Scaphopoda is the sister taxon to Bivalvia: Evidence of ancient incomplete lineage sorting.

The almost simultaneous emergence of major animal phyla during the early Cambrian shaped modern animal biodiversity. Reconstructing evolutionary relationships among such closely spaced branches in the animal tree of life has proven to be a major challenge, hindering understanding of early animal evolution and the fossil record. This is particularly true in the species-rich and highly varied Mollusca where dramatic inconsistency among paleontological, morphological, and molecular evidence has led to a long-standing debate about the group's phylogeny and the nature of dozens of enigmatic fossil taxa. A critical step needed to overcome this issue is to supplement available genomic data, which is plentiful for well-studied lineages, with genomes from rare but key lineages, such as Scaphopoda. Here, by presenting chromosome-level genomes from both extant scaphopod orders and leveraging complete genomes spanning Mollusca, we provide strong support for Scaphopoda as the sister taxon of Bivalvia, revitalizing the morphology-based Diasoma hypothesis originally proposed 50 years ago. Our molecular clock analysis confidently dates the split between Bivalvia and Scaphopoda at ~520 Ma, prompting a reinterpretation of controversial laterally compressed Early Cambrian fossils, including Anabarella, Watsonella, and Mellopegma, as stem diasomes. Moreover, we show that incongruence in the phylogenetic placement of Scaphopoda in previous phylogenomic studies was due to ancient incomplete lineage sorting (ILS) that occurred during the rapid radiation of Conchifera. Our findings highlight the need to consider ILS as a potential source of error in deep phylogeny reconstruction, especially in the context of the unique nature of the Cambrian Explosion.

Checklist of the marine malacofauna of Culuccia Peninsula (NW Sardinia, Italy), with notes on relevant species.

Background: Culuccia is a small peninsula of about 3 km2 placed in north-western Sardinia (Italy) at the margin of the Maddalena Archipelago. The marine area surrounding this Peninsula is a Special Area of Conservation, included in the European Natura 2000 Ecological Network of protected areas, but until now, no information on biodiversity of this area is available. In 2021, a research project to study both terrestrial and marine biodiversity of Culuccia has started in order to fill this gap of knowledge. New information: This work provides the first inventory of the marine malacofauna of the coast of Culuccia. Fifteen sites were sampled seasonally for one-year by using different sampling methods and the present study shows the results from approximately 50 scientific SCUBA and free dive surveys, carried out in all main marine habitats of the studied area. In total, 259 species of molluscs were recorded along the coasts of the Culuccia Peninsula (0-25 m depth), belonging to the classes Bivalvia, Gastropoda, Polyplacophora and Scaphopoda. Amongst the four classes recorded, gastropods were the most represented (66.90%; 173 species), followed by bivalves (28.10%; 73 species), polyplacophorans (4.60%; 12 species) and scapophods (0.40%; 1 species). Notes about distribution, conservation status and ecology for some valuable species are provided, together with images of representative species, consisting mainly of in situ photographs. Additionally, the present investigation recorded the presence of four alien species, whose Mediterranean distribution was extended to north-western Sardinia.

The Complete Mitochondrial Genome and Gene Arrangement of the Enigmatic Scaphopod Pictodentalium vernedei.

The enigmatic scaphopods, or tusk shells, are a small and rare group of molluscs whose phylogenomic position among the Conchifera is undetermined, and the taxonomy within this class also needs revision. Such work is hindered by there only being a very few mitochondrial genomes in this group that are currently available. Here, we present the assembly and annotation of the complete mitochondrial genome from Dentaliida Pictodentalium vernedei, whose mitochondrial genome is 14,519 bp in size, containing 13 protein-coding genes, 22 tRNA genes and two rRNA genes. The nucleotide composition was skewed toward A-T, with a 71.91% proportion of AT content. Due to the mitogenome-based phylogenetic analysis, we defined P. vernedei as a sister to Graptacme eborea in Dentaliida. Although a few re-arrangements occurred, the mitochondrial gene order showed deep conservation within Dentaliida. Yet, such a gene order in Dentaliida largely diverges from Gadilida and other molluscan classes, suggesting that scaphopods have the highest degree of mitogenome arrangement compared to other molluscs.

Mollusca collected by Agassiz trawl from the 2016 SO-AntEco (JR15005) expedition to the South Orkney Islands, Antarctica - data.

Background: This dataset contributes to the knowledge of macro- and megafaunal Mollusca associated with a range of benthic habitat types in the South Orkney Islands, Antarctica, an exceptionally diverse region of the Southern Ocean. The information presented is derived from Agassiz trawl samples collected on the archipelago's shelf plateau and slope, within and outside of the South Orkney Islands Southern Shelf Marine Protected Area (SOISS MPA). Sampling was conducted in the framework of the British Antarctic Survey/SCAR "South Orkneys - State of the Antarctic Ecosystem" (SO-AntEco) project aboard RRS James Clark Ross during expedition JR15005 in Austral summer 2016. This dataset is published by the British Antarctic Survey under the licence CC-BY 4.0. We would appreciate it if you could follow the guidelines from the SCAR Data Policy (SCAR 2023) when using the data. If you have any questions regarding this dataset, do not hesitate to contact us via the contact information provided in the metadata or via data-biodiversity-aq@naturalsciences.be. Issues with the dataset can be reported at https://github.com/biodiversity-aq/data-publication/. This dataset is part of the Biodiversity, Evolution and Adaptation Project of the Environmental Change and Evolution Program of the British Antarctic Survey. The cruise report of the expedition is available at https://www.bodc.ac.uk/resources/inventories/cruise_inventory/reports/jr15005.pdf. New information: We report occurrences of Mollusca from individual samples taken with a 2 m-wide Agassiz trawl (AGT) in the framework of the February - March 2016 research expedition JR15005 of RRS James Clark Ross to the SOISS MPA and adjacent shelf and slope areas. Of 78 successful AGT deployments, 44 trawls at depths ranging from 235-2194 m yielded living Mollusca, totalling 2276 individuals, 67 morphospecies and 163 distributional records. One hundred and fifteen empty shells were also collected and recorded in the dataset. Three morphospecies (one Bivalvia and two Gastropoda) were sampled exclusively as empty shells, yielding a total of 70 morphospecies and 2391 specimens represented in the dataset. All specimens were preserved in 96% undenatured ethanol and are stored as vouchers in the collections of the British Antarctic Survey (BAS), Cambridge, United Kingdom. The publication of this dataset aims at increasing the knowledge on the biodiversity, abundance and geographical and bathymetric distribution of larger-sized epi- and shallow infaunal Mollusca of the South Orkney Islands.

Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae).

Many species of the gastropod genus Philine have been named from northeastern Asia but scanty descriptions based predominantly on shells make it difficult to determine which are valid. This, plus the sporadic anatomical and genetic information available for many of these species has led to what may be described as an un-integrated taxonomy. In this situation, it is generally preferable to postpone dissection of rare and unusual specimens until relevant diagnostic characters can be established in broader studies. Micro-CT scanning and DNA sequencing were used to examine such a specimen collected recently from deep waters off northeastern Taiwan. Micro-CT examination of the morphology of the internal shell and gizzard plates suggested that, among named species, the sequenced specimen is most similar to P.otukai. It cannot, however, be definitively referred to P.otukai as that species lacks adequate anatomical description or known DNA sequences. Phylogenetic analyses of newly collected DNA sequences show the specimen to be most closely related to, but distinct from the northern Atlantic Ocean and Mediterranean species, Philinequadripartita. The sequences also confirm genetically that five or more species of Philine occur in northeast Asia, including at least three subject to considerable taxonomic uncertainty.

Type specimens in the molluscan collection of the Bailey-Matthews National Shell Museum, Florida, USA.

This article lists and comments on the primary and secondary types represented in the collection of the Bailey-Matthews National Shell Museum (BMSM), on Sanibel, Florida, USA. The collection includes 464 type specimens, of which 15 are holotypes, representing 149 taxa, of which 145 are species and four subspecies. The BMSM collection is fully catalogued and posted online via the Museum's website, in addition to iDigBio and GBIF. The publication of this annotated list intends to improve on the accessibility and promote this important group of name-bearing specimens, which includes, among other cases, types originating from orphaned collections and material poorly documented in the original descriptions. Eighty-two types were selected for illustration, and the photos of all BMSM types are available as part of the BMSM online collection catalog.

Species richness and biogeographical affinities of the marine molluscs from Bahía de Chamela, Mexico.

For more than 10 years (2007-2018), the benthic macroinvertebrates of Bahía de Chamela (Mexican Pacific) were sampled at 31 sites (0-25 m depth). A total of 308 species of the five main classes of benthic molluscs were obtained (106 bivalves, 185 gastropods, 13 polyplacophorans, two scaphopods and two cephalopods). This is a significant increase in the number of species (246 new records) compared to the 62 species previously recorded more than 10 years ago. The distribution in the 31 localities of the bay is given for the first time for most of the species, together with information on its ecological rarity (incidence in the samples). Two families of bivalves (Veneridae and Mytilidae) and three families of gastropods (Calyptraeidae, Muricidae and Collumbellidae) comprised ~ 30% of all species. Ecological rarity was evident with 45 families (45.0%) with only one species and 178 species (57.8%) collected in one site and 67 (21.8%) in two sites. The molluscs of Bahía de Chamela represent 12.2% of all species recorded in the Mexican Pacific. Their biogeographic affinities are mostly related to the Tropical Eastern Pacific (TEP) including the oceanic islands and a few are restricted to the Tropical Mexican Pacific (TMP). Some have broader distributions to adjacent northern and southern temperate regions of the American Pacific, one to the western Atlantic, two pantropical (PAN) and two cosmopolitans (COS). The range distribution of each species was reviewed and updated, thus finding that seven species have extended their ranges of geographic distribution.

Complete mitochondrial genomes of two scaphopod molluscs.

Complete mitochondrial genomes were determined for two scaphopod molluscs: the dentaliid Antalis entalis and an unidentified Antarctic gadilid. Both genomes are complete except, in Gadilida sp. indet., a short stretch of nad5 was undetermined and trnR could not be annotated. Organization of the Gadilida sp. genome is nearly identical to that previously reported for the gadilid Siphonodentalium whereas trnK, nad5, trnD, nad4, and nad4l are transposed to the opposite strand in the previously published Graptacme genome relative to that of Antalis. Phylogenetic analysis of the 13 protein-coding and 2 rRNA genes recovered Scaphopoda, Gadilida, and Dentaliida monophyletic with maximal support.

Catalogue of the primary types of marine molluscan taxa described by Tommaso Allery Di Maria, Marquis of Monterosato, deposited in the Museo Civico di Zoologia, Roma.

We have compiled a complete list of new marine molluscan taxa introduced by Tommaso Allery Di Maria, Marquis of Monterosato (1841-1927). The dates of publication of every single work have been checked against available evidence, and an updated bibliography is also presented. Finally, the type material of all marine taxa expected to be in the collection Monterosato (presently preserved in the Museo Civico di Zoologia in Rome) has been searched in the main collection, and all retrieved specimens have been catalogued. A large majority of the material has been found, representative specimens of each taxon have been illustrated, and remarks on nomenclature and taxonomy have been provided yielding 42 new synonymies, 46 nominal taxa rediscovered, and 6 new combinations.

A systematic review of animal predation creating pierced shells: implications for the archaeological record of the Old World.

BACKGROUND: The shells of molluscs survive well in many sedimentary contexts and yield information about the diet of prehistoric humans. They also yield evidence of symbolic behaviours through their use as beads for body adornments. Researchers often analyse the location of perforations in shells to make judgements about their use as symbolic objects (e.g., beads), the assumption being that holes attributable to deliberate human behaviour are more likely to exhibit low variability in their anatomical locations, while holes attributable to natural processes yield more random perforations. However, there are non-anthropogenic factors that can cause perforations in shells and these may not be random. The aim of the study is compare the variation in holes in shells from archaeological sites from the Old World with the variation of holes in shells pierced by mollusc predators. METHODS: Three hundred and sixteen scientific papers were retrieved from online databases by using keywords, (e.g., 'shell beads'; 'pierced shells'; 'drilling predators'); 79 of these publications enabled us to conduct a systematic review to qualitatively assess the location of the holes in the shells described in the published articles. In turn, 54 publications were used to assess the location of the holes in the shells made by non-human predators. RESULTS: Almost all archaeological sites described shells with holes in a variety of anatomical locations. High variation of hole-placement was found within the same species from the same site, as well as among sites. These results contrast with research on predatory molluscs, which tend to be more specific in where they attacked their prey. Gastropod and bivalve predators choose similar hole locations to humans. DISCUSSION: Based on figures in the analysed articles, variation in hole-location on pierced shells from archaeological sites was similar to variation in the placement of holes created by non-human animals. Importantly, we found that some predators choose similar hole locations to humans. We discuss these findings and identify factors researchers might want to consider when interpreting shells recovered from archaeological contexts.

Abyssal fauna of the UK-1 polymetallic nodule exploration area, Clarion-Clipperton Zone, central Pacific Ocean: Mollusca.

We present the first DNA taxonomy publication on abyssal Mollusca from the Clarion-Clipperton Zone (CCZ), central Pacific ocean, using material collected as part of the Abyssal Baseline (ABYSSLINE) environmental survey cruise 'AB01' to the UK Seabed Resources Ltd (UKSRL) polymetallic-nodule exploration area 'UK-1' in the eastern CCZ. This is the third paper in a series to provide regional taxonomic data for a region that is undergoing intense deep-sea mineral exploration for high-grade polymetallic nodules. Taxonomic data are presented for 21 species from 42 records identified by a combination of morphological and genetic data, including molecular phylogenetic analyses. These included 3 heterodont bivalves, 5 protobranch bivalves, 4 pteriomorph bivalves, 1 caudofoveate, 1 monoplacophoran, 1 polyplacophoran, 4 scaphopods and 2 solenogastres. Gastropoda were recovered but will be the subject of a future study. Seven taxa matched published morphological descriptions for species with deep Pacific type localities, and our sequences provide the first genetic data for these taxa. One taxon morphologically matched a known cosmopolitan species but with a type locality in a different ocean basin and was assigned the open nomenclature 'cf' as a precautionary approach in taxon assignments to avoid over-estimating species ranges. One taxon is here described as a new species, Ledella knudseni sp. n. For the remaining 12 taxa, we have determined them to be potentially new species, for which we make the raw data, imagery and vouchers available for future taxonomic study. The Clarion-Clipperton Zone is a region undergoing intense exploration for potential deep-sea mineral extraction. We present these data to facilitate future taxonomic and environmental impact study by making both data and voucher materials available through curated and accessible biological collections.

Bathyal Mollusca from the cold-water coral biotope of Santa Maria di Leuca (Apulian margin, southern Italy).

This paper describes 97 molluskan species (45 Bivalvia, 3 Scaphopoda, 49 Gastropoda) recovered from bathyal bottoms off Santa Maria di Leuca (Puglia, Italy), in the northern Ionian Sea, and provides data about their taxonomy, geographical distribution, habitat, ecological requirements and fossil record. Only 6 species remain unidentified, and all are illustrated. The bivalve-dominated assemblages belong to the so-called "cold-water coral ecosystem". They appear to depend mainly on substrate characteristics, with faunas related to hard substrate around coral-colonized mound tops, and mud-related ones in inter-mound areas, respectively. Nuculanoida and Pectinoidea among bivalves, and Conoidea and Pyramidelloidea among gastropods are the most diverse suprafamilial groups. The present paper is the first comprehensive taxonomic overview of Mediterranean bathyal mollusks including larval shell characters.

The ParaHox gene Gsx patterns the apical organ and central nervous system but not the foregut in scaphopod and cephalopod mollusks.

BACKGROUND: It has been hypothesized that the ParaHox gene Gsx patterned the foregut of the last common bilaterian ancestor. This notion was corroborated by Gsx expression in three out of four lophotrochozoan species, several ecdysozoans, and some deuterostomes. Remarkably, Gsx is also expressed in the bilaterian anterior-most central nervous system (CNS) and the gastropod and annelid apical organ. To infer whether these findings are consistent with other mollusks or even lophotrochozoans, we investigated Gsx expression in developmental stages of representatives of two other molluscan classes, the scaphopod Antalis entalis and the cephalopod Idiosepius notoides. RESULTS: Gsx is not expressed in the developing digestive tract of Antalis entalis and Idiosepius notoides. Instead, it is expressed in cells of the apical organ in the scaphopod trochophore and in two cells adjacent to this organ. Late-stage trochophores express Aen-Gsx in cells of the developing cerebral and pedal ganglia and in cells close to the pavilion, mantle, and foot. In postmetamorphic specimens, Aen-Gsx is expressed in the cerebral and pedal ganglia, the foot, and the nascent captacula. In early squid embryos, Ino-Gsx is expressed in the cerebral, palliovisceral, and optic ganglia. In late-stage embryos, Ino-Gsx is additionally expressed close to the eyes and in the supraesophageal and posterior subesophageal masses and optic lobes. Developmental stages close to hatching express Ino-Gsx only close to the eyes. CONCLUSIONS: Our results suggest that Gsx expression in the foregut might not be a plesiomorphic trait of the Lophotrochozoa as insinuated previously. Since neither ecdysozoans nor deuterostomes express Gsx in their gut, a role in gut formation in the last common bilaterian ancestor appears unlikely. Gsx is consistently expressed in the bilaterian anterior-most CNS and the apical organ of lophotrochozoan larvae, suggesting a recruitment of Gsx into the formation of this organ in the Lophotrochozoa. The cephalopod posterior subesophageal mass and optic ganglia and the scaphopod pedal ganglia also express Gsx. In summary, Gsx expression only appears to be conserved in the anterior-most brain region during evolution. Accordingly, Gsx appears to have been recruited into the formation of other expression domains, e.g., the apical organ or the foregut, in some lophotrochozoans.

Amundsen Sea Mollusca from the BIOPEARL II expedition.

Information regarding the molluscs in this dataset is based on the epibenthic sledge (EBS) samples collected during the cruise BIOPEARL II / JR179 RRS James Clark Ross in the austral summer 2008. A total of 35 epibenthic sledge deployments have been performed at five locations in the Amundsen Sea at Pine Island Bay (PIB) and the Amundsen Sea Embayment (ASE) at depths ranging from 476 to 3501m. This presents a unique and important collection for the Antarctic benthic biodiversity assessment as the Amundsen Sea remains one of the least known regions in Antarctica. Indeed the work presented in this dataset is based on the first benthic samples collected with an EBS in the Amundsen Sea. However we assume that the data represented are an underestimation of the real fauna present in the Amundsen Sea. In total 9261 specimens belonging to 6 classes 55 families and 97 morphospecies were collected. The species richness per station varied between 6 and 43. Gastropoda were most species rich 50 species followed by Bivalvia (37), Aplacophora (5), Scaphopoda (3) and one from each of Polyplacophora and Monoplacophora.

Ross Sea Mollusca from the Latitudinal Gradient Program: R/V Italica 2004 Rauschert dredge samples.

Information regarding the molluscs in this dataset is based on the Rauschert dredge samples collected during the Latitudinal Gradient Program (LGP) on board the R/V "Italica" in the Ross Sea (Antarctica) in the austral summer 2004. A total of 18 epibenthic dredge deployments/samplings have been performed at four different locations at depths ranging from 84 to 515m by using a Rauschert dredge with a mesh size of 500µm. In total 8,359 specimens have been collected belonging to a total of 161 species. Considering this dataset in terms of occurrences, it corresponds to 505 discrete distributional records (incidence data). Of these, in order of abundance, 5,965 specimens were Gastropoda (accounting for 113 species), 1,323 were Bivalvia (accounting for 36 species), 949 were Aplacophora (accounting for 7 species), 74 specimens were Scaphopoda (3 species), 38 were Monoplacophora (1 species) and, finally, 10 specimens were Polyplacophora (1 species). This data set represents the first large-scale survey of benthic micro-molluscs for the area and provides important information about the distribution of several species, which have been seldom or never recorded before in the Ross Sea. All vouchers are permanently stored at the Italian National Antarctic Museum (MNA), Section of Genoa, enabling future comparison and crosschecking. This material is also currently under study, from a molecular point of view, by the barcoding project "BAMBi" (PNRA 2010/A1.10).