Sipunculan phylogeny based on six genes, with a new classification and the descriptions of two new families

Distribution of Antillesoma (Stephen & Edmonds, 1972) (Sipuncula, Antillesomatidae) in the Southwest Atlantic: New Records and Morphological Notes

Sipuncula, a marine annelid group, remains poorly known, particularly in the Southwestern Atlantic. This study focuses on the family Antillesomatidae (Kawauchi, Sharma, & Giribet 2012) and the cosmopolitan species Antillesoma antillarum (Grube & Öersted 1858) to enhance our understanding of its distribution, morphology, and population-level variations. We document A. antillarum at thirteen localities in the Southwestern Atlantic, extending its known range. This work was enabled by reviewing specimens from Brazilian scientific collections, which previously lacked formal records. Detailed morphological analysis and examination of population variations reveal the species' morphological plasticity and refine its distribution limits. Our findings improve the taxonomic framework for A. antillarum and significantly advance the understanding of Sipuncula diversity and distribution in the region, providing new insights into distribution patterns.

Redescription of Aspidosiphon (Paraspidosiphon) steenstrupii Diesing, 1859 (Sipuncula: Aspidosiphonidae) and the reinstatement of three species

Sipuncula, specifically the family Aspidosiphonidae, faces taxonomic challenges due to brief original descriptions and the poor condition or loss of the type material. Detailed standardized redescriptions are essential to understanding the diversification in this group. Herein, a comprehensive redescription of Aspidosiphon (Paraspidosiphon) steenstrupii based on an extensive material collection from the tropical Western Atlantic is provided. Based on morphological data and the analysis of COI sequences, we delimited A. (P.) steenstrupii morphologically, restricting its distribution to the tropical Western Atlantic. Also, the redescriptions and proposals for reinstatement of A. (P.) exostomum, A. (P.) ochrus, and A. (P.) speculator, previously considered junior synonyms of A. (P.) steenstrupii, are included. Furthermore, a comprehensive discussion on diagnostic morphological features to recognize aspidosiphonid species and a detailed revision of synonyms of A. (P.) steenstrupii are included. Notable differences in morphology and genetic data suggest the need for revising the taxonomic status of several synonyms within the family, highlighting underestimated diversity in sipunculans.

Reeling them in: taxonomy of marine annelids used as bait by anglers in the Western Cape Province, South Africa

Background

Common names are frequently used inconsistently for marine annelid species used as bait in the peer-reviewed literature, field guides and legislative material. The taxonomy of many such species based on morphology only also ignores cryptic divergences not yet detected. Such inconsistencies hamper effective management of marine annelids, especially as fishing for recreation and subsistence is increasing. This study investigates the scale of the problem by studying the use and names of bait marine annelids in the Western Cape Province of South Africa.

Methods

Fifteen recreational and six subsistence fishers at 12 popular fishing sites in the Western Cape Province donated 194 worms which they identified by common name. Worms were assigned scientific names according to a standard identification key for polychaetes from South Africa, and mitochondrial cytochrome oxidase I (COI) amplified and sequenced.

Results

This study identified 11 nominal species known by 10 common names, in the families Siphonosomatidae, Arenicolidae, Sabellaridae, Lumbrineridae, Eunicidae, Onuphidae and Nereididae. Cryptic diversity was investigated through employing mitochondrial COI sequences and these data will facilitate future identifications among widely distributed species. Several species (Siphonosoma dayi, Abarenicola gilchristi, Scoletoma species, Marphysa corallina, Lysidice natalensis, Heptaceras quinquedens, Perinereis latipalpa) are reported as bait for the first time, and while the names blood- and moonshineworms were consistently applied to members of Arenicolidae and Onuphidae, respectively, coralworm was applied to members of Sabellaridae and Nereididae. Analysis of COI sequences supported morphological investigations that revealed the presence of two taxonomic units each for specimens initially identified as Gunnarea gaimardi and Scoletoma tetraura according to identification keys. Similarly, sequences for Scoletoma species and Lysidice natalensis generated in this study do not match those from specimens in China and India, respectively. Further research is required to resolve the species complexes detected and also to refine the use of names by fishermen over a wider geographic range.

Annelids of the eastern Australian abyss collected by the 2017 RV 'Investigator' voyage

In Australia, the deep-water (bathyal and abyssal) benthic invertebrate fauna is poorly known in comparison with that of shallow (subtidal and shelf) habitats. Benthic fauna from the deep eastern Australian margin was sampled systematically for the first time during 2017 RV 'Investigator' voyage 'Sampling the Abyss'. Box core, Brenke sledge, and beam trawl samples were collected at one-degree intervals from Tasmania, 42°S, to southern Queensland, 24°S, from 900 to 4800 m depth. Annelids collected were identified by taxonomic experts on individual families around the world. A complete list of all identified species is presented, accompanied with brief morphological diagnoses, taxonomic remarks, and colour images. A total of more than 6000 annelid specimens consisting of 50 families (47 Polychaeta, one Echiura, two Sipuncula) and 214 species were recovered. Twenty-seven species were given valid names, 45 were assigned the qualifier cf., 87 the qualifier sp., and 55 species were considered new to science. Geographical ranges of 16 morphospecies extended along the eastern Australian margin to the Great Australian Bight, South Australia; however, these ranges need to be confirmed with genetic data. This work providing critical baseline biodiversity data on an important group of benthic invertebrates from a virtually unknown region of the world's ocean will act as a springboard for future taxonomic and biogeographic studies in the area.

How Many Sipunculan Species Are Hiding in Our Oceans?

Sipuncula, long considered a separate phylum, are now commonly included in the Annelida based on phylogenomic analyses. The sipunculan body consists of an unsegmented trunk and a retractable introvert, usually with a set of tentacles at its anterior end. Unlike other annelids, they have no chaetae, but the introvert is often adorned with proteinaceous hooks that can be important taxonomic characters. Other external taxonomic characters include the tentacles (number, shape and arrangement), body papillae and, in some cases, hardened shields, as well as length ratios. Many species require dissection for correct identification to reveal internal characteristics, such as introvert retractor muscles, nephridia and contractile vessels. Here we summarize the state of the current knowledge of species diversity in sipunculans. We emphasize molecular studies, conducted over the past two decades, that have revealed multiple complexes of cryptic or pseudocryptic species. It has become obvious that diversity is significantly higher than the current taxonomic scheme accounts for, but formal species descriptions are lagging behind. Although the major branches in the sipunculan phylogeny have become increasingly consolidated, the internal relationships within most branches are still in flux.

Reinstatement of Phascolosoma (Phascolosoma) varians Keferstein, 1865 (Sipuncula: Phascolosomatidae) based on morphological and molecular data

Phascolosoma (P.) varians, a sipunculan species known from the Greater Caribbean, was designated as a synonym of Phascolosoma (P.) nigrescens, which was originally described from Fiji. Their synonymy was primarily based upon an interpretation that these two species were morphologically indistinguishable. After its designation as a synonym, no further detailed analyses of morphological or molecular characteristics were performed to corroborate the assumed widespread distribution of Phascolosoma (P.) nigrescens. In this study, Phascolosoma (P.) varians is redescribed, and notable differences between this species and its proposed senior synonym are presented. These two species differ in the shape of their hooks, the spatial attachment of nephridia to the body wall, and the morphology of the contractile vessel. Additionally, there is high genetic divergence between nucleotide sequences within their respective cytochrome c oxidase subunit 1 (COI) genes, which supports the morphological data. Herein, the synonymy of Phascolosoma (P.) varians with Phascolosoma (P.) nigrescens is rejected due to morphological and molecular differences. Furthermore, the assumed widespread distribution of Phascolosoma (P.) nigrescens is still considered as questionable.

The first complete mitochondrial genome of Siphonosoma from Siphonosoma cumanense (Sipuncula, Sipunculidae)

Siphonosoma cumanense is economic important species in the fishery of southeast China. However, the current classification and the phylogeny of genus Siphonosoma had not been verified yet. Here, we report the complete mitochondrial genome sequence of S. Siphonosoma. The mitogenome has 15,917 base pairs and made up of total of 38 genes (13 protein-coding, 23 transfer RNAs and 2 ribosomal RNAs), and a putative control region. This study was the first available complete mitogenomes of Siphonosoma and will provide useful genetic information for future phylogenetic and taxonomic classification of Sipuncula.

The complete mitogenome of a peanut worm Phascolosoma pacificum (Sipuncula, Phascolosomatida, Phascolosomatidea)

Sipuncula (peanut worms) is a traditional phylum which consists of unsegmented bilateral symmetric marine worms. Although it is accepted as a phylum, the phylogenetic position of Sipuncula has been questionable. There is lack of molecular record on Sipuncula species while morphological data is not enough to distinguish the closer relationships between Annelida and Sipuncula. In order to add more data to genomic library of sipunculan species, Phascolosoma pacificum (Keferstein, 1866) was collected from seagrass area of Chuuk lagoon/Micronesia and its complete mitochondrial genome sequenced. Furthermore, phylogenetic relationship of the phylum Sipuncula and the other Trochozoan phyla investigate due to mitochondrial protein coding genes. Although there is lack of recorded data, our results support the idea that Sipuncula are nested within Annelida according to phylogenetic analyses of mitochondrial protein coding genes.

Complete mitochondrial genome analysis of Phascolosoma sp. (Sipuncula, Phascolosomatida, Phascolosomatidea) from Micronesia

In this study a Sipuncula species Phascolosoma sp. was collected from seagrass area from Chuuk lagoon Micronesia and its complete mitochondrial genome analyzed. This is the second complete mitochondrial genome record from the genus after Phascolosoma esculenta. The total length of mitochondrial genome of the species is 16,571 bp, which is longer than P. esculenta record. Also, locations of tRNA-Gly and putative control region are different between two records. Furthermore, phylogenetic relationship of Phascolosoma sp. are investigated due to protein-coding genes of mitochondrial genome. Due to the lack of recorded data, P. esculenta has been observed is the closest species to Phascolosoma sp. and they are belonging to the monophyletic group.

Reciprocal Symbiont Sharing in the Lodging Mutualism between Walking Corals and Sipunculans

Solitary scleractinian corals of the genera Heterocyathus and Heteropsammia inhabit soft marine bottoms without attaching to hard substrata. The corallums of these genera contain a coiled cavity inhabited by a sipunculan that roams the seafloor, carrying the host coral with it. The coral serves as a sturdy shelter that protects the sipunculan from possible predators. At the same time, the sipunculan maintains the coral in an upright position on the soft bottom. This coral–sipunculan association is unique because two phylogenetically distant coral genera have developed convergent associations with sipunculans. We investigate the process of convergent evolution of two coral species, Hc. aequicostatus and Hp. cochlea, in Okinawa, Japan, with their symbiotic sipunculans, using phylogenetic and morphological analyses. Phylogenetic analyses clarified that the symbiotic sipunculans comprise two distinct clades, surprisingly both of which are associated with both coral species. The bodily habitus of the sipunculan differed between coral species and fit the morphologies of the coiled cavities of their respective host corals. Our results suggest that the two coral species share two sipunculan clades and that sipunculan morphology is plastic and determined by the internal structure of their host corals.

Re-evaluating the phylogeny of Sipuncula through transcriptomics

Sipunculans (also known as peanut worms) are an ancient group of exclusively marine worms with a global distribution and a fossil record that dates back to the Early Cambrian. The systematics of sipunculans, now considered a distinct subclade of Annelida, has been studied for decades using morphological and molecular characters, and has reached the limits of Sanger-based approaches. Here, we reevaluate their family-level phylogeny by comparative transcriptomic analysis of eight species representing all known families within Sipuncula. Two data matrices with alternative gene occupancy levels (large matrix with 675 genes and 62% missing data; reduced matrix with 141 genes and 23% missing data) were analysed using concatenation and gene-tree methods, yielding congruent results and resolving each internal node with maximum support. We thus corroborate prior phylogenetic work based on molecular data, resolve outstanding issues with respect to the familial relationships of Aspidosiphonidae, Antillesomatidae and Phascolosomatidae, and highlight the next area of focus for sipunculan systematics.

Investigating the Bivalve Tree of Life – an exemplar-based approach combining molecular and novel morphological characters

To re-evaluate the relationships of the major bivalve lineages, we amassed detailed morpho-anatomical, ultrastructural and molecular sequence data for a targeted selection of exemplar bivalves spanning the phylogenetic diversity of the class. We included molecular data for 103 bivalve species (up to five markers) and also analysed a subset of taxa with four additional nuclear protein-encoding genes. Novel as well as historically employed morphological characters were explored, and we systematically disassembled widely used descriptors such as gill and stomach ‘types’. Phylogenetic analyses, conducted using parsimony direct optimisation and probabilistic methods on static alignments (maximum likelihood and Bayesian inference) of the molecular data, both alone and in combination with morphological characters, offer a robust test of bivalve relationships. A calibrated phylogeny also provided insights into the tempo of bivalve evolution. Finally, an analysis of the informativeness of morphological characters showed that sperm ultrastructure characters are among the best morphological features to diagnose bivalve clades, followed by characters of the shell, including its microstructure. Our study found support for monophyly of most broadly recognised higher bivalve taxa, although support was not uniform for Protobranchia. However, monophyly of the bivalves with protobranchiate gills was the best-supported hypothesis with incremental morphological and/or molecular sequence data. Autobranchia, Pteriomorphia, Heteroconchia, Palaeoheterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata and Imparidentia new clade ( = Euheterodonta excluding Anomalodesmata) were recovered across analyses, irrespective of data treatment or analytical framework. Another clade supported by our analyses but not formally recognised in the literature includes Palaeoheterodonta and Archiheterodonta, which emerged under multiple analytical conditions. The origin and diversification of each of these major clades is Cambrian or Ordovician, except for Archiheterodonta, which diverged from Palaeoheterodonta during the Cambrian, but diversified during the Mesozoic. Although the radiation of some lineages was shifted towards the Palaeozoic (Pteriomorphia, Anomalodesmata), or presented a gap between origin and diversification (Archiheterodonta, Unionida), Imparidentia showed steady diversification through the Palaeozoic and Mesozoic. Finally, a classification system with six major monophyletic lineages is proposed to comprise modern Bivalvia: Protobranchia, Pteriomorphia, Palaeoheterodonta, Archiheterodonta, Anomalodesmata and Imparidentia.

Into the deep: a phylogenetic approach to the bivalve subclass Protobranchia

A molecular phylogeny of Protobranchia, the subclass of bivalve mollusks sister to the remaining Bivalvia, has long proven elusive, because many constituent lineages are deep-sea endemics, which creates methodological challenges for collecting and preserving genetic material. We obtained 74 representatives of all 12 extant protobranch families and investigated the internal phylogeny of this group using sequence data from five molecular loci (16S rRNA, 18S rRNA, 28S rRNA, cytochrome c oxidase subunit I, and histone H3). Model-based and dynamic homology parsimony approaches to phylogenetic reconstruction unanimously supported four major clades of Protobranchia, irrespective of treatment of hypervariable regions in the nuclear ribosomal genes 18S rRNA and 28S rRNA. These four clades correspond to the superfamilies Nuculoidea (excluding Sareptidae), Nuculanoidea (including Sareptidae), Solemyoidea, and Manzanelloidea. Salient aspects of the phylogeny include (1) support for the placement of the family Sareptidae with Nuculanoidea; (2) the non-monophyly of the order Solemyida (Solemyidae+Nucinellidae); (3) and the non-monophyly of most nuculoid and nuculanoid genera and families. In light of this first family-level phylogeny of Protobranchia, we present a revised classification of the group. Estimation of divergence times in concert with analyses of diversification rates demonstrate the signature of the end-Permian mass extinction in the phylogeny of extant protobranchs.

Sipunculan larvae and "cosmopolitan" species

Sipuncula is a relatively small taxon with roughly 150 recognized species. Many species are geographically widespread or "cosmopolitan." The pelagosphera larvae of some species are estimated to spend several months in the plankton. However, recent molecular evidence suggests that many of the "cosmopolitan" species actually represent species-complexes, some not even monophyletic. Herein, we present data on three sipunculan species with different developmental modes that occur both in the Sea of Japan and in the Northeast Pacific. The development of the three species-Phascolosoma agassizii, Thysanocardia nigra, and Themiste pyroides-is exceptionally well studied in both regions of the Pacific. Significant differences have been observed between the two regions with respect to egg size, developmental mode, and developmental timing. In general, eggs are larger and development slower in the Northeast Pacific when compared with the Sea of Japan. These differences have been explained as a result of phenotypic plasticity exhibited under different environmental conditions, in particular temperature, but we show that the populations of all three species are also remarkably distinct genetically and that gene flow between the two regions is extremely unlikely. In Thysanocardia nigra, we even found two very distinct genetic lineages within the same location in the Northeast Pacific. The amount of genetic divergence between populations from the Sea of Japan and those from the Northeast Pacific is not correlated with developmental mode. Themiste pyroides, the species with the most abbreviated development, actually has the least degree of genetic divergence between the regions. Analyses of molecular variance show that the majority of the observed variation in all three species is between the regions. We conclude that all three "cosmopolitan" species actually represent complexes of cryptic or pseudo-cryptic species. These examples demonstrate that a solid taxonomic framework based on molecular and morphological evidence is a prerequisite for evaluating relationships between dispersal capabilities, species' ranges, and the connectivity of populations.