Comparative anatomy of siphons in tellinoidean clams (Bivalvia, Tellinoidea)

Siphons are tubular organs formed by fusion and posterior extension of the marginal mantle folds. They are supposed to have performed key roles in the evolution of bivalves by enabling these animals to occupy several ecological niches. However, anatomical details of these organs are scarce for one of the most diverse lineages of tropical bivalves, the superfamily Tellinoidea. We investigated the siphonal morphology of 15 species, sampling five tellinoidean families, by integrating scanning electron microscopy, confocal microscopy, and histology. The siphons revealed variations in length, pigmentation, tentacles, papillae, and number of nerve cords. Due to the presence of sensorial structures, such as papillae and tentacles, we reclassify the siphons of Tellinoidea from type A to A+. Additional anatomical patterns were identified at family and genus levels. For example, the incurrent siphon shorter than the excurrent and 24 tentacles are putative synapomorphies of Donacidae. We also highlight shared siphonal traits between Donacidae and Solecurtidae as well as between Semelidae and Tellinidae. In addition, our data support the idea of Psammobiidae as a paraphyletic lineage. Overall, we provide an extensive comparative data set on siphonal traits with significant relevance for bivalve taxonomy, functional anatomy, and evolutionary investigations.

The Complete Mitochondrial Genome and Phylogenetic Analysis of the Freshwater Shellfish Novaculina chinensis (Bivalvia: Pharidae)

Razor clams, belonging to the Pharidae and Solenidae families, are ecologically and economically important; however, very little research has been conducted on the Pharidae family. The genus Novaculina is a marine-derived freshwater lineage, and Novaculina chinensis is a rare freshwater species of the Pharidae family. In order to understand the phylogenetic relationships of N. chinensis, we sequenced the mitochondrial genome of the genus Novaculina, which is 16,262 bp in length and consists of 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The phylogenetic relationships of 69 Imparidentian mitochondrial genomes (mitogenomes) indicated that N. chineisis is closely related to Sinonovacula constricta of the order Adapedonta. Our study also found that the Ka/Ks ratios of 12 protein-coding genes in the Pharidae family are lower than one, indicating the occurrence of negative purification selection. Morphological observations of the siphons of N. chinensis, Novaculina myanmarensis, and Novaculina gangetica indicate that N. chinensis may be the ancestral clade of the genus Novaculina, which has not been proposed in previous studies. Our study provides useful molecular information on the phylogenetic and evolutionary relationships of Pharidae and also contributes to the conservation and management of the germplasm resources of N. chinensis.

The Complete Genome Sequences of 2 Species of Geukensia (Brachidontinae, Mytilidae)

We present the complete genome sequences of Geukensia demissa and Geukensia granosissima. Illumina sequencing was performed on genetic material from museum specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are available via Genbank.

Latitudinal variation and plasticity in response to temperature in Geukensia demissa

As global temperatures warm, species must adapt to a changing climate or transition to a different location suitable for their survival. Understanding the extent to which species are able to do so, particularly keystone species, is imperative to ensuring the survival of key ecosystems. The ribbed mussel Geukensia demissa is an integral part of salt marshes along the Atlantic coast of North America. Spatial patterns of genomic and phenotypic divergence have been previously documented, although their link with coastal environmental variation is unknown. Here, we study how populations of G. demissa in the northern (Massachusetts) and southern (Georgia) portions of the species range respond to changes in temperature. We combine assays of variation in oxygen consumption and RNA transcriptomic data with genomic divergence analyses to identify how separate populations of G. demissa may vary in distinct thermal environments. Our results show differences in constitutive oxygen consumption between mussels from Georgia and Massachusetts, as well as shared and disparate patterns of gene expression across temperature profiles. We also find that metabolic genes seem to be a strong component of divergence between these two populations. Our analysis highlights the importance of studying integrative patterns of genomic and phenotypic variation in species that are key for particular ecosystems, and how they might respond to further changes in climate.

Nanocrystalline fluorapatite mineralization in the calciphile rock-boring bivalve Lithophaga: functional and phylogenetic significance

Phosphate mineralization as a skeletal material is uncommon in invertebrate animals and rare in Mollusca. Remarkably, apatite minerals were first reported more than 30 years ago in the periostracum of two species of the mytilid bivalve Lithophaga where shells are mostly constructed of calcium carbonate. This discovery extended the range of biominerals secreted by molluscs but has attracted no subsequent research. In this study we review the occurrence of phosphate mineralization in Lithophaga and putatively allied taxa. Lithophagine bivalves, particularly Lithophaga and the more diverse Leiosolenus species, are well known for their endolithic chemical dissolution of calcareous rocks and corals with calcium-binding lipoproteins secreted by mantle glands. Fluorapatite was identified by X-ray diffraction in an outer layer of the periostracum in six species of Lithophaga. Morphological study by scanning electron microscopy of four species showed the fluorapatite crystals embedded in periostracal material in a layer 10–20 µm thick. Dilute bleach treatment revealed the crystals as densely packed euhedral prisms 250–400 nm in size. The succeeding inner layers of the periostracum were unmineralized. Observations of the developing periostracum of Lithophaga teres suggest that the initial mineralization is in the form of amorphous granules that coalesce and transform into euhedral crystals. Periostracal phosphate was not recorded in other members of the Lithophaginae – Leiosolenus, Botula or Zelithophaga species. Leiosolenus species characteristically have extraperiostracal aragonitic encrustations that can be thick and structurally complex. Published molecular phylogenies of Mytilidae bivalves show a division into two major clades with Lithophaga species in one clade and Leiosolenus species in the other, indicating that the subfamily Lithophaginae as presently understood is polyphyletic. This result implies that the two genera have independent evolutionary pathways to endolithic occupation of calcareous substrates although using similar mantle gland secretions to excavate their crypts. Because fluorapatite is considerably less soluble and harder than calcium carbonate, it is suggested that the phosphate layer of Lithophaga is a functional adaptation to protect their shells from self-dissolution from their rock-dissolving glandular secretions and may also act as defence against other shell-eroding organisms.

Mitochondrial genomic analyses provide new insights into the "missing" atp8 and adaptive evolution of Mytilidae

Background

Mytilidae, also known as marine mussels, are widely distributed in the oceans worldwide. Members of Mytilidae show a tremendous range of ecological adaptions, from the species distributed in freshwater to those that inhabit in deep-sea. Mitochondria play an important role in energy metabolism, which might contribute to the adaptation of Mytilidae to different environments. In addition, some bivalve species are thought to lack the mitochondrial protein-coding gene ATP synthase F0 subunit 8. Increasing studies indicated that the absence of atp8 may be caused by annotation difficulties for atp8 gene is characterized by highly divergent, variable length.

Results

In this study, the complete mitochondrial genomes of three marine mussels (Xenostrobus securis, Bathymodiolus puteoserpentis, Gigantidas vrijenhoeki) were newly assembled, with the lengths of 14,972 bp, 20,482, and 17,786 bp, respectively. We annotated atp8 in the sequences that we assembled and the sequences lacking atp8. The newly annotated atp8 sequences all have one predicted transmembrane domain, a similar hydropathy profile, as well as the C-terminal region with positively charged amino acids. Furthermore, we reconstructed the phylogenetic trees and performed positive selection analysis. The results showed that the deep-sea bathymodiolines experienced more relaxed evolutionary constraints. And signatures of positive selection were detected in nad4 of Limnoperna fortunei, which may contribute to the survival and/or thriving of this species in freshwater.

Conclusions

Our analysis supported that atp8 may not be missing in the Mytilidae. And our results provided evidence that the mitochondrial genes may contribute to the adaptation of Mytilidae to different environments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08940-8.

Form and function of the mantle edge in Protobranchia (Mollusca: Bivalvia)

We analyzed, by optical and transmission electron microscopy, the morphology and function of the mantle edge, including the formation of the periostracum, of ten species of protobranchs. Five species from the order Nuculida, four species from the order Nuculanida and one species from the order Solemyida were studied. A second outer fold, which seems to function as a template for the internal marginal crenulations of the valves, is present in the crenulated species of Nucula. The minute non-crenulated Ennucula aegeensis shows the glandular basal cells displaced toward the periostracal groove, resembling a minute additional fold between the outer and middle folds. Intense secretion of glycocalyx, together with active uptake of particles, have been observed in the inner epithelium of the middle mantle fold and the whole epithelium of the inner mantle fold in all the studied species. Contrary to the rest of the bivalves, all the protobranchs analyzed have two basal cells involved in the formation of the external nanometric pellicle of the periostracum, a character that would support the monophyly of protobranchs. A three-layered pattern is the general rule for the periostracum in protobranchs, like for other bivalves. The presence of pouches of translucent layer inside the tanned dark layer under periostracal folds is characteristic of the species with a folded periostracum; its function is unclear but could give flexibility to the periostracum. The non-nacreous internal shell layer and the presence of translucent pouches under periostracal folds in Sarepta speciosa resemble those found in nuculanids. However, the free periostracum is rather similar to those of N. hanleyi and E. aegeensis, with a continuous vesicular layer. All the latter supports the inclusion of Sarepta in the order Nuculanida but could indicate either a basal lineage or that the translucent vesicular layer is an adaptive trait.

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.

Combined threats to native smooth-shelled mussels (genus Mytilus) in Australia: bioinvasions and hybridization

Human-mediated pressures, including bioinvasions, threaten the biotas of every continent. Hybridization and introgression between invasive and native species may result in loss of genetic integrity of native taxa but, in many cases, these events are hard to detect because the invader is impossible to tell apart from the native taxon. The problem of cryptic invasive taxa and its importance for biodiversity protection have been underestimated, because of the limited number of studies of broadly distributed taxa using sensitive nuclear DNA markers. We employed a panel of 51 single nucleotide polymorphism (SNP) markers to examine genetic interactions between Australian native smooth-shelled mussels, Mytilus planulatus, and invasive and cryptic Northern Hemisphere M. galloprovincialis along 4400 km of coastline from the Pacific to the Indian Ocean. Overall, 20.8% of mussels from ten sites were native species. The centre of distribution of M. planulatus is in south-eastern Australia, in particular in Tasmania. We suggest that ongoing spatial and temporal monitoring of Tasmanian sites is required to test for the presence of M. galloprovincialis and its possible further spread, and that hatchery production of M. planulatus for farming and reseeding into the wild may help reduce the likelihood of its loss.