Complete mtDNA sequence of the North American freshwater mussel,Lampsilis ornata (Unionidae): an examination of the evolution and phylogenetic utility of mitochondrial genome organization in Bivalvia (Mollusca)

Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. Two factors inhibiting our understanding the evolution of gene rearrangement in bivalves are inadequate taxonomic sampling and failure to examine gene order in a phylogenetic framework. Here, we report the first complete nucleotide sequence (16,060 bp) of the mitochondrial (mt) genome of a North American freshwater bivalve, Lampsilis ornata (Mollusca: Paleoheterodonta: Unionidae). Gene order and mt genome content is examined in a comparative phylogenetic framework for Lampsilis and five other bivalves, representing five families. Mitochondrial genome content is shown to vary by gene duplication and loss among taxa and between male and female mitotypes within a species. Although mt gene arrangement is highly variable among bivalves, when optimized on an independently derived phylogenetic hypothesis, it allows for the reconstruction of ancestral gene order states and indicates the potential phylogenetic utility of the data. However, the interpretation of reconstructed ancestral gene order states must take in to account both the accuracy of the phylogenetic estimation and the probability of character state change across the topology, such as the presence/absence of atp8 in bivalve lineages. We discuss what role, if any, doubly uniparental inheritance (DUI) and recombination between sexual mitotypes may play in influencing gene rearrangement of the mt genome in some bivalve lineages.     

On the controversial questions of the taxonomy of Bivalvia (Mollusca): Too many species or too few characters?

Problems emerging in the course of taxonomic studies and species diagnostics of freshwater bivalves are discussed by the example of one of the bivalve groups (the family Unionidae). It is shown that one of the causes of the current, diametrically opposing views on specific and generic systematics of Bivalvia is the fact that researchers revising taxonomic groups ignore complex analysis of several independent characters (conchological, anatomical, biochemical, genetic, etc.).     

中国寒武纪双壳类研究之评述

长期以来,双壳类研究者虽未将扬于蛤(Yangtzedonta Yu)纳入到双壳类早期系统演化的研究范畴,支却又难以予以完全否定。最近,钱逸的工作终于解决了这一悬案,这是寒武纪带壳软体动物研究的一项重要进展。然而,钱逸对双壳类早期演化的理解仍存在着误解,例如,将Xianfengoconcha Zhang当作是“最古老的双壳类”,为此有必要对近二十年来我国寒武纪双壳类的研究进行回顾与总结。Xianfengoconcha发育有两侧对称排列的所谓“片状齿”,实属腕足类小圆货贝型铰合构造。化石证据表明,真正的片状齿是由古栉齿型铰齿演化而来,因此,古异齿型不是双壳类最古老的铰齿类型。目前,我国没有争议的寒武纪双壳类只有．Pojetaia Jell一属。     

Calcification in the bivalve periostracum

The periostracum in certain bivalves is imbedded with calcified, spiculelike structures analogous if not homologous to cuticular spicules found in the Aplacophora and Polyplacophora (chitons). Although rare or absent in most living bivalves, calcified periostracal structures are apparently an ancestral feature in some bivalve groups, i.e. the Mytilacea, Permophoridae, Myoida. and Anomalodesmata. Ancestors of the Bivalvia and Polyplacophora may have been covered with a flexible, spiculestudded cuticle. Shell plates in these two classes may have originated through a modification of the mechanism of spiculelike cuticular calcification. resulting in a primordial shell with simple prismatic structure.     

Spatio‐temporal transitions in Paleozoic Bivalvia: A field comparison of upper Ordovician and upper Paleozoic bivalve‐dominated fossil assemblages

Because of the uncertain relationship between relative abundance and taxonomic richness, abundance data are potentially critical components in any analysis of faunal dominance within fossil assemblages. However, such data are often not available in the literature. In this paper, relative abundance data collected during field work at 25 Upper Ordovician and 22 Upper Pennsylvanian to mid‐Permian localities are used to evaluate Paleozoic transitions in the environmental distributions of bivalve molluscs. On the basis of multivariate analyses of these data, it is shown that even early in their history, during the Ordovician, bivalves were generally not restricted in abundance to just marginal environments. They apparently thrived in terrigenous—dominated regions, both nearshore and offshore, but were less abundant in carbonate settings. However, by the late Paleozoic, bivalve abundances had increased in some carbonate environments, in part because of the growing abundances of free‐burrowing suspension‐feeders, which had been substantially less abundant even in terrigenous environments earlier in the Paleozoic. The results of this study corroborate those of a companion analysis, using literature‐derived data, of paleoenvironmental diversity transitions exhibited by Paleozoic Bivalvia.     

Stages in the ontogeny and a model of the evolution of bivalves (Mollusca)

Comparison of the ontogenies of bivalves of different habitats and systematic position provide two main conclusions. The first is that bivalves stick to a certain basic program of ontogeny which can be divided into six phases. The first three phases are parallel to those of some other invertebrates, the 4th phase is parallel to that of conchiferan molluscs, with, the 5th phase, bivalve characters are acquired, and in the 6th phase, genus-specific adult organization is reached. The second is that within this basic developmental programm specific differences occur. The ontogeny ofTeredora is similar to that of many marine bivalves and is characterized by a strong plasticity. The adult, in contrast, is highly specialized for living within wood. InAnodonta, the opposite is true and embryonic development even includes a parasitic stage, while the adult is of a more general organization. Due to brood-protection and embryonic nursing, the whole organogenesis ofSphaerium becomes directed towards adult organization. Ontogenetic development of a general body plan of the Bivalvia provides a model for the evolution of the first bivalves (protobranchs excluded) from univalves by a one-step alteration connected with shell mineralization and loss of the buccal mass affecting the embryo near end of embryogenesis.     

双壳纲贝类18S rRNA基因序列变异及系统发生

双壳纲贝类栖息于环境多变的海域,是一个形态学和生态学都具有多样性的类群,清晰而可靠的进化关系对于养殖与相关种类的管理具重要意义。然而,目前对双壳类宏观分子系统学研究的报道较少。研究用18S rRNA基因(18S)分析了双壳类3个亚纲贝类的系统发育关系。从GenBank下载帘蛤目、海螂目、贻贝目、胡桃蛤目、蚶目、珍珠贝目6个目94个种类的18S全/部分序列107个,通过ClustalX软件进行序列比对, 用MEGA4.1软件和PHyML软件计算遗传距离, 构建系统发育树, 研究了双壳类18S变异规律及其在系统发生研究中的应用。结果显示18S有插入/缺失序列, 存在长度多态性。序列比对显示有5段约30 70bp的保守区, 4段约130 550bp的高变区。碱基组成平均为T:24.4%, C:23.6%, A:24.5%, G:27.5%。G+C含量为51.1%。在1796个比对位点中, 变异位点占31.7%, 简约信息位点占24.0%。目内科间遗传距离为0.003 0.043, 目间遗传距离为0.026 0.093。NJ树和ML树显示贻贝目、珍珠贝目、胡桃蛤目、蚶目和海螂目的缝栖蛤科先分别聚为支持率很高(BPN=94 100)的单系支, 后聚为一大支(BPN=100)。蛤蜊科与帘蛤目的其他科分离形成一置信度很高的单系支(BPN=93)。帘蛤科种类聚为置信度较低(BPN=60)的一支。海螂目、帘蛤目的种类没能完全聚到所属支系, 彼此嵌套,缝栖蛤科的种类从海螂目中分离出来。18S资料揭示帘蛤目的蛤蜊科、海螂目的缝栖蛤科已经进化为独立的支系。     

Phylogenetic analysis of four nuclear protein-encoding genes largely corroborates the traditional classification of Bivalvia (Mollusca)

Revived interest in molluscan phylogeny has resulted in a torrent of molecular sequence data from phylogenetic, mitogenomic, and phylogenomic studies. Despite recent progress, basal relationships of the class Bivalvia remain contentious, owing to conflicting morphological and molecular hypotheses. Marked incongruity of phylogenetic signal in datasets heavily represented by nuclear ribosomal genes versus mitochondrial genes has also impeded consensus on the type of molecular data best suited for investigating bivalve relationships. To arbitrate conflicting phylogenetic hypotheses, we evaluated the utility of four nuclear protein-encoding genes-ATP synthase β, elongation factor-1α, myosin heavy chain type II, and RNA polymerase II-for resolving the basal relationships of Bivalvia. We sampled all five major lineages of bivalves (Archiheterodonta, Euheterodonta [including Anomalodesmata], Palaeoheterodonta, Protobranchia, and Pteriomorphia) and inferred relationships using maximum likelihood and Bayesian approaches. To investigate the robustness of the phylogenetic signal embedded in the data, we implemented additional datasets wherein length variability and/or third codon positions were eliminated. Results obtained include (a) the clade (Nuculanida+Opponobranchia), i.e., the traditionally defined Protobranchia; (b) the monophyly of Pteriomorphia; (c) the clade (Archiheterodonta+Palaeoheterodonta); (d) the monophyly of the traditionally defined Euheterodonta (including Anomalodesmata); and (e) the monophyly of Heteroconchia, i.e., (Palaeoheterodonta+Archiheterodonta+Euheterodonta). The stability of the basal tree topology to dataset manipulation is indicative of signal robustness in these four genes. The inferred tree topology corresponds closely to those obtained by datasets dominated by nuclear ribosomal genes (18S rRNA and 28S rRNA), controverting recent taxonomic actions based solely upon mitochondrial gene phylogenies.     

On bivalve phylogeny: a high-level analysis of the Bivalvia (Mollusca) based on combined morphology and DNA sequence data

Abstract. Bivalve classification has suffered in the past from the crossed-purpose discussions among paleontologists and neontologists, and many have based their proposals on single character systems. More recently, molecular biologists have investigated bivalve relationships by using only gene sequence data, ignoring paleontological and neontological data. In the present study we have compiled morphological and anatomical data with mostly new molecular evidence to provide a more stable and robust phylogenetic estimate for bivalve molluscs. The data here compiled consist of a morphological data set of 183 characters, and a molecular data set from 3 loci: 2 nuclear ribosomal genes (18S rRNA and 28S rRNA), and 1 mitochondrial coding gene (cytochrome c oxidase subunit I), totaling ∼3 Kb of sequence data for 76 molluscs (62 bivalves and 14 outgroup taxa). The data have been analyzed separately and in combination by using the direct optimization method of Wheeler (1996), and they have been evaluated under 12 analytical schemes. The combined analysis supports the monophyly of bivalves, paraphyly of protobranchiate bivalves, and monophyly of Autolamellibranchiata, Pteriomorphia, Heteroconchia, Palaeoheterodonta, and Heterodonta s.l., which includes the monophyletic taxon Anomalodesmata. These analyses strongly support the conclusion that Anomalodesmata should not receive a class status, and that the heterodont orders Myoida and Veneroida are not monophyletic. Among the most stable results of the analysis are the monophyly of Palaeoheterodonta, grouping the extant trigoniids with the freshwater unionids, and the sister-group relationship of the heterodont families Astartidae and Carditidae, which together constitute the sister taxon to the remaining heterodont bivalves. Internal relationships of the main bivalve groups are discussed on the basis of node support and clade stability.     

Doubly uniparental inheritance (DUI) of mitochondrial DNA in Donax trunculus (Bivalvia: Donacidae) and the problem of its sporadic detection in Bivalvia

Mitochondrial DNA is transmitted maternally in metazoan species. This rule does not hold in several species of bivalves that have two mtDNA types, one that is transmitted maternally and the other paternally. This system of mitochondrial DNA transmission is known as doubly uniparental inheritance (DUI). Here we present evidence of DUI in the clam Donax trunculus making Donacidae the sixth bivalve family in which the phenomenon has been found. In addition, we present the taxonomic affiliation of all species in which DUI is currently known to occur and construct a phylogeny of the maternal and paternal genomes of these species. We use this information to address the question of a single or multiple origins of DUI and to discuss whether failed attempts to demonstrate the presence of DUI in several bivalve species might be due to problems of detection or to genuine absence of the phenomenon.     

LVTree Viewer:An Interactive Display for the All-Species Living Tree Incorporating Automatic Comparison with Prokaryotic Systematics

We describe an interactive viewer for the All-Species Living Tree (LVTree). The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. It also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. The system reports taxon statistics at all ranks automatically after each collapsing and re-collapsing. These features greatly facilitate the compar-ison of the 16S rRNA sequence phylogeny with prokaryotic taxonomy in a taxon by taxon manner. In view of the fact that the present prokaryotic systematics is largely based on 16S rRNA sequence analysis, the current viewer may help reveal discrepancies between phylogeny and taxonomy. As an application, we show that in the latest release of LVTree, based on 11,939 rRNA sequences, as few as 24 lineage modifications are enough to bring all but two phyla (Proteobacteria and Firmicutes) to monophyletic clusters.     

Metabolic dominance of bivalves predates brachiopod diversity decline by more than 150 million years

Brachiopods and bivalves feed in similar ways and have occupied the same environments through geological time, but brachiopods were far more diverse and abundant in the Palaeozoic whereas bivalves dominate the post-Palaeozoic, suggesting a transition in ecological dominance 250 Ma. However, diversity and abundance data alone may not adequately describe key changes in ecosystem function, such as metabolic activity. Here, we use newly compiled body size data for 6066 genera of bivalves and brachiopods to calculate metabolic rates and revisit this question from the perspective of energy use, finding that bivalves already accounted for a larger share of metabolic activity in Palaeozoic oceans. We also find that the metabolic activity of bivalves has increased by more than two orders of magnitude over this interval, whereas brachiopod metabolic activity has declined by more than 50%. Consequently, the increase in bivalve energy metabolism must have occurred via the acquisition of new food resources rather than through the displacement of brachiopods. The canonical view of a mid-Phanerozoic transition from brachiopod to bivalve dominance results from a focus on taxonomic diversity and numerical abundance as measures of ecological importance. From a metabolic perspective, the oceans have always belonged to the clams.     

Reconstruction of phylogenetic relationships within Grapsidae (Crustacea: Brachyura) and comparison of trans-isthmian versus amphi-atlantic gene flow based on mtDNA

Following taxonomic revisions in recent years, the originally large family Grapsidae MacLeay, 1838 has become a relatively small and morphologically homogeneous family in terms of adult and larval morphology. Most available molecular studies including more than one genus of the family have also suggested monophyly of the corresponding taxa. However, no single phylogenetic study has ever included all constituent genera of the Grapsidae. In the current study, a molecular phylogeny based on sequences of the mitochondrial 16S rRNA gene from all eight grapsid genera and 34 species is presented and suggests that up to four genera are not monophyletic. This is mainly due to the polyphyletic nature of the genus Pachygrapsus which can be found in six different lineages of the phylogeny, suggesting that the genus currently does not represent a single evolutionary lineage and is in need of taxonomic revision. Amphi-atlantic and trans-isthmian species pairs or populations in four genera are compared and reveal relatively constant and pronounced divergences across the Panama Isthmus as opposed to moderate divergences across the Atlantic Ocean, thereby suggesting occurrence of gene flow across the Atlantic Ocean during the past three million years.     

The broadcast spawning Caribbean shipworm,Teredothyra dominicensis (Bivalvia,Teredinidae), has invaded and become established in the eastern Mediterranean Sea

Teredinids, commonly referred to as shipworms, are wood-boring bivalves estimated to cause over one billion dollars’ worth of damage to submerged wooden structures per annum. This paper reports the detection and establishment of the Caribbean shipworm Teredothyra dominicensis (Bivalvia, Teredinidae) in the eastern Mediterranean Sea. Identification was confirmed using an integrative taxonomical approach combining morphology, morphometry and molecular markers (COI-5P and 18S), thus improving both the taxonomic resolution and tractability of this invasive species. Sequence comparisons between indigenous Caribbean and Mediterranean specimens were at least 99 % identical. Wooden panels placed at the site of discovery were infested exclusively by T. dominicensis with specimens of varying size and age, indicating multiple settlement events and the presence of breeding populations in the region. Anatomical and behavioural observations confirm the species as a broadcast spawner with larvae undergoing planktotrophic development, thus distribution range is potentially extensive. Of the possible introduction vectors, transport via ballast water is proposed as the most likely. The establishment of breeding populations of a tropical teredinid in the Mediterranean is of considerable concern as tropical species are particularly destructive and degrade wood more rapidly than the species currently found in the region. This threat is likely to increase in severity due to global warming, as increases in temperature and salinity may lead to an increase in the distribution range, development rate and boring activity of teredinids.     

Species composition,richness, and distribution of marine bivalve molluscs in Bahía de Mazatlán,México

We describe the composition and distribution of bivalve molluscs from the sandy and rocky intertidal and the shallow subtidal environments of Bahía de Mazatlán, México. The bivalve fauna of the bay is represented by 89 living species in 28 families, including 37 new records and four range extensions: Lithophaga hastasia, Adula soleniformis, Mactrellona subalata, and Strigilla ervilia. The number of species increases from the upper (44) and lower intertidal (53) to the shallow subtidal (76), but only 11 (17%) have a wide distribution in the bay (i.e., found in all sampling sites and environments). The bivalve assemblages are composed of four main life forms: 27 epifaunal species, 26 infaunal, 16 semi-infaunal, and 20 endolithic. A taxonomic distinctness analysis identified the sampling sites and environments that contribute the most to the taxonomic diversity (species to suborder categories) of the bay. The present work increased significantly (31%) to 132 species previous inventories of bivalves of Bahía de Mazatlán. These species represent 34% of the bivalve diversity of the southern Golfo de California and approximately 15% of the Eastern Tropical Pacific region.     

Evidence of predation in Early Cretaceous unionoid bivalves from freshwater sediments in the Cameros Basin,Spain

Here, we present evidence of possible vertebrate predation on freshwater bivalves from the Lower Cretaceous strata of the Cameros Basin (Spain). The described collection contains the largest number of vertebrate‐inflicted shell injuries in freshwater bivalve shells yet reported in the Mesozoic continental record. Several types of shell damage on fossil shells of Protopleurobema numantina (Bivalvia: Unionoida) are described and their respective modes of formation interpreted in the context of morphological attributes of the shell injuries and the inferred tooth morphology of predators that could have inflicted such injuries. Detailed study of these bite marks shows similarities with the well‐documented injuries in the shells of marine molluscs, namely ammonoids, that have likewise been attributed to reptilian predators. The most parsimonious interpretation suggests crocodiles as the vertebrates interacting with the bivalves in the Cameros Basin. □Barremian–Aptian; bite marks; freshwater bivalves; predation; reptile; Unionoida.     

Bayesian estimation of ancestral character states on phylogenies

Biologists frequently attempt to infer the character states at ancestral nodes of a phylogeny from the distribution of traits observed in contemporary organisms. Because phylogenies are normally inferences from data, it is desirable to account for the uncertainty in estimates of the tree and its branch lengths when making inferences about ancestral states or other comparative parameters. Here we present a general Bayesian approach for testing comparative hypotheses across statistically justified samples of phylogenies, focusing on the specific issue of reconstructing ancestral states. The method uses Markov chain Monte Carlo techniques for sampling phylogenetic trees and for investigating the parameters of a statistical model of trait evolution. We describe how to combine information about the uncertainty of the phylogeny with uncertainty in the estimate of the ancestral state. Our approach does not constrain the sample of trees only to those that contain the ancestral node or nodes of interest, and we show how to reconstruct ancestral states of uncertain nodes using a most-recent-common-ancestor approach. We illustrate the methods with data on ribonuclease evolution in the Artiodactyla. Software implementing the methods (BayesMultiState) is available from the authors.     

What can 18S rDNA do for bivalve phylogeny?

Molecular characteristics, especially 18S rDNA sequences, may be of great value for the study of bivalve evolution and its numerous morphological convergencies once the reliability of these data can be evaluated. The analysis of 11 published complete molluscan sequences and two new ones,Arca noae andAtrina pectinata, reveals considerable differences in relative substitution rates. The gastropod and eulamellibranch species have the fastest and Atrina species have the slowest rates. Two methods are used to assess the information contents of the dataset in addition to bootstrap analysis, spectral analysis, and the “pattern of resolved nodes” technique. Tree reconstructions by parsimony, neighbor-joining, and maximum-likelihood differ in regard to the position of the eulamellibranch family Mactridae and ofCrassostrea. Although there is a signal for the monophyly of Bivalvia, Mactridae cluster with Gastropoda in most runs, rendering Bivalvia diphyletic. The position ofCrassostrea was extremely variable, probably due to the high substitution rate of this species.Atrina roots deeper thanArca in all trees, although a corresponding signal in spectral analysis is absent. Phylogenetic signals among the three pectinid species are low but sufficient to resolve the branching pattern. The tree inferred from the 18S rDNA and from morphological data has Bivalvia monophyletic with a basal polytomy of Mactridae,Crassostrea, and the remaining Pteriomorphia, whereArca branches off before Atrina and the Pectinidae.Argopecten is sister group to the other two pectinids; 18S sequence data will have great impact on our understanding of bivalve phylogeny, but only when more sequences of similar substitution rates are available. Correspondence to: G. Steiner     

Phylogenetic relationships of the globally distributed freshwater prawn genus Macrobrachium (Crustacea: Decapoda: Palaemonidae): biogeography, taxonomy and the convergent evolution of abbreviated larval development

There has hitherto been little research into evolutionary and taxonomic relationships amongst species of the freshwater prawn genus Macrobrachium Bate across its global distribution. Previous work by the authors demonstrated that the endemic Australian species did not evolve from a single ancestral lineage. To examine whether other regional Macrobrachium faunas also reflect this pattern of multiple origins, the phylogeny of 30 Macrobrachium species from Asia, Central/South America and Australia was inferred from mitochondrial 16S rRNA sequences. Phylogenetic relationships demonstrate that, despite some evidence for regional diversification, Australia, Asia and South America clearly contain Macrobrachium species that do not share a common ancestry, suggesting that large-scale dispersal has been a major feature of the evolutionary history of the genus. The evolution of abbreviated larval development (ALD), associated with the transition from an estuarine into a purely freshwater lifecycle, was also mapped onto the phylogeny and was shown to be a relatively homoplasious trait and not taxonomically informative. Other taxonomic issues, as well as the evolutionary origins of Macrobrachium , are also discussed.