Validating a molecular clock for nudibranchs-No fossils to the rescue

Time calibrated phylogenies are typically reconstructed with fossil information but for soft-bodied marine invertebrates that lack hard parts, a fossil record is lacking. In these cases, biogeographic calibrations or the rates of divergence for related taxa are often used. Although nudibranch phylogenies have advanced with the input of molecular data, no study has derived a divergence rate for this diverse group of invertebrates. Here, we use an updated closure date for the Isthmus of Panama (2.8 Ma) to derive the first divergence rates for chromodorid nudibranchs using multigene data from a geminate pair with broad phylogeographic sampling. Examining the species Chromolaichma sedna (Marcus & Marcus, 1967), we uncover deep divergences among eastern Pacific and western Atlantic clades and we erect a new species designation for the latter (Chromolaichma hemera sp. nov.). Next, we discover extensive phylogeographic structure within C. hemera sp. nov. sensu lato, thereby refuting the hypothesis of a recent introduction. Lastly, we derive divergence rates for mitochondrial and nuclear loci that exceed known rates for other gastropods and we highlight significant rate heterogeneity both among markers and taxa. Together, these findings improve understanding of nudibranch systematics and provide rates useful to apply to divergence scenarios in this diverse group.

A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes

BACKGROUND

How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum have long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species.

RESULTS

The final assembled and filtered Berghia genome is comparable to other high-quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes) and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low.

CONCLUSIONS

Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.

A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes

How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum has long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. The final assembled and filtered Berghia genome is comparable to other high quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes), and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.

Peruvian nudibranchs (Mollusca, Gastropoda, Heterobranchia): an updated literature review-based list of species

Nudibranchs, as a group, have received limited attention in terms of scientific study along the coastline of Peru. Here, an updated and comprehensive list of nudibranch species found in the Peruvian sea is presented, compiled through an extensive review of relevant literature. This compilation encompasses a total of 31 species, classified into two suborders, 10 superfamilies, 20 families, and 28 genera. With respect to the biogeographic provinces along the Peruvian coast, 23 species inhabit the Warm Temperate Southeastern Pacific province, 18 species occur in the Tropical Eastern Pacific province, and 10 species are found in both provinces, crossing the transitional zone between them. In terms of distribution patterns, two species exhibit a cosmopolitan distribution (Glaucusatlanticus and Fionapinnata), while two species display a circumtropical distribution (Cephalopygetrematoides and Phylliroebucephala). One species exhibits a bipolar distribution in the Eastern Pacific and possesses an amphi-South American distribution (Rostangapulchra). Additionally, six species exhibit an amphi-South American distribution (Rostangapulchra, Diaululapunctuolata, Dotouva, Tyrinnaevelinae, Tyrinnadelicata, and Dorisfontainii), and two species are endemic to Peru (Corambemancorensis and Felimaresechurana). This study provides comprehensive information on biogeographical aspects, geographical distributions, and taxonomic updates within the nudibranch species documented in Peru. Furthermore, we discuss the status of species listed in previous literature that have not been confirmed by collections, referring to them as potentially occurring species.

Coping with abrasive food: diverging composition of radular teeth in two Porifera-consuming nudibranch species (Mollusca, Gastropoda)

Molluscs forage with their radula, a chitinous membrane with teeth. Adaptations to hard or abrasive ingesta were well studied in Polyplacophora and Patellogastropoda, but for other taxa there are large gaps in knowledge. Here, we investigated the nudibranch gastropods Felimare picta and Doris pseudoargus, both of which feed on Porifera. Tooth morphologies were documented by scanning electron microscopy, and mechanical properties were tested by nanoindentation. We found that these parameters are rather similar in both species, indicating that teeth are similar in their function. To study the composition, teeth were visualized using confocal laser scanning microscopy (CLSM), to determine the degree of tanning, and analysed with energy-dispersive X-ray spectroscopy, to test the elemental composition. The emitted autofluorescence signal and the inorganic content differed between the species. This was especially prominent when studying the inner and outer tooth surfaces (leading and trailing edges). In F. picta, we detected high proportions of Si, whereas teeth of D. pseudoargus contained high amounts of Ca, which influenced the autofluorescence signal in CLSM. Employing nanoindentation, we determined high Young's modulus and hardness values for the leading edges of teeth, which relate to the Si and Ca content. This highlights that teeth with a similar morphology and mechanical properties can be mechanically enhanced via different chemical pathways in Nudibranchia.

Tracing RNA viruses associated with Nudibranchia gastropods

Background

Nudibranchia is an under-studied taxonomic group of gastropods, including more than 3,000 species with colourful and extravagant body shapes and peculiar predatory and defensive strategies. Although symbiosis with bacteria has been reported, no data are available for the nudibranch microbiome nor regarding viruses possibly associated with these geographically widespread species.

Methods

Based on 47 available RNA sequencing datasets including more than two billion reads of 35 nudibranch species, a meta-transcriptome assembly was constructed. Taxonomic searches with DIAMOND, RNA-dependent-RNA-polymerase identification with palmscan and viral hallmark genes identification by VirSorter2 in combination with CheckV were applied to identify genuine viral genomes, which were then annotated using CAT.

Results

A total of 20 viral genomes were identified as bona fide viruses, among 552 putative viral contigs resembling both RNA viruses of the Negarnaviricota, Pisuviricota, Kitrinoviricota phyla and actively transcribing DNA viruses of the Cossaviricota and Nucleocytoviricota phyla. The 20 commonly identified viruses showed similarity with RNA viruses identified in other RNA-seq experiments and can be putatively associated with bacteria, plant and arthropod hosts by co-occurence analysis. The RNA samples having the highest viral abundances showed a heterogenous and mostly sample-specific distribution of the identified viruses, suggesting that nudibranchs possess diversified and mostly unknown viral communities.

A comparison of food sources of nudibranch mollusks at different depths off the Kuril Islands using fatty acid trophic markers

Gastropod molluscs such as nudibranchs are important members of deep-sea benthic ecosystems. However, data on the trophic ecology and feeding specialization of these animals are limited to date. The method of fatty acid trophic markers (FATM) was applied to determine the dietary preferences of nudibranchs off the Kuril Islands. Fatty acid (FA) compositions of Dendronotus sp., Tritonia tetraquetra, and Colga pacifica collected from deep waters were analyzed and compared with those of Aeolidia papillosa and Coryphella verrucosa from the offshore zone. The high level of FATM such as 22:5n-6 and C₂₀ monounsaturated FAs indicated that Dendronotus sp. preys on sea anemones and/or anthoathecates hydroids similarly to that of shallow-water species A. papillosa and C. verrucosa. The high percentage of tetracosapolyenoic acids and the ratio 24:6n-3/24:5n-6 indicated that T. tetraquetra preys on soft corals such as Gersemia and/or Acanella at a depth of 250 m, but soft corals of the family Primnoidae may be the main item in the diet of T. tetraquetra at a depth of 500 m. The high content of Δ 7,13-22:2 and 22:6n-3 shows that C. pacifica can feed on bryozoans. In C. pacifica, 22:5n-6 may be synthesized intrinsically by the mollusks, whereas odd-chain and branched saturated FAs originate from associated bacteria.

Looking at the Nudibranch Family Myrrhinidae (Gastropoda, Heterobranchia) from a Mitochondrial '2D Folding Structure' Point of View

Integrative taxonomy is an evolving field of multidisciplinary studies often utilised to elucidate phylogenetic reconstructions that were poorly understood in the past. The systematics of many taxa have been resolved by combining data from different research approaches, i.e., molecular, ecological, behavioural, morphological and chemical. Regarding molecular analysis, there is currently a search for new genetic markers that could be diagnostic at different taxonomic levels and that can be added to the canonical ones. In marine Heterobranchia, the most widely used mitochondrial markers, COI and 16S, are usually analysed by comparing the primary sequence. The 16S rRNA molecule can be folded into a 2D secondary structure that has been poorly exploited in the past study of heterobranchs, despite 2D molecular analyses being sources of possible diagnostic characters. Comparison of the results from the phylogenetic analyses of a concatenated (the nuclear H3 and the mitochondrial COI and 16S markers) dataset (including 30 species belonging to eight accepted genera) and from the 2D folding structure analyses of the 16S rRNA from the type species of the genera investigated demonstrated the diagnostic power of this RNA molecule to reveal the systematics of four genera belonging to the family Myrrhinidae (Gastropoda, Heterobranchia). The "molecular morphological" approach to the 16S rRNA revealed to be a powerful tool to delimit at both species and genus taxonomic levels and to be a useful way of recovering information that is usually lost in phylogenetic analyses. While the validity of the genera Godiva, Hermissenda and Phyllodesmium are confirmed, a new genus is necessary and introduced for Dondice banyulensis, Nemesis gen. nov. and the monospecific genus Nanuca is here synonymised with Dondice, with Nanuca sebastiani transferred into Dondice as Dondice sebastiani comb. nov.

Mimicry and mitonuclear discordance in nudibranchs: New insights from exon capture phylogenomics

Phylogenetic inference and species delimitation can be challenging in taxonomic groups that have recently radiated and where introgression produces conflicting gene trees, especially when species delimitation has traditionally relied on mitochondrial data and color pattern. Chromodoris, a genus of colorful and toxic nudibranch in the Indo-Pacific, has been shown to have extraordinary cryptic diversity and mimicry, and has recently radiated, ultimately complicating species delimitation. In these cases, additional genome-wide data can help improve phylogenetic resolution and provide important insights about evolutionary history. Here, we employ a transcriptome-based exon capture approach to resolve Chromodoris phylogeny with data from 2,925 exons and 1,630 genes, derived from 15 nudibranch transcriptomes. We show that some previously identified mimics instead show mitonuclear discordance, likely deriving from introgression or mitochondrial capture, but we confirm one "pure" mimic in Western Australia. Sister-species relationships and species-level entities were recovered with high support in both concatenated maximum likelihood (ML) and summary coalescent phylogenies, but the ML topologies were highly variable while the coalescent topologies were consistent across datasets. Our work also demonstrates the broad phylogenetic utility of 149 genes that were previously identified from eupulmonate gastropods. This study is one of the first to (a) demonstrate the efficacy of exon capture for recovering relationships among recently radiated invertebrate taxa, (b) employ genome-wide nuclear markers to test mimicry hypotheses in nudibranchs and (c) provide evidence for introgression and mitochondrial capture in nudibranchs.

agaricina (Demospongiae, Dictyoceratida)

Investigations on the biochemical relationship between Doriprismatica stellata (Chromodorididae, Doridoidea) nudibranchs, their egg ribbons, and the associated dietary sponge Spongia cf. agaricina (Demospongiae, Porifera) led to the isolation of the structurally new scalarane-type sesterterpene 12-deacetoxy-4-demethyl-11,24-diacetoxy-3,4-methylenedeoxoscalarin, with an unprecedented position of the cyclopropane ring annelated to the ring A. Unlike other scalaranes, which are most often functionalized at C-12 of ring C, it bears two acetoxy groups at C-11 and C-24 instead. The compound was present in all three samples, supporting the dietary relationship between chromodorid nudibranchs of the genus Doriprismatica and scalarane-containing dictyoceratid sponges of the Spongiidae family. The results also indicate that D. stellata passes the scalarane metabolite on to its egg ribbons, most likely for protective purposes. The scalarane showed antibacterial activity against the Gram-positive bacteria Arthrobacter crystallopoietes (DSM 20117) and Bacillus megaterium (DSM 32).

with the addition of two new species from Japan (Mollusca, Nudibranchia)

Morphological and molecular data are presented for the first time in an integrative way for the genus Myja Bergh, 1896. In accordance with the new molecular phylogenies, the traditional Facelinidae is paraphyletic. Herein is presented the phylogenetic placement of true Facelinidae s. str., including the first molecular data for F.auriculata (Müller, 1776), type species of the genus Facelina Alder & Hancock, 1855. The taxonomic history of F.auriculata is reviewed. The genus Myja is related to the clade Facelinidae s. str., but shows disparate morphological traits. Two new species of the genus Myja, M.karinsp. n., and M.hyotansp. n., are described from the Pacific waters of Japan (middle Honshu), and M.cf.longicornis Bergh, 1896 is investigated from Thailand. According to molecular analysis and review of available morphological information, the genus Myja contains more hidden diversity. The family-level relationship within aeolidacean nudibranchs with emphasis on the family Facelinidae is outlined. The problem of the relationship between Facelinidae Bergh, 1889 and Glaucidae Gray, 1827 is discussed. The family Glaucidae has precedence over Facelinidae and is phylogenetically related to the core group of Facelinidae s. str., but has a profoundly modified aberrant external morphology, thus making a purely molecular-based approach to the taxonomy an unsatisfactory solution. To accommodate recently discovered hidden diversity within glaucids, the genus Glaucilla Bergh, 1861 is restored. The family Facelinidae s. str. is separate from, and not closely related to, a clade containing the genera Dondice Marcus, 1958, Godiva MacNae 1954, Hermissenda Bergh, 1879, and Phyllodesmium Ehrenberg, 1831 (= Myrrhine Bergh, 1905). The oldest valid available name for the separate ex-facelinid paraphyletic clade that contains several facelinid genera is Myrrhinidae Bergh, 1905, and resurrection of this family name under provision of the ICZN article 40.1 can preliminarily solve the problem of paraphyly of the traditional Facelinidae. “Facelinidae” s. l. needs to be further divided into several separate families, pending further study.

Lomanoticola nishiharai n. sp., a New Species of Copepod Parasitic on the Facelinid Nudibranch, Sakuraeolis enosimensis (Baba, 1930), from the Seto Inland Sea, Western Japan, Including Histological Observations of the Female Lateral Body Process

Splanchnotrophidae Norman and Scott, 1906 is a family of parasitic copepods that infest nudibranchian and sacoglossan sea slugs. In this study, a new species of splanchnotrophid copepod, Lomanoticola nishiharai n. sp., is described based on specimens of both sexes collected from the facelinid nudibranch, Sakuraeolis enosimensis (Baba, 1930), in the Seto Inland Sea off Hiroshima, central Japan. It represents the third species of Lomanoticola Scott and Scott, 1895 and is characterized by the following female characters: the cephalosome distinctly protruded; the second and third lateral processes on the body originated from same bases; the caudal rami bears a seta V which almost same as long as the rami. Ultrastructural observations revealed that the cuticular surface of the lateral process on the female body is covered with numerous protuberances that may have protective functions against the cellular immune system of the host.

Antimicrobial Potential of Bacteria Associated with Marine Sea Slugs from North Sulawesi, Indonesia

Nudibranchia, marine soft-bodied organisms, developed, due to the absence of a protective shell, different strategies to protect themselves against putative predators and fouling organisms. One strategy is to use chemical weapons to distract predators, as well as pathogenic microorganisms. Hence, these gastropods take advantage of the incorporation of chemical molecules. Thereby the original source of these natural products varies; it might be the food source, de novo synthesis from the sea slug, or biosynthesis by associated bacteria. These bioactive molecules applied by the slugs can become important drug leads for future medicinal drugs. To test the potential of the associated bacteria, the latter were isolated from their hosts, brought into culture and extracts were prepared and tested for antimicrobial activities. From 49 isolated bacterial strains 35 showed antibiotic activity. The most promising extracts were chosen for further testing against relevant pathogens. In that way three strains showing activity against methicillin resistant Staphylococcus aureus and one strain with activity against enterohemorrhagic Escherichia coli, respectively, were identified. The obtained results indicate that the sea slug associated microbiome is a promising source for bacterial strains, which hold the potential for the biotechnological production of antibiotics.

Secondary metabolome and its defensive role in the aeolidoidean Phyllodesmium longicirrum, (Gastropoda, Heterobranchia, Nudibranchia)

Phyllodesmium longicirrum is the largest aeolidoidean species known to date, and extremely rich in terpenoid chemistry. Herein we report the isolation of a total of 19 secondary metabolites from a single specimen of this species, i.e., steroids 1-4, cembranoid diterpenes 5-13, complex biscembranoids 14 and 15, and the chatancin-type diterpenes 16-19. These compounds resemble those from soft corals of the genus Sarcophyton, of which to date, however, only S. trocheliophorum is described as a food source for P. longicirrum. Fish feeding deterrent activity was determined using the tropical puffer fish Canthigaster solandri, and showed activity for (2S)-isosarcophytoxide (10), cembranoid bisepoxide 12 and 4-oxochatancin (16). Determining the metabolome of P. longicirrum and its bioactivity, makes it evident that this seemingly vulnerable soft bodied animal is well protected from fish by its chemical arsenal.

Shallow water sea slugs (Gastropoda: Heterobranchia) from the northwestern coast of the Sea of Japan, north of Peter the Great Bay, Russia

The coast of northern Primorye region, north of Peter the Great Bay has been sparsely studied in regards to its molluscan fauna, with just a few works reviewing the distribution of local mollusks. This work presents a survey of the shallow water heterobranch sea slugs currently occurring around Kievka Bay to Oprichnik Bay, Russia. Thirty-nine species of sea slugs were found in this study and the new species Cadlina olgae sp. nov., described herein. Most (24) of the species occurring in the area have widespread ranges in the northern Pacific Ocean. The eight species are endemic for the Sea of Japan and adjacent part of the Sea of Okhotsk. Seven other occur also in northern Atlantic and Arctic waters. Thirteen found species are not known from Peter the Great Bay but known from adjacent northern Pacific waters. The finding of a previously undescribed species emphasizes the need of further surveys, particularly in subtidal and deeper waters, in order to improve the knowledge on this neglected fauna in Primorye.

dudkai (Nudibranchia)

Morphological and molecular data of type material of the nudibranch mollusc Dendronotus primorjensis Martynov, Sanamyan, Korshunova, 2015 from the Sea of Japan are summarised and compared with those of Dendronotus dudkai Ekimova, Schepetov, Chichvarkhina, Chichvarkhin, 2016. The clear conclusion is that the latter is a junior synonym of Dendronotus primorjensis.

Two new species and a remarkable record of the genus Dendronotus from the North Pacific and Arctic oceans (Nudibranchia)

Two new species of the nudibranch genus Dendronotus, Dendronotus arcticussp. n. and Dendronotus robilliardisp. n., are described from the Arctic and North Pacific oceans respectively, based on morphological and molecular data, and the North Pacific Dendronotus albus is revealed to be a species complex. The species Dendronotus robilliardisp. n. is described from the northwestern Pacific (Kamchatka) differing from the northeastern Pacific Dendronotus albus by molecular and morphological data. The synonymy of Dendronotus diversicolor with Dendronotus albus is confirmed by analysis of their original descriptions. An endemic Arctic species Dendronotus arcticussp. n. is also described here, differing substantially from all species of the genus Dendronotus using morphological and molecular data. An unusual record of the recently described Dendronotus kamchaticus Ekimova, Korshunova, Schepetov, Neretina, Sanamyan, Martynov, 2015 is also presented, the first from the northeastern Pacific, geographically separated from the type locality of this species in the northwestern Pacific by a distance ca. 6000 km; molecular data show them to belong to the same species.

Opisthobranchs from the western Indian Ocean, with descriptions of two new species and ten new records (Mollusca, Gastropoda)

Seventy species of opisthobranchs are described in this work based on collections from the Persian Gulf, Socotra, Kenya, Zanzibar, Madagascar, La Réunion, Mauritius, the Seychelles, the Maldives, and Sri Lanka. Ten species are newly recorded from the western Indian Ocean and four species are recorded in the scientific literature for the first time since their original descriptions. Two species are described as new: Cyerce bourbonicasp. n. from La Réunion and Doriopsilla nigrocerasp. n. from the Persian Gulf coast of Saudi Arabia. Chromodoris cavae is removed from its synonymy with Chromodoris tennentana and redescribed from specimens from La Réunion, while several new synonyms are proposed for some commonly occurring species. Risbecia bullockii is recorded for the second time from the Indian Ocean and assigned to its correct genus.