Resolving the relationships of clams and cockles: dense transcriptome sampling drastically improves the bivalve tree of life.

Bivalvia has been the subject of extensive recent phylogenetic work to attempt resolving either the backbone of the bivalve tree using transcriptomic data, or the tips using morpho-anatomical data and up to five genetic markers. Yet the first approach lacked decisive taxon sampling and the second failed to resolve many interfamilial relationships, especially within the diverse clade Imparidentia. Here we combine dense taxon sampling with 108 deep-sequenced Illumina-based transcriptomes to provide resolution in nodes that required additional study. We designed specific data matrices to address the poorly resolved relationships within Imparidentia. Our results support the overall backbone of the bivalve tree, the monophyly of Bivalvia and all its main nodes, although the monophyly of Protobranchia remains less clear. Likewise, the inter-relationships of the six main bivalve clades were fully supported. Within Imparidentia, resolution increases when analysing Imparidentia-specific matrices. Lucinidae, Thyasiridae and Gastrochaenida represent three early branches. Gastrochaenida is sister group to all remaining imparidentians, which divide into six orders. Neoheterodontei is always fully supported, and consists of Sphaeriida, Myida and Venerida, with the latter now also containing Mactroidea, Ungulinoidea and Chamidae, a family particularly difficult to place in earlier work. Overall, our study, by using densely sampled transcriptomes, provides the best-resolved bivalve phylogeny to date.

The families Carditidae and Condylocardiidae in the Magellan and Perú-Chile provinces (Bivalvia: Carditoidea).

Based on the study of available types and extant collections, this paper provides a systematic revision of the living species of Carditoidea occurring in the Magellan and Perú-Chile Provinces. Out of the 19 nominal species reported for the area, eight species are recognized as valid: Cyclocardia compressa, C. spurca, C. thouarsii, C. velutina, Carditella naviformis, C. semen, C. tegulata and Carditopsis flabellum. Other eight nominal species are regarded as synonyms: Cardita magellanica of Cyclocardia velutina; Carditella pallida of C. tegulata; Cardita australis and Actinobolus philippi of Carditella naviformis; Cardium pygmaeum of Carditella semen; Cardita paeteliana of Cyclocardia spurca; Carditella pallida duodecimcostata of Carditopsis flabellum; and Cardita congelascens of Cyclocardia thouarsii. Furthermore, Cardita malvinae and Cardium parvulum are nomina dubia, and the occurrence of Carditella exulata in Magellanic waters is doubtful.

Phylogenetic study and barcoding of the blood cockle, Tegillarca granosa, found on the west coast of peninsular Malaysia using the COI gene.

Blood cockles are among the most economically important brackish water invertebrates found in Malaysia. However, our knowledge of blood cockle phylogeny and systematics is rudimentary, especially for the species Tegillarca granosa. It is unclear, for instance, whether the cockles occurring on the west coast of peninsular Malaysia constitute a single species, or multiple, phylogenetically distinct species. We performed the first DNA molecular phylogenetic analysis of T. granosa to distinguish it from other related species found in other parts of the world and to create a DNA database for the species. An approximately 585-nucleotide fragment of the mitochondrial DNA (cytochrome oxidase I, COI) was sequenced for 150 individual cockles, representing 10 populations: three from the north, four from the central part and three from the southern part of peninsular Malaysia. Phylogenetic analyses of the resulting dataset yielded tree topologies that not only showed the relationship between T. granosa and its closest relatives but its position in the evolutionary tree. Three mitochondrial clades were evident, each containing an individual genus. Using the mutation rate of the COI gene, the divergence time between T. granosa and its closest related species was estimated to be 460 thousand years ago. This study provides a phylogenetic framework for this ecologically prominent and commercially important cockle species.

Isolation and characterization of the first microsatellite markers for the endangered relict mussel Hypanis colorata (Mollusca: Bivalvia: Cardiidae).

Hypanis colorata (Eichwald, 1829) (Cardiidae: Lymnocardiinae) is a bivalve relict species with a Ponto-Caspian distribution and is under strict protection in Romania, according to national regulations. While the species is depressed in the western Black Sea lagoons from Romania and Ukraine, it is also a successful invader in the middle Dniepr and Volga regions. Establishing a conservation strategy for this species or studying its invasion process requires knowledge about the genetic structure of the species populations. We have isolated and characterized nine polymorphic microsatellite markers in H. colorata. The number of alleles per locus ranged from 4 to 28 and the observed heterozygosity ranged from 0.613 to 1.000. The microsatellites developed in the present study are highly polymorphic and they should be useful for the assessment of genetic variation within this species.

A Useful SNP Panel to Distinguish Two Cockle Species, Cerastoderma edule and C. glaucum, Co-Occurring in Some European Beds, and Their Putative Hybrids.

Cockles are highly appreciated mollusks and provide important services in coastal areas. The two European species, edible (Cerastodermaedule) and lagoon (Cerastodermaglaucum) cockles, are not easily distinguishable, especially when young. Interestingly, the species show different resistance to Marteilia cochillia, the parasite responsible for marteiliosis outbreaks, which is devastating cockle production in some areas. C.edule is severely affected by the parasite, while C. glaucum seems to be resistant, although underlying reasons are still unknown. Hybrids between both species might be interesting to introgress allelic variants responsible for tolerance, either naturally or through artificial selection, from lagoon into edible cockle. Here, we used 2b restriction site-associated DNA sequencing (2b-RAD) to identify single nucleotide polymorphisms (SNP) diagnostic for cockle discrimination (fixed for alternative allelic variants). Among the nine diagnostic SNPs selected, seven were validated using a SNaPshot assay in samples covering most of the distribution range of both species. The validated SNPs were used to check cockles that were suggested to be hybrids by a claimed diagnostic tool based on the internal transcribed spacers of the ribosomal RNA. Although these were shown to be false positives, we cannot rule out the fact that hybrids can occur and be viable. The SNP tool here developed will be valuable for their identification and management.

Bucardium grateloupianum n. sp. from the Lower Miocene of Aquitaine with taxonomic comments on some fossil species from Europe (Bivalvia, Cardiidae).

The genus Bucardium J. E. Gray, 1853 has been widely used in the past literature, either for living and fossil cardiids, but only a single species was known, its type species B. ringens (Bruguière, 1789), living in the tropical waters of West Africa. Another species, from the Lower Miocene of the Aquitaine Basin, turned out to be undescribed, though known since the 19th century. It is herein described as Bucardium grateloupianum n. sp. The genus seems to have always had a low diversity and a tropical distribution. Its disappearance in Europe coincides with the general cooling trend recorded after the Middle Miocene. Several poorly known cardiids from the Lower-Middle Miocene of France and Austria and from the Upper Oligocene of Hungary show closer morphological affinities with the living Cardium indicum Lamarck, 1819, rather than with the genus Bucardium or with Cardium costatum Linnaeus, 1758, the type species of Cardium Linnaeus, 1758. These affinities suggest the need of a systematic reappraisal of the living and fossil species currently assigned to Cardium.