla, of which more than one-third (13) are part of a single radiation here named the Thuridilla gracilis (Risbec, 1928) species-complex. This complex includes T. gracilis, T. splendens (Baba, 1949), T. bayeri (Er. Marcus, 1965), and T. ratna (Er. Marcus, 1965), plus nine additional undescribed species. All 13 species are distinguishable by radular characters, external morphology and their DNA. The detection of this radiation led diversity of Thuridilla to be underestimated by about 25% and provides a new comparative system for studying the role of colour patterns in marine diversification.

An updated inventory of sea slugs from Koh Tao, Thailand, with notes on their ecology and a dramatic biodiversity increase for Thai waters

Improved access to field survey infrastructure throughout South-East Asia has allowed for a greater intensity of biodiversity surveys than ever before. The rocky bottoms and coral reef habitats across the region have been shown to support some of the highest sea slug biodiversity on the planet, with ever increasing records. During the past ten years, intensive SCUBA surveys have been carried out at Koh Tao, in the Gulf of Thailand, which have yielded remarkable findings in sea slug biology and ecology. In this work a brief history of sea slug biodiversity research from Thailand is covered and a complete inventory of sea slugs from Koh Tao, Gulf of Thailand is provided. This inventory is based on surveys from 2012 to 2020, with previously unreported findings since 2016. Habitat specificity and species-specific ecology are reported where available with a focused comparison of coral reef habitats and deeper soft-sediment habitats. The findings contribute 90 new species records for Thai waters (92 for the Gulf of Thailand) and report a remarkable consistency in the proportional diversity found to be exclusive to one habitat type or another. Additionally, taxonomic remarks are provided for species documented from Koh Tao that have not been discussed in past literature from Thailand, and a summary of previous records in the Indo-West Pacific is given.

Metabolome of the Phyllidiella pustulosa Species Complex (Nudibranchia, Heterobranchia, Gastropoda) Reveals Rare Dichloroimidic Sesquiterpene Derivatives from a Phylogenetically Distinct and Undescribed Clade

Phyllidiid nudibranchs are brightly colored gastropod mollusks, frequently encountered in coral reefs of the tropical Indo-Pacific. The lack of a protective shell is suggested to be compensated by toxic secondary metabolites that are sequestered from specific prey sponges. Our ongoing reconstruction of phyllidiid phylogeny using molecular data of more than 700 specimens, based on published data and newly collected specimens in various seasons and localities around North Sulawesi (Indonesia), demonstrates that Phyllidiella pustulosa is a species complex with at least seven well-supported clades. A metabolomic analysis of 52 specimens from all seven clades of P. pustulosa was performed. Secondary metabolite profiles were found to correlate with the phylogenetic study and not the prevailing food sponges as expected. GNPS molecular networking revealed a unique chemotype in clade 6. Detailed chemical analysis of a specimen from this chemically and genetically distinct P. pustulosa clade led to the identification of seven new sesquiterpenoids with a rare dichloroimidic moiety (1 and 4) and derivatives thereof (2, 3, 5-7). Our findings suggest that P. pustulosa clades should be raised to the species level.

On the Plakobranchidae (Gastropoda, Sacoglossa) from soft sediment habitats of Koh Tao, Gulf of Thailand, with descriptions of two new species

Research in recent years have provided rapid advances in biogeographic and taxonomic documentation of sea slugs around the world. However, efforts are lacking in surveying most coastlines and habitats in South-East Asia. Recent studies from the Gulf of Thailand have indicated that a wealth of unexplored sea slug diversity and ecology may be gained from an investigation of soft sediment habitats beyond the reef slopes. Additionally, the waters of Koh Tao have been found to host regionally high levels of sea slug diversity with several species awaiting taxonomic clarification. In this work the initial findings of an expanded survey effort from the waters around Koh Tao are provided, with the identity of two soft sediment-associated sacoglossan species in the family Plakobranchidae being investigated. By integrating morphological and molecular analyses, the species Plakobranchusnoctisstellatussp. nov. and Elysiaaowthaisp. nov. are described and species complexes surrounding Plakobranchusocellatus van Hasselt, 1824 and Elysiajaponica Eliot, 1913 are discussed. The topics of morphological variability and the cryptic species problem are also discussed.

From Persian Gulf to Indonesia: interrelated phylogeographic distance and chemistry within the genus Peronia (Onchidiidae, Gastropoda, Mollusca)

The knowledge of relationships between taxa is essential to understand and explain the chemical diversity of the respective groups. Here, twelve individuals of the panpulmonate slug Peronia persiae from two localities in Persian Gulf, and one animal of P. verruculata from Bangka Island, Indonesia, were analyzed in a phylogenetic and chemotaxonomic framework. Based on the ABGD test and haplotype networking using COI gene sequences of Peronia specimens, nine well-supported clades were found. Haplotype network analysis highlighted a considerable distance between the specimens of P. persiae and other clades. Metabolomic analysis of both species using tandem mass spectrometry-based GNPS molecular networking revealed a large chemical diversity within Peronia of different clades and localities. While P. persiae from different localities showed a highly similar metabolome, only few identical chemical features were found across the clades. The main common metabolites in both Peronia species were assigned as polypropionate esters of onchitriols and ilikonapyrones, and osmoprotectant amino acid-betaine compounds. On the other hand, the isoflavonoids genistein and daidzein were exclusively detected in P. persiae, while cholesterol and conjugated chenodeoxycholic acids were only found in P. verruculata. Flavonoids, bile acids, and amino acid-betaine compounds were not reported before from Onchidiidae, some are even new for panpulmonates. Our chemical analyses indicate a close chemotaxonomic relation between phylogeographically distant Peronia species.