The genome sequence of a heart cockle, Fragum fragum (Linnaeus, 1758).

We present a genome assembly from an individual specimen of Fragum fragum (a heart cockle; Mollusca; Bivalvia; Veneroida; Cardiidae). The genome sequence is 1,153.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 22.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,262 protein coding genes.

Genomic data reveals habitat partitioning in massive Porites on Guam, Micronesia.

Corals in marginal reef habitats generally exhibit less bleaching and associated mortality compared to nearby corals in more pristine reef environments. It is unclear, however, if these differences are due to environmental differences, including turbidity, or genomic differences between the coral hosts in these different environments. One particularly interesting case is in the coral genus Porites, which contains numerous morphologically similar massive Porites species inhabiting a wide range of reef habitats, from turbid river deltas and stagnant back reefs to high-energy fore reefs. Here, we generate ddRAD data for 172 Porites corals from river delta and adjacent (<0.5 km) fore reef populations on Guam to assess the extent of genetic differentiation among massive Porites corals in these two contrasting environments and throughout the island. Phylogenetic and population genomic analyses consistently identify seven different clades of massive Porites, with the two largest clades predominantly inhabiting either river deltas or fore reefs, respectively. No population structure was detected in the two largest clades, and Cladocopium was the dominant symbiont genus in all clades and environments. The perceived bleaching resilience of corals in marginal reefs may therefore be attributed to interspecific differences between morphologically similar species, in addition to potentially mediating environmental differences. Marginal reef environments may therefore not provide a suitable refuge for many reef corals in a heating world, but instead host additional cryptic coral diversity.

Boring life: early colony formation and growth in the endolithic bryozoan genus Penetrantia Silén, 1946.

As in most colonial and sessile marine invertebrates, bryozoan life history is characterized by asexual propagation of zooids for colonial growth and by sexual production of larvae for dispersal. However, comprehensive life histories, particularly in cryptic species such as endolithic (boring) bryozoans, remain poorly understood. The ctenostome family Penetrantiidae is widespread from temperate to tropical waters and often found in molluscan shells, offering an opportunity to study the boring lifestyle and its potential impact on bioerosion through growth and settlement experiments. Our research focused on Penetrantia clionoides from Guam in the Pacific Ocean, Penetrantia japonica from Japan, and a Penetrantia species from France in the Atlantic Ocean. We found distinct life histories and reproductive patterns potentially influenced by environmental factors such as temperature and food availability. The tropical P. clionoides displayed higher rates of larval production and growth compared to its temperate counterpart. For instance, the mean stolon extension was 335.2 µm/week in P. clionoides versus 232.1 µm/week in Penetrantia sp. Autozooid development took 13 days in P. clionoides and 31 days in Penetrantia sp. Anatomical features like apertural rims aided in species identification and in understanding larval settlement preferences, suggesting a tendency for philopatric settlement behavior. The bioerosional impact of penetrantiids remains little understood, but we generated first projections of bioerosion rates and a protocol for keeping Penetrantia under laboratory conditions, laying a foundation for further research in this field.

Boring systematics: A genome skimmed phylogeny of ctenostome bryozoans and their endolithic family Penetrantiidae with the description of one new species.

Ctenostomes are a group of gymnolaemate bryozoans with an uncalcified chitinous body wall having few external, skeletal characters. Hence, species identification is challenging and their systematics remain poorly understood, even more so when they exhibit an endolithic (boring) lifestyle. Currently, there are four Recent families of endolithic bryozoans that live inside mineralized substrates like mollusk shells. In particular, Penetrantiidae Silén, 1946 has received considerable attention and its systematic affinity to either cheilostomes or ctenostomes has been debated. Species delimitation of penetrantiids remains difficult, owing to a high degree of colonial and zooidal plasticity. Consequently, an additional molecular approach is essential to unravel the systematics of penetrantiids, their phylogenetic placement and their species diversity. We therefore sequenced the mitochondrial (mt) genomes and two nuclear markers of 27 ctenostome species including nine penetrantiids. Our phylogeny supports the Penetrantiidae as a monophyletic group placed as sister taxon to the remaining ctenostomes alongside paludicellids, arachnidioids and terebriporids. The boring family Terebriporidae d'Orbigny, 1847 were previously considered to be among vesicularioids, but our results suggest an arachnidioid affinity instead. Ctenostome paraphyly is supported by our data, as the cheilostomes nest within them. A Multiporata clade is also well supported, including the former victorelloid genus Sundanella. Altogether, this study provides new insights into ctenostome systematics, assists with species delimitation and contributes to our understanding of the bryozoan tree of life.

Boring bryozoans: an investigation into the endolithic bryozoan family Penetrantiidae.

An endolithic lifestyle in mineralized substrates has evolved multiple times in various phyla including Bryozoa. The family Penetrantiidae includes one genus with ten extant and two fossil species. They predominantly colonize the shells of molluscs and establish colonies by chemical dissolution of calcium carbonate. Based on several morphological characters, they were described to be either cheilostome or ctenostome bryozoans. For more than 40 years, neither the characters of species identity and systematics nor the problem of their phylogeny was approached. Consequently, the aim of this study is to reevaluate species identities and the systematic position of the genus Penetrantia by analyzing at least six different species from eight regions with the aid of modern methods such as confocal laser scanning microscopy and 3D-reconstruction techniques. This study demonstrates that the musculature associated with the operculum and brood chamber shows significant differences from the cheilostome counterparts and seems to have evolved independently. Together with the presence of other ctenostome-like features such as true polymorphic stolons and uncalcified body wall, this finding supports a ctenostome affinity. Operculum morphology reveals many new species-specific characters, which, together with information about gonozooid morphology, tentacle number, and zooid size ranges, will enhance species identification. It also revealed a probable new species in Japan as well as potential cryptic species in France and New Zealand. In addition, this study increases the known distribution range of the family and its substrate diversity. Altogether, the new information collated here provides the basis for future work on a neglected taxon. Supplementary Information: The online version contains supplementary material available at 10.1007/s13127-023-00612-z.

Genomic signatures suggesting adaptation to ocean acidification in a coral holobiont from volcanic CO2 seeps.

Ocean acidification, caused by anthropogenic CO2 emissions, is predicted to have major consequences for reef-building corals, jeopardizing the scaffolding of the most biodiverse marine habitats. However, whether corals can adapt to ocean acidification and how remains unclear. We addressed these questions by re-examining transcriptome and genome data of Acropora millepora coral holobionts from volcanic CO2 seeps with end-of-century pH levels. We show that adaptation to ocean acidification is a wholistic process involving the three main compartments of the coral holobiont. We identified 441 coral host candidate adaptive genes involved in calcification, response to acidification, and symbiosis; population genetic differentiation in dinoflagellate photosymbionts; and consistent transcriptional microbiome activity despite microbial community shifts. Coral holobionts from natural analogues to future ocean conditions harbor beneficial genetic variants with far-reaching rapid adaptation potential. In the face of climate change, these populations require immediate conservation strategies as they could become key to coral reef survival.

Three new species of Nautilus Linnaeus, 1758 (Mollusca, Cephalopoda) from the Coral Sea and South Pacific.

Nautiloids are a charismatic group of marine molluscs best known for their rich fossil record, but today they are restricted to a handful of species in the family Nautilidae from around the Coral Triangle. Recent genetic work has shown a disconnect between traditional species, originally defined on shell characters, but now with new findings from genetic structure of various Nautilus populations. Here, three new species of Nautilus from the Coral Sea and South Pacific region are formally named using observations of shell and soft anatomical data augmented by genetic information: N.samoaensissp. nov. (from American Samoa), N.vitiensissp. nov. (from Fiji), and N.vanuatuensissp. nov. (from Vanuatu). The formal naming of these three species is timely considering the new and recently published information on genetic structure, geographic occurrence, and new morphological characters, including color patterns of shell and soft part morphology of hood, and will aid in managing these possibly endangered animals. As recently proposed from genetic analyses, there is a strong geographic component affecting taxonomy, with the new species coming from larger island groups that are separated by at least 200 km of deep water (greater than 800 m) from other Nautilus populations and potential habitats. Nautilid shells implode at depths greater than 800 m and depth therefore acts as a biogeographical barrier separating these species. This isolation, coupled with the unique, endemic species in each locale, are important considerations for the conservation management of the extant Nautilus species and populations.

Effects of elevated temperature on reproduction and larval settlement in Leptastrea purpurea.

As global ocean temperatures continue to rise, severe declines in coral reef health and diversity are reported on a global scale. Recovery of coral reefs relies on reproduction and increased rates of successful recruitment, which can vary tremendously across coral species. We investigated the effects of increased temperatures in the environment of parental colonies on larval production, size, settlement and survival, in the heat-resistant coral Leptastrea purpurea in Guam. Thanks to two tank experiments (eleven and four weeks, respectively) conducted over two consecutive years we found that larvae released by heat-treated parents (30 °C) were significantly smaller in size but greater in number, had normal settlement behavior and increased post-settlement survival rates compared to those released by control parent colonies (28 °C). We conclude that changes in the environment of parental L. purpurea colonies trigger an anticipatory maternal effect which leads to the release of preconditioned larvae with an increased chance of survival. Supplementary Information: The online version contains supplementary material available at 10.1007/s00338-022-02241-y.

Diversity and toxicity of Pacific strains of the benthic dinoflagellate Coolia (Dinophyceae), with a look at the Coolia canariensis species complex.

Coolia Meunier 1919 from benthic assemblages of Hawai'i and Guam were isolated and clonal cultures were established from single cells. Cultures were identified to species-level based on 28S rRNA and ITS-5.8S rRNA genes and tested for toxicity. In Hawai'i, two strains of C. malayensis were isolated. In Guam, a high biodiversity was identified: four strains of C. malayensis, one strain of C. palmyrensis, one strain of C. tropicalis, one strain of C. canariensis phylogroup III, and two strains forming a new phylogroup (phylogroup IV) of nontoxic C. canariensis. Morphology of the new C. canariensis phylogroup was described using light microscopy and scanning electron microscopy. Mass cultures and methanol extracts of representative cultures (C. malayensis, C. palmyrensis, C. canariensis, C. tropicalis) from Guam were prepared for liquid chromatography-mass spectrometry analysis. Chemical analyses revealed yessotoxin analogue C56H78O18S2 is produced by C. malayensis, C. canariensis phylogroup IV and C. palmyrensis, but other analogues, C57H80O18S2 and C58H86O18S2, were only found in C. malayensis (Okinawa) and C. canariensis phylogroup IV. Individual toxin profiles were also different over time for an Okinawa strain of C. malayensis (NIES-3637), highlighting intra and inter-species variation in Yessotoxin-analogue expression. Biological activity was tested using Artemia bioassay and toxicity was observed in Guam and Okinawa strains of C. malayensis. Strong support of four distinct clades within the C. canariensis species complex was recovered in phylogenetic analyses, despite morphological similarities.

Evolutionary management of coral-reef fisheries using phylogenies to predict density dependence.

Harvesting models are based upon the ideology that removing large, old individuals provides space for young, fast-growing counterparts that can maximize (fisheries) yields while maintaining population stability and ecosystem function. Yet, this compensatory density dependent response has rarely been examined in multispecies systems. We combined extensive data sets from coral-reef fisheries across a suite of Pacific islands and provided unique context to the universal assumptions of compensatory density dependence. We reported that size-and-age truncation only existed for 49% of target coral-reef fishes exposed to growing fishing pressure across a suite of Pacific islands. In contrast, most of the remaining species slowly disappeared from landings and reefs with limited change to their size structure (i.e., little to no compensation), often becoming replaced by smaller-bodied sister species. To understand these remarkable and disparate differences, we constructed phylogenies for dominant fish families and discovered that large patristic distances between sister species, or greater phylogenetic isolation, predicted size-and-age truncation. Isolated species appeared to have greater niche dominance or breadth, supported by their faster growth rates compared to species with similar sizes and within similar guilds, and many also have group foraging behavior. In contrast, closely related species may have more restricted, realized niches that led to their disappearance and replacement. We conclude that phylogenetic attributes offered novel guidance to proactively manage multispecies fisheries and improve our understanding of ecological niches and ecosystem stability.

Phylogeny of Micronesian emperor fishes and evolution of trophic types.

Island communities that rely on reef fish are currently faced with declining marine resources due to unsustainable fishing and climate change. Identification of genetic stocks through phylogenetic analyses has become a growing field of study with conservation implications, but genetic information on reef fish in Micronesia is limited. In this study we focus on Lethrinidae, one of the most commonly fished reef fish families in Micronesia. Our main goal was to establish a phylogeny for Lethrinidae based on Micronesian data with the intent to help future conservation efforts and clarify the evolutionary history of trophic types in this family. Thirty-eight Lethrinidae specimens collected across five Micronesian islands were used to build a phylogeny with three mitochondrial and one nuclear gene. The phylogenetic analyses allowed us to clarify the identity and position of 11 commonly harvested species and provided a novel genetic identification for Monotaxis heterodon in Micronesia. Our improved and dated phylogeny supports a new hypothesis for the ancestral trophic type of emperor fishes: "stalkers" with low-bodies and conical teeth. We correlated the radiation of most Lethrinidae species with the radiation of major scleractinian coral lineages in the middle Miocene, highlighting the tight relationships between declining reefs and the survival of emperor fishes.

Going with the flow: How corals in high-flow environments can beat the heat.

Coral reefs are experiencing unprecedented declines in health on a global scale leading to severe reductions in coral cover. One major cause of this decline is increasing sea surface temperature. However, conspecific colonies separated by even small spatial distances appear to show varying responses to this global stressor. One factor contributing to differential responses to heat stress is variability in the coral's micro-environment, such as the amount of water flow a coral experiences. High flow provides corals with a variety of health benefits, including heat stress mitigation. Here, we investigate how water flow affects coral gene expression and provides resilience to increasing temperatures. We examined host and photosymbiont gene expression of Acropora cf. pulchra colonies in discrete in situ flow environments during a natural bleaching event. In addition, we conducted controlled ex situ tank experiments where we exposed A. cf. pulchra to different flow regimes and acute heat stress. Notably, we observed distinct flow-driven transcriptomic signatures related to energy expenditure, growth, heterotrophy and a healthy coral host-photosymbiont relationship. We also observed disparate transcriptomic responses during bleaching recovery between the high- and low-flow sites. Additionally, corals exposed to high flow showed "frontloading" of specific heat-stress-related genes such as heat shock proteins, antioxidant enzymes, genes involved in apoptosis regulation, innate immunity and cell adhesion. We posit that frontloading is a result of increased oxidative metabolism generated by the increased water movement. Gene frontloading may at least partially explain the observation that colonies in high-flow environments show higher survival and/or faster recovery in response to bleaching events.

Shedding light: a phylotranscriptomic perspective illuminates the origin of photosymbiosis in marine bivalves.

BACKGROUND: Photosymbiotic associations between metazoan hosts and photosynthetic dinoflagellates are crucial to the trophic and structural integrity of many marine ecosystems, including coral reefs. Although extensive efforts have been devoted to study the short-term ecological interactions between coral hosts and their symbionts, long-term evolutionary dynamics of photosymbiosis in many marine animals are not well understood. Within Bivalvia, the second largest class of mollusks, obligate photosymbiosis is found in two marine lineages: the giant clams (subfamily Tridacninae) and the heart cockles (subfamily Fraginae), both in the family Cardiidae. Morphologically, giant clams show relatively conservative shell forms whereas photosymbiotic fragines exhibit a diverse suite of anatomical adaptations including flattened shells, leafy mantle extensions, and lens-like microstructural structures. To date, the phylogenetic relationships between these two subfamilies remain poorly resolved, and it is unclear whether photosymbiosis in cardiids originated once or twice. RESULTS: In this study, we establish a backbone phylogeny for Cardiidae utilizing RNASeq-based transcriptomic data from Tridacninae, Fraginae and other cardiids. A variety of phylogenomic approaches were used to infer the relationship between the two groups. Our analyses found conflicting gene signals and potential rapid divergence among the lineages. Overall, results support a sister group relationship between Tridacninae and Fraginae, which diverged during the Cretaceous. Although a sister group relationship is recovered, ancestral state reconstruction using maximum likelihood-based methods reveals two independent origins of photosymbiosis, one at the base of Tridacninae and the other within a symbiotic Fraginae clade. CONCLUSIONS: The newly revealed common ancestry between Tridacninae and Fraginae brings a possibility that certain genetic, metabolic, and/or anatomical exaptations existed in their last common ancestor, which promoted both lineages to independently establish photosymbiosis, possibly in response to the modern expansion of reef habitats.

Revisiting metazoan phylogeny with genomic sampling of all phyla.

Proper biological interpretation of a phylogeny can sometimes hinge on the placement of key taxa-or fail when such key taxa are not sampled. In this light, we here present the first attempt to investigate (though not conclusively resolve) animal relationships using genome-scale data from all phyla. Results from the site-heterogeneous CAT + GTR model recapitulate many established major clades, and strongly confirm some recent discoveries, such as a monophyletic Lophophorata, and a sister group relationship between Gnathifera and Chaetognatha, raising continued questions on the nature of the spiralian ancestor. We also explore matrix construction with an eye towards testing specific relationships; this approach uniquely recovers support for Panarthropoda, and shows that Lophotrochozoa (a subclade of Spiralia) can be constructed in strongly conflicting ways using different taxon- and/or orthologue sets. Dayhoff-6 recoding sacrifices information, but can also reveal surprising outcomes, e.g. full support for a clade of Lophophorata and Entoprocta + Cycliophora, a clade of Placozoa + Cnidaria, and raising support for Ctenophora as sister group to the remaining Metazoa, in a manner dependent on the gene and/or taxon sampling of the matrix in question. Future work should test the hypothesis that the few remaining uncertainties in animal phylogeny might reflect violations of the various stationarity assumptions used in contemporary inference methods.

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.

Putting keyhole limpets on the map: phylogeny and biogeography of the globally distributed marine family Fissurellidae (Vetigastropoda, Mollusca).

Fissurellidae are marine gastropods with a worldwide distribution and a rich fossil record. We integrate molecular, geographical and fossil data to reconstruct the fissurellid phylogeny, estimate divergence times and investigate historical routes of oceanic dispersal. With five molecular markers for 143 terminals representing 27 genera, we resolve deep nodes and find that many genera (e.g., Emarginula, Diodora, Fissurella) are not monophyletic and need systematic revision. Several genera classified as Emarginulinae are recovered in Zeidorinae. Future work should prioritize emarginuline genera to improve understanding of ancestral traits and the early evolution of fissurellids. Tree calibration with the fossilized birth-death model indicates that crown fissurellids originated around 175 Ma, and generally resulted in younger ages for the earliest nodes than the node dating approach. Model-based biogeographic reconstruction, supported by fossils, infers an Indo-West Pacific origin, with a westward colonization of new oceans via the Tethys Seaway upon the breakup of Pangea. Western Atlantic clades then served as source for dispersal towards other parts of the globe. As the sister group to all other fissurellids, Rimula is ranked in its own subfamily, Rimulinae stat. nov. New synonyms: Hemitominae syn. nov. of Zeidorinae stat. nov.; Cranopsissyn. nov. of Puncturella; Variegemarginulasyn. nov. of Montfortula.

Genomic signatures of evolution in Nautilus-An endangered living fossil.

Living fossils are survivors of previously more diverse lineages that originated millions of years ago and persisted with little morphological change. Therefore, living fossils are model organisms to study both long-term and ongoing adaptation and speciation processes. However, many aspects of living fossil evolution and their persistence in the modern world remain unclear. Here, we investigate three major aspects of the evolutionary history of living fossils: cryptic speciation, population genetics and effective population sizes, using members of the genera Nautilus and Allonautilus as classic examples of true living fossils. For this, we analysed genomewide ddRAD-Seq data for all six currently recognized nautiloid species throughout their distribution range. Our analyses identified three major allopatric Nautilus clades: a South Pacific clade, subdivided into three subclades with no signs of admixture between them; a Coral Sea clade, consisting of two genetically distinct populations with significant admixture; and a widespread Indo-Pacific clade, devoid of significant genetic substructure. Within these major clades, we detected five Nautilus groups, which likely correspond to five distinct species. With the exception of Nautilus macromphalus, all previously described species are at odds with genomewide data, testifying to the prevalence of cryptic species among living fossils. Detailed FST analyses further revealed significant genome-wide and locus-specific signatures of selection between species and differentiated populations, which is demonstrated here for the first time in a living fossil. Finally, approximate Bayesian computation (ABC) simulations suggest large effective population sizes, which may explain the low levels of population differentiation commonly observed in living fossils.

A family-level Tree of Life for bivalves based on a Sanger-sequencing approach.

The systematics of the molluscan class Bivalvia are explored using a 5-gene Sanger-based approach including the largest taxon sampling to date, encompassing 219 ingroup species spanning 93 (or 82%) of the 113 currently accepted bivalve families. This study was designed to populate the bivalve Tree of Life at the family level and to place many genera into a clear phylogenetic context, but also pointing to several major clades where taxonomic work is sorely needed. Despite not recovering monophyly of Bivalvia or Protobranchia-as in most previous Sanger-based approaches to bivalve phylogeny-our study provides increased resolution in many higher-level clades, and supports the monophyly of Autobranchia, Pteriomorphia, Heteroconchia, Palaeoheterodonta, Heterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata, Imparidentia, and Neoheterodontei, in addition to many other lower clades. However, deep nodes within some of these clades, especially Pteriomorphia and Imparidentia, could not be resolved with confidence. In addition, many families are not supported, and several are supported as non-monophyletic, including Malletiidae, Nuculanidae, Yoldiidae, Malleidae, Pteriidae, Arcidae, Propeamussiidae, Iridinidae, Carditidae, Myochamidae, Lyonsiidae, Pandoridae, Montacutidae, Galeommatidae, Tellinidae, Semelidae, Psammobiidae, Donacidae, Mactridae, and Cyrenidae; Veneridae is paraphyletic with respect to Chamidae, although this result appears to be an artifact. The denser sampling however allowed testing specific placement of species, showing, for example, that the unusual Australian Plebidonax deltoides is not a member of Donacidae and instead nests within Psammobiidae, suggesting that major revision of Tellinoidea may be required. We also showed that Cleidothaerus is sister group to the cementing member of Myochamidae, suggesting that Cleidothaeridae may not be a valid family and that cementation in Cleidothaerus and Myochama may have had a single origin. These results highlight the need for an integrative approach including as many genera as possible, and that the monophyly and relationships of many families require detailed reassessment. NGS approaches may be able to resolve the most recalcitrant nodes in the near future.

Cementing mussels to oysters in the pteriomorphian tree: a phylogenomic approach.

Mussels (Mytilida) are a group of bivalves with ancient origins and some of the most important commercial shellfish worldwide. Mytilida consists of approximately 400 species found in various littoral and deep-sea environments, and are part of the higher clade Pteriomorphia, but their exact position within the group has been unstable. The multiple adaptive radiations that occurred within Pteriomorphia have rendered phylogenetic classifications difficult and uncertainty remains regarding the relationships among most families. To address this phylogenetic uncertainty, novel transcriptomic data were generated to include all five orders of Pteriomorphia. Our results, derived from complex analyses of large datasets from 41 transcriptomes and evaluating possible pitfalls affecting phylogenetic reconstruction (matrix occupancy, heterogeneity, evolutionary rates, evolutionary models), consistently recover a well-supported phylogeny of Pteriomorphia, with the only exception of the most complete but smallest data matrix (Matrix 3: 51 genes, 90% gene occupancy). Maximum-likelihood and Bayesian mixture model analyses retrieve strong support for: (i) the monophyly of Pteriomorphia, (ii) Mytilida as a sister group to Ostreida, and (iii) Arcida as sister group to all other pteriomorphians. The basal position of Arcida is congruent with its shell microstructure (solely composed of aragonitic crystals), whereas Mytilida and Ostreida display a combination of a calcitic outer layer with an aragonitic inner layer composed of nacre tablets, the latter being secondarily lost in Ostreoidea.