Molecular Data from the 16S rRNA Gene for the Phylogeny of Pectinidae (Mollusca: Bivalvia)

The phylogenetic relationships among the species belonging to the family Pectinidae are still an issue of debate. The mitochondrial DNA sequences from the large ribosomal RNA gene may be of great value for systematic and phylogenetic studies within families. Partial sequences of the 16S rRNA gene were obtained for the scallop species Adamussium colbecki, Aequipecten opercularis, Chlamys glabra, C. islandica, C. varia, and Pecten jacobeus and compared with the published sequence of Pecten maximus. The present molecular data show that Chlamys are polyphyletic and do not support the assignment of these species to the two subfamilies Chlamydinae and Pectininae. Moreover, the minimal genetic distance between P. maximus and P. jacobeus suggests that they could belong to the same species. Received: 24 May 1999 / Accepted: 1 September 1999     

Phylogeny of families in the Pectinoidea (Mollusca: Bivalvia): importance of the fossil record

The Triassic fossil record points to the monophyly of the Pectinoidea (scallops), all members of which have a triangular resilium with a nonmineralized medial core that functions below the hinge line. The elastic properties of this resilium in extant taxa predict that the initial adaptation of the Pectinoidea was to swimming. This is indeed corroborated by the shell form of Pernopecten , the earliest known pectinoidean genus, which ranged from late Devonian to earliest Triassic. The new family Entolioididae, a largely Triassic group, provides the missing link between the Pernopectinidae and the families Propeamussiidae, Entoliidae, and Pectinidae, all of which originated by the Middle Triassic and survive to the present day. A new Triassic genus Filamussium shows that the Propeamussiidae originated from the Entolioididae, not directly from the Pernopectinidae as previously supposed. Evidence from morphology, the fossil record, and molecular genetics indicates that the family Spondylidae originated in the Middle Jurassic from an ancestor within the Pectinidae, possibly the genus Spondylopecten , which was already present in the Late Triassic. Journal compilation © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 148 , 313–342. No claim to original US government works     

Early Miocene Mollusca from McMurdo Sound,Antarctica (ANDRILL 2A drill core), with a review of Antarctic Oligocene and Neogene Pectinidae (Bivalvia)

Retrotapes andrillorum sp. nov., Hiatella cf. arctica (Linnaeus, 1767), ?Yoldia sp. (internal mould) and six taxa of Pectinidae are reported from the Burdigalian section of the ANDRILL 2A core, drilled in McMurdo Sound, Ross Sea. The pectinids are Adamussium cf. jonkersi Quaglio et al., 2010, Antarctipecten gen. nov. alanbeui (Jonkers, 2003), Austrochlamys forticosta sp. nov., Austrochlamys cf. marisrossensis Jonkers, 2003, Ruthipecten gen. nov., sp. nov. (not named) and a fragmentary specimen representing an unnamed genus and species. In a revision of Antarctic Pectinidae, Austrochlamys Jonkers, 2003, Ruthipecten gen. nov. (proposed for Chlamys (Zygochlamys) tuftsensis Turner, 1967, reported only from Wright Valley and the Vestfold Hills, not present in ANDRILL 2A), Leoclunipecten gen. nov. (proposed for Austrochlamys gazdzickii Jonkers, 2003, reported only from Oligocene rocks of King George Island, not present in ANDRILL 2A) and the unnamed genus in ANDRILL 2A are assigned to subfamily Chlamydinae, tribe Chlamydini, whereas Adamussium Thiele, 1934 and Antarctipecten gen. nov. are assigned to subfamily Palliolinae, tribe Adamussiini. The diverse Pectinidae in ANDRILL 2A suggest sea temperatures roughly 5°C warmer than at present in the Ross Sea during Early Miocene time.     

Ciliary ultrastructure of protobranchs (Mollusca, Bivalvia)

Abstract. The external epithelial cilia and other surface structures of the nuculoid protobranchs Nuculana pernula and Nucula nitidosa were studied. The gill lamellae and labial palps are partly covered with very long cilia. These have a modified slender distal portion, an ordinary metazoan-type basal body, a basal foot. and a single, long cross-striated rootlet. In cilia on the gills of N. nitidosa , the basal foot is thick and attaches to the next basal body directly behind. Unciliated surface areas on the gills, labial palps, and foot are covered with a dense brushborder of microvilli. We observed no specific homologies between the cilia of the protobranchs studied and the epidermal cilia of the enigmatic Xenoturbella bocki , hence the recent hypothesis of a close connection of the latter to the protobranch bivalves is questioned.     

Phylogeny of Veneroidea (Mollusca: Bivalvia) based on morphology and molecules

The largest Recent family of Bivalvia, the marine Veneridae with approximately 800 species, comprises one of the least understood and most poorly defined molluscan taxa, despite including some of the most economically important and abundant bivalves, for example quahog, Pismo clams, and Manila clams. A review of previous phylogenetic analyses including the superfamily Veneroidea (Veneridae, Petricolidae, Glauconomidae, Turtoniidae, Neoleptonidae) and within the Veneridae shows minimal taxon sampling leading to weak conclusions and few supported synapomorphies. New phylogenetic analyses on 114 taxa tested the monophyly of Veneroidea, Veneridae, and 17 nominal venerid subfamilies, using morphological (conchological, anatomical) data and molecular sequences from mitochondrial (16S, cytochrome oxidase I) and nuclear (28S, histone 3) genes. Morphological analyses using 45 exemplar taxa and 23 traditional characters were highly homoplastic and failed to reconstruct traditional veneroid classification. Full morphological analyses (31 characters) supported the monophyly of Veneroidea and Veneridae but only when certain taxa were excluded, revealing analytical difficulties caused by a suite of characters associated with neotenous or miniaturized morphology. Molecular analyses resulted in substantially higher clade consistency. The combined molecular data set resulted in significant support for a particular topology. The monophyly of Veneridae was supported only when Petricolidae and Turtoniidae were subsumed, and recognized as members with derived or neotenous morphologies, respectively. Morphological character mapping on molecular trees retained a high level of homoplasy, but revealed synapomorphies for major branch points and supported six subfamily groups (Dosiniinae, Gemminae, Samarangiinae, Sunettinae, Tapetinae, combined Chioninae + Venerinae). Glauconomidae and Neoleptonidae are provisionally maintained in Veneroidea pending further study; Petricolinae and Turtoniinae are placed in Veneridae. © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society, 2006, 148 , 439–521.     

软体动物系统发育研究进展

软体动物是动物界仅次于节肢动物的第二大门类.长期以来,其系统位置及其系统发育关系一直争议颇多.简述了软体动物的分类及系统学研究概况,重点介绍了近年来18SrRNA和28SrRNA基因的分子系统学研究进展.同时就软体动物系统学研究中存在的问题和前景作了分析和展望.     

Type specimens of Pectinidae (Mollusca: Bivalvia) described by Linnaeus (1758–1771)

Linnaeus listed and described (as Ostrea species) 20 recent pectinid species in the 10th edition of his Systema Naturae and one pectinid species in his Mantissa. These are now placed in 17 genera of the family Pectinidae. Nine species are cited to Museum Ludovicae Ulricae. Ten primary types are present in the Linnéan Society of London, and the same number in die Zoological Museum of die Uppsala University. Two lectotypes were designated recendy by Smith and Waller; 18 lectotypes and one neotype are selected herein. Nine of the species are type species of currently accepted pectinid genera. Seven new type localities are also designated for species which had unknown or erroneous type localities, and six are more restricted. Potential type material of eight species is also traced in the Gualtieri collection of the Museo di Storia Naturale e del Territorio at Certosi di Calci (Italy).     

Reconstructing the Anomalodesmata (Mollusca: Bivalvia): morphology and molecules

The extant anomalodesmatan bivalves have always proved rather enigmatic and difficult to interpret, both in terms of their relationships to other bivalve taxa and the interrelationships of the constituent families. These difficulties stem from their diverse and often highly specialized life habits which have resulted in a wide array of disparate morphologies, and also from the fact that many are extremely rare. Classifications based on morphological characters have been dogged by fears that convergent and parallel evolution has masked phylogenetic signals. Molecular surveys of members of 12 of the 15 constituent families, using the 18S rRNA gene, have revealed that anomalodesmatans are robustly monophyletic and lie within the basal heterodonts. The Anomalodesmata should no longer be regarded as a subclass, but as a part of the Heterodonta. Here we present an enhanced analysis of 32 anomalodesmatan species (representatives of 12 families). Our results, subjected to Maximum Parsimony, Maximum Likelihood and Bayesian analyses, challenge our understanding of the internal relationships within the Anomalodesmata. In particular they indicate the need for a re-distribution of the families traditionally placed in the Thracioidea and Pandoroidea into a 'thraciid' lineage (Thraciidae + Cleidothaeridae + Myochamidae) and a 'lyonsiid' lineage (polyphyletic Lyonsiidae + Clavagellidae + Laternulidae + Pandoridae). The endolithic Clavagella and endobenthic Brechites and Penicillus form a robust clade. The hypothesis that the carnivorous septibranchs are monophyletic can, thus far, be neither supported nor rejected. Mapping critical morphological characters onto our molecular results provides evidence of multiple loss of some characters (e.g. prismato-nacreous shell microstructure and shell spicules) and also multiple gain of others (e.g. chondrophores).  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 148 , 395–420.     

Phylogeny of Veneridae (Bivalvia) based on mitochondrial genomes

Veneridae is one of the most diverse families of bivalve molluscs. However, their phylogenetic relationships among subfamilies have been debated for years. To explore phylogenetic relationships of Veneridae, we sequenced 13 complete mitochondrial genome sequences from eight subfamilies and compared with available complete mitochondrial genome of other Veneridae taxa (18 previously reported sequences). Phylogenetic analyses using probabilistic methods recovered two highly supported clades. In addition, the protein‐coding gene order revealed a highly conserved pattern among the same subclade lineages. According to our molecular analyses, Tapetinae should be recognized as a valid subfamily, but the genera formed para‐polyphyletic clades. Chioninae was recovered not monophyletic that differs from a previously molecular phylogeny. Furthermore, the reconstructed chronogram calibrated with fossils recovered the Veneridae have originated during the early Permian (about 290 million years ago). Noticeably, programmed frameshift was found in the nad4 gene of Leukoma jedoensis, Anomalodiscus squamosus and Antigona lamellaris and cob gene of L. jedoensis. This is the first time that the presence of the programmed frameshift has been found in the protein‐coding genes of Heterodonta species. Our results improved the phylogenetic resolution within Veneridae, and a more taxonomic sampling analysis of the subfamily Chioninae is supposed to construct.     

Chromosome rearrangements in Pectinidae (Bivalvia: Pteriomorphia) implied based on chromosomal localization of histone H3 gene in four scallops

Chromosomal structural rearrangement in four scallops, Chlamys farreri (n = 19), Patinopecten yessoensis (n = 19), Chlamys nobilis (n = 16) and Argopecten irradians (n = 16), was studied by fluorescence in situ hybridization using histone H3 gene probes. The results show that histone H3 gene sites differ strikingly with regard to number, location, and intensity among, or even within these species. For example, two histone H3 gene loci were detected on the metaphase chromosomes of P. yessoensis, while one locus was found in the others. In P. yessoensis, differing intensities of hybridization signals were detected between homologues 5 and 11, and within homologue 11. These data suggest that the histone H3 gene is a qualified chromosome marker for the preliminary understanding of the historical chromosomal reconstructing of the Pectinidae family. The variable distribution patterns of the histone H3 gene suggest that gene duplication/diminution as well as chromosome rearrangements by inversion and translocation may have played important roles in the genomic evolution of Pectinidae. We also compiled our present results with former published data regarding the chromosome mapping of rDNAs in species of the Pectinidae family. Such comparative chromosomal mapping should improve our understanding of historical chromosomal reconstructions of modern-day scallops.     

Morphological perspective on the classification and evolution of Recent Pterioidea (Mollusca: Bivalvia)

The evolutionary relationships of the Recent Pterioidea are inferred from a phylogenetic analysis of representatives of all pterioidean genera based on original observations of anatomy and shell morphology, and an extensive survey of bivalve literature. The well-resolved cladogram supports monophyly for the superfamily, but renders all but one family (the monotypic Pulvinitidae) polyphyletic. In addition, these results reveal a considerable level of convergence and parallelisms through the Pterioidea. The branching order of pterioid genera in the morphological analysis is largely corroborated by the sequence of their appearance in the fossil record. The palaeontological evidence provides important information on dating lineage splitting events and transitional taxa. The proposed phylogeny integrates the cladistic analysis of the Recent Pterioidea with the fossil record and suggests that the crown-group pterioideans probably originated in the Triassic from the Bakevelliidae, an extinct paraphyletic stem group from which the Ostreoidea are also ultimately derived.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 148 , 253–312.     

The karyotype of Nodipecten nodosus (Bivalvia: Pectinidae)

Earlier karyotypical work on Nodipecten nodosus embryos indicated that this species has a diploid number of 38, with six pairs respectively of metacentric and submetacentric chromosomes and seven pairs of subtelocentric chromosomes, although there were some difficulties in obtaining complete metaphases. The present work provides additional results on specific regions of the chromosomes in N. nodosus and, by meiotic studies, confirms the chromosome number with more reliability. Active nucleolar organizer regions (NOR), detected in mitotic metaphases from embryos, can be characterized in N. nodosus by a high level of heteromorphism of NOR-sites, indicating that these regions are not appropriate as chromosomal markers in this species. The procedure for detecting constitutive heterochromatin of chromosomes allowed us to observe most of the heterochromatic blocks at a pericentromeric position and some at telomeric and interstitial positions. The analysis of meiotic chromosomes from gonad tissue revealed the presence of 19 bivalents during metaphase I, all homomorphic and isopicnotic, confirming the previously described diploid chromosomal number of 38 for N. nodosus. From these results, some evolutionary aspects of the Pectinidae are briefly discussed.     

DNA barcoding and phylogenetic analysis of Pectinidae (Mollusca: Bivalvia) based on mitochondrial COI and 16S rRNA genes

DNA sequence data enable not only the inference of phylogenetic relationships but also provide an efficient method for species-level identifications under the terms DNA barcoding or DNA taxonomy. In this study, we have sequenced partial sequences of mitochondrial COI and 16S rRNA genes from 63 specimens of 8 species of Pectinidae to assess whether DNA barcodes can efficiently distinguish these species. Sequences from homologous regions of four other species of this family were gathered from GenBank. Comparisons of within and between species levels of sequence divergence showed that genetic variation between species exceeds variation within species. When using neighbour-joining clustering based on COI and 16S genes, all species fell into reciprocally monophyletic clades with high bootstrap values. These evidenced that these scallop species can be efficiently identified by DNA barcoding. Evolutionary relationships of Pectinidae were also examined using the two mitochondrial genes. The results are almost consistent with Waller’s classification, which was proposed on the basis of shell microstructure and the morphological characteristics of juveniles.     

Phylogeny and comparative genomic analysis of Pteriomorphia (Mollusca: Bivalvia) based on complete mitochondrial genomes

The subclass Pteriomorphia is a morphologically diverse and economically important group of Mollusca. We retrieved 42 mitochondrial genomes (mtGenomes) of Pteriomorphia and concatenated protein-coding genes, rRNAs and tRNAs to assess phylogenetic relationships and divergence times among the families with maximum likelihood (ML) and Bayesian inference (BI) analyses. Both ML and BI analyses strongly support the same topology except for the position of Atrina pectinata. Our study confirms the monophyly of the families Arcidae, Mytilidae, Pteriidae, Ostreidae and Pectinidae. Within Pteriomorphia, we recovered two clusters, one comprising Mytilidae, Arcidae and Pectinidae, the other consisting of Ostreidae, Pteriidae and Pinnidae, but we did not confirm a basal position for any family. The phylogenetic trees suggest that Ostreidae, Pteriidae and Pinnidae should be grouped as the order Ostreoida. Divergence times of major families are estimated as follows: Arcidae, 315.9 Ma; Pectinidae, 384.4 Ma; Ostreidae, 240.8 Ma; Mytilidae, 390.8 Ma. Comparative analysis indicates a low-level codon usage bias (with an average of 50.29) in mtGenomes of Pteriomorphia. In Mytilidae and Ostreidae, the codon usage bias was under mutation pressure rather than selection. Contrastingly, mutation is not the main factor in defining the codon usage in Pectinidae and Pteriidae. Among Ostreidae, Pectinidae and Mytilidae, Ka/Ks ratios range from 0.00 to 1.22 and most values (89.11%) are less than 0.20, indicating that most genes are under strong negative or purifying selection. The protein-coding gene orders show dramatically different patterns in Pteriomorphia. There is no gene block even consisting of two genes that is shared by five families.     

Molecular phylogeny of the family Pectinidae (Mollusca: Bivalvia) based on mitochondrial 16S and 12S rRNA genes

Pectinidae is a large bivalve family characterised by almost circular, flat shells. Species are distributed worldwide and fall into three life-styles: swimming, byssally attached to hard substrates, and cemented to rocks with one valve. Despite these very different life strategies, pectinid shells are highly conservative in shape and offer few clues for the unravelling of phylogenetic issues. Consequently, phylogenetic studies based on morphological features have not yielded conclusive results. We thus set out to analyse partial sequences of mitochondrial 12S and 16S rRNA genes from 23 species of 16 genera with molecular techniques. The results are largely in contrast, both at the genus and the subfamily level, with the systematic classifications based on adult morphological characters, whereas they agree with the morphological classifications based on the more conserved non-adaptive features.     

Molecular phylogenetics of the Pectinidae (Mollusca: Bivalvia) and effect of increased taxon sampling and outgroup selection on tree topology

Evolutionary relationships of the Pectinidae were examined using two mitochondrial genes (12S rRNA, 16S rRNA) and one nuclear gene (Histone H3) for 46 species. Outgroup taxa from Propeamussidae, Spondylidae and Limidae were also sequenced to examine the impact of outgroup choice on pectinid topologies. Our phylogenetic analyses resolved the Pectinidae as monophyletic, but many of the subfamilies and tribes within the family do not form monophyletic clades. The paraphyletic Aequipectinini group is the most basal member of the Pectinidae, with the Chlamydinae and Palliolinae representing the most recently derived pectinid groups. These results are in contrast with the current morphological hypothesis of Pectinidae evolution, which suggests the Chlamydinae and Pallioline are basal groups within the Pectinidae. Ingroup topology was found to be sensitive to outgroup choice and increasing taxon sampling within the Pectinidae resulted in more robust phylogenies.     

Molecular phylogeny of Anomalodesmata (Mollusca: Bivalvia) inferred from 18S rRNA sequences

The origin of the anomalodesmatan bivalves and the relationships of the constituent families are far from being settled. Phylogenetic uncertainties result from the morphological heterogeneity of the Anomalodesmata and from parallel/convergent evolution of several character complexes due to similar life habits. Here, we assess these problems with 26 near-complete anomalodesmatan 18S rRNA sequences from 12 out of 15 families and a selection of heteroconch outgroup taxa. The robustly monophyletic Anomalodesmata share insertions in the V2 and V4 expansion regions. Both parsimony and maximum-likelihood analyses confirm their position among the basal heterodonts rooting between Carditidae and Lucinidae or, together with the latter, between Carditidae and the remaining Heterodonta. There is no support for monophyletic Myoida, nor for a close relationship of Anomalodesmata with any myoid taxon. At the base of the Anomalodesmata is an unstable cluster of long-branch species belonging to the Poromyidae, Verticordiidae, Lyonsiellidae and Thraciidae. The remaining Anomalodesmata split consistently but with varying branch support into three major clades: the Cuspidariidae excluding Myonera ; a 'thraciid' clade consisting of (Euciroidae, ( Myonera ( Thracia, Cleidothaerus , Myochamidae))); and a 'lyonsiid' clade with Laternulidae, Pandoridae, diphyletic Lyonsiidae due to a robust clade of Lyonsia norwegica and the clavagellid Brechites vaginiferus . Tests of various alternative topologies showed that all are significantly longer but optimal likelihood trees with monophyletic carnivorous taxa and/or Thraciidae are not significantly less likely. These results differ greatly from previous morphological studies. Palaeontological data and homology decisions for selected characters are evaluated in the light of the molecular trees.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 139 , 229–246.     

Spermatozoa of the Anomalodesmata (Bivalvia, Mollusca) with special reference to relationships within the group

Sperm ultrastructure in the marine bivalve order Anomalodesmata is considered in the light of new information for Australian Myochama anomioides and Cuspidaria latesulcata . In M. anomioides , the acrosomal complex lies posterior to the nucleus, in contact with the asymmetrical midpiece mitochondria – an unusual configuration reported from most of the studied Anomalodesmata. Spermatozoa of M. anomioides resemble those of Myadora brevis (both in family Myochamidae). Myochamid spermatozoa are considerably less modified than those of the Lyonsiidae or Laternulidae, and may prove a basal type within the non-septibranch anomalodesmatans. In contrast, C. latesulcata differs from other examined anomalodesmatans in having an anterior acrosomal complex and radial midpiece mitochondria (classic aquasperm features). Sperm data for the Anomalodesmata are limited but congruent with the most recent phylogenetic analyses that recognize distinct 'thraciid' and 'lyonsiid' clades. Results for C. latesulcata suggest septibranch origins before the development of a posteriorly positioned acrosomal complex and mitochondrial asymmetry.