Sinanodonta woodiana (Lea, 1834) is a large Unionid species with a real invasion success. It colonized Europe, Central America, the Indonesian Islands and recently North America. The species life cycle involves a larval parasitic stage on freshwater fish species which contributes to the spread of the mussel. In this paper we describe, for the first time, eight polymorphic microsatellite loci for the species Sinanodonta woodiana. The genetic screening of individuals confirmed that all loci were highly polymorphic. The number of alleles per locus ranged from 7 to 14 and the observed heterozygosity ranged from 0.650 to 0.950. These loci should prove useful to study the species population genetics which could help to infer important aspects of the invasion process.
invasive species; microsatellite; population genetics; range expansion; native area
Unionid shells are characterized by an outer aragonitic prismatic layer and an inner nacreous layer. The prisms of the outer shell layer are composed of single-crystal fibres radiating from spheruliths. During prism development, fibres progressively recline to the growth front. There is competition between prisms, leading to the selection of bigger, evenly sized prisms. A new model explains this competition process between prisms, using fibres as elementary units of competition. Scanning electron microscopy and X-ray texture analysis show that, during prism growth, fibres become progressively orientated with their three crystallographic axes aligned, which results from geometric constraints and space limitations. Interestingly transition to the nacreous layer does not occur until a high degree of orientation of fibres is attained. There is no selection of crystal orientation in the nacreous layer and, as a result, the preferential orientation of crystals deteriorates. Deterioration of crystal orientation is most probably due to accumulation of errors as the epitaxial growth is suppressed by thick or continuous organic coats on some nacre crystals. In conclusion, the microstructural arrangement of the unionid shell is, to a large extent, self-organized with the main constraints being crystallographic and geometrical laws.
Several clades of bivalve molluscs have invaded freshwaters at various times throughout Phanerozoic history. The most successful freshwater clade in the modern world is the Unionoida. Unionoids arose in the Triassic Period, sometime after the major extinction event at the End-Permian boundary and are now widely distributed across all continents except Antarctica. Until now, no freshwater bivalves of any kind were known to exist in the Early Triassic.
Here we report on a faunule of two small freshwater bivalve species preserved in vertebrate coprolites from the Olenekian (Lower Triassic) of the Burgersdorp Formation of the Karoo Basin, South Africa. Positive identification of these bivalves is not possible due to the limited material. Nevertheless they do show similarities with Unionoida although they fall below the size range of extant unionoids. Phylogenetic analysis is not possible with such limited material and consequently the assignment remains somewhat speculative.
Bivalve molluscs re-invaded freshwaters soon after the End-Permian extinction event, during the earliest part of the recovery phase during the Olenekian Stage of the Early Triassic. If the specimens do represent unionoids then these Early Triassic examples may be an example of the Lilliput effect. Since the oldest incontrovertible freshwater unionoids are also from sub-Saharan Africa, it is possible that this subcontinent hosted the initial freshwater radiation of the Unionoida. This find also demonstrates the importance of coprolites as microenvironments of exceptional preservation that contain fossils of organisms that would otherwise have left no trace.
Doubly uniparental inheritance (DUI) is an atypical system of animal mtDNA inheritance found only in some bivalves. Under DUI, maternally (F genome) and paternally (M genome) transmitted mtDNAs yield two distinct gender-associated mtDNA lineages. The oldest distinct M and F genomes are found in freshwater mussels (order Unionoida). Comparative analyses of unionoid mitochondrial genomes and a robust phylogenetic framework are necessary to elucidate the origin, function and molecular evolutionary consequences of DUI. Herein, F and M genomes from three unionoid species, Venustaconcha ellipsiformis, Pyganodon grandis and Quadrula quadrula have been sequenced. Comparative genomic analyses were carried out on these six genomes along with two F and one M unionoid genomes from GenBank (F and M genomes of Inversidens japanensis and F genome of Lampsilis ornata).
Compared to their unionoid F counterparts, the M genomes contain some unique features including a novel localization of the trnH gene, an inversion of the atp8-trnD genes and a unique 3'coding extension of the cytochrome c oxidase subunit II gene. One or more of these unique M genome features could be causally associated with paternal transmission. Unionoid bivalves are characterized by extreme intraspecific sequence divergences between gender-associated mtDNAs with an average of 50% for V. ellipsiformis, 50% for I. japanensis, 51% for P. grandis and 52% for Q. quadrula (uncorrected amino acid p-distances). Phylogenetic analyses of 12 protein-coding genes from 29 bivalve and five outgroup mt genomes robustly indicate bivalve monophyly and the following branching order within the autolamellibranch bivalves: ((Pteriomorphia, Veneroida) Unionoida).
The basal nature of the Unionoida within the autolamellibranch bivalves and the previously hypothesized single origin of DUI suggest that (1) DUI arose in the ancestral autolamellibranch bivalve lineage and was subsequently lost in multiple descendant lineages and (2) the mitochondrial genome characteristics observed in unionoid bivalves could more closely resemble the DUI ancestral condition. Descriptions and comparisons presented in this paper are fundamental to a more complete understanding regarding the origins and consequences of DUI.
Vesicomyid bivalves are a consistent component of communities of sulphide-rich reducing environments distributed worldwide from 77° N to 70°S at depths from 100 to 9050 m. Up-to-now the taxonomy of the family has been uncertain. In this paper, the current state of vesicomyid taxonomy and distribution at the generic rank are considered. This survey is founded on a database including information both from literature sources and also unpublished data of the authors on all recent species of vesicomyids. We suggest that the Vesicomyidae is not a synonym of Kelliellidae, and is therefore a valid family name. We propose to divide the family Vesicomyidae into two subfamilies: Vesicomyinae and Pliocardiinae. The Vesicomyinae includes one genus, Vesicomya, which comprises small-sized bivalves characterized by non-reduced gut and the absence of subfilamental tissue in gills. Symbiosis with chemoautotrophic bacteria has, so far, not been proved for Vesicomya and the genus is not restricted to sulphide-rich reducing habitats. The subfamily Pliocardiinae currently contains about 15 genera with mostly medium or large body size, characterized by the presence of subfilamental tissue in the gills. The Pliocardiinae are highly specialized for sulphide-rich reducing environments, harbouring chemoautrophic bacteria in their gills. This is the first summary of the generic structure of the family Vesicomyidae that allow us to analyze the distribution of vesicomyids at the generic level. We recognize here five different distribution patterns that are related to the specific environmental demands. The general trends in the distribution patterns of the vesicomyids are an occurrence of the majority of genera in broad geographical ranges and the prevalence of near continental type of distribution.
The superfamily Pterioidea is a morphologically and ecologically diverse lineage of epifaunal marine bivalves distributed throughout the tropical and subtropical continental shelf regions. This group includes commercially important pearl culture species and model organisms used for medical studies of biomineralization. Recent morphological treatment of selected pterioideans and molecular phylogenetic analyses of higher-level relationships in Bivalvia have challenged the traditional view that pterioidean families are monophyletic. This issue is examined here in light of molecular data sets composed of DNA sequences for nuclear and mitochondrial loci, and a published character data set of anatomical and shell morphological characters.
The present study is the first comprehensive species-level analysis of the Pterioidea to produce a well-resolved, robust phylogenetic hypothesis for nearly all extant taxa. The data were analyzed for potential biases due to taxon and character sampling, and idiosyncracies of different molecular evolutionary processes. The congruence and contribution of different partitions were quantified, and the sensitivity of clade stability to alignment parameters was explored.
Four primary conclusions were reached: (1) the results strongly supported the monophyly of the Pterioidea; (2) none of the previously defined families (except for the monotypic Pulvinitidae) were monophyletic; (3) the arrangement of the genera was novel and unanticipated, however strongly supported and robust to changes in alignment parameters; and (4) optimizing key morphological characters onto topologies derived from the analysis of molecular data revealed many instances of homoplasy and uncovered synapomorphies for major nodes. Additionally, a complete species-level sampling of the genus Pinctada provided further insights into the on-going controversy regarding the taxonomic identity of major pearl culture species.
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.
Monodacna; Ponto-Caspian; invasive species; population genetics; repetitive elements; genetic diversity
Solenidae are deep burrowing bivalves inhabiting intertidal and shallow sub-tidal soft bottom sediments mostly in tropical and sub-tropical areas. Solen dactylus has a restricted distribution within the Indian Ocean. Solen dactylus is frequently found on the sandy-muddy coast of the northern Persian Gulf, Iran. Specimens of S. dactylus were collected since 2006 from Bandar Abbas to study their biology and ecology. During these studies, an unexpected pair of anterior pallial tentacles at the dorsal end of the anterior pallial crest of the mantle was found. In the tentacles, two kinds of epithelial cells (pyramidal and vacuolated) and fibres (radial and longitudinal), and a branch of the pallial nerve located in the centre of a haemocoel, were determined. A possible coherence of a furrow parallel to the anterior shell margin with the presence of anterior pallial tentacles is discussed. All species with long anterior pallial tentacles have anterior shell furrows. Anterior pallial tentacles were found in 10 species of Solenidae from Asia to the Middle East and Europe. The function of the tentacles is unknown. However, more species need to be examined for anterior pallial tentacles and anterior shell furrows to determine if they reflect a common evolutionary history or ecology.
Mitochondrial (mt) function depends critically on optimal interactions between components encoded by mt and nuclear DNAs. mitochondrial DNA (mtDNA) inheritance (SMI) is thought to have evolved in animal species to maintain mito-nuclear complementarity by preventing the spread of selfish mt elements thus typically rendering mtDNA heteroplasmy evolutionarily ephemeral. Here, we show that mtDNA intraorganismal heteroplasmy can have deterministic underpinnings and persist for hundreds of millions of years. We demonstrate that the only exception to SMI in the animal kingdom, that is, the doubly uniparental mtDNA inheritance system in bivalves, with its three-way interactions among egg mt-, sperm mt- and nucleus-encoded gene products, is tightly associated with the maintenance of separate male and female sexes (dioecy) in freshwater mussels. Specifically, this mother-through-daughter and father-through-son mtDNA inheritance system, containing highly differentiated mt genomes, is found in all dioecious freshwater mussel species. Conversely, all hermaphroditic species lack the paternally transmitted mtDNA (=possess SMI) and have heterogeneous macromutations in the recently discovered, novel protein-coding gene (F-orf) in their maternally transmitted mt genomes. Using immunoelectron microscopy, we have localized the F-open reading frame (ORF) protein, likely involved in specifying separate sexes, in mitochondria and in the nucleus. Our results support the hypothesis that proteins coded by the highly divergent maternally and paternally transmitted mt genomes could be directly involved in sex determination in freshwater mussels. Concomitantly, our study demonstrates novel features for animal mt genomes: the existence of additional, lineage-specific, mtDNA-encoded proteins with functional significance and the involvement of mtDNA-encoded proteins in extra-mt functions. Our results open new avenues for the identification, characterization, and functional analyses of ORFs in the intergenic regions, previously defined as “noncoding,” found in a large proportion of animal mt genomes.
mtDNA; doubly uniparental inheritance; open reading frame; sex determination; heteroplasmy; Bivalvia
Freshwater mussels (order Unionoida) represent one of the most severely endangered groups of animals due to habitat destruction, introduction of nonnative species, and loss of host fishes, which their larvae (glochidia) are obligate parasites on. Conservation efforts such as habitat restoration or restocking of host populations are currently hampered by difficulties in unionoid species identification by morphological means. Here we present the first complete molecular identification key for all seven indigenous North and Central European unionoid species and the nonnative Sinanodonta woodiana, facilitating quick, low-cost, and reliable identification of adult and larval specimens. Application of this restriction fragment length polymorphisms (RFLP) key resulted in 100% accurate assignment of 90 adult specimens from across the region by digestion of partial ITS-1 (where ITS is internal transcribed spacer) polymerase chain reaction (PCR) products in two to four single digestions with five restriction endonucleases. In addition, we provide protocols for quick and reliable extraction and amplification of larval mussel DNA from complete host fish gill arches. Our results indicate that this new method can be applied on infection rates as low as three glochidia per gill arch and enables, for the first time, comprehensive, large-scale assessments of the relative importance of different host species for given unionoid populations.
Host–parasite interactions; morphological variability; PCR-RFLP; species identification; Unionidae; wildlife management
The linkage between 5S ribosomal DNA and other multigene families has been detected in many eukaryote lineages, but whether it provides any selective advantage remains unclear. In this work, we report the occurrence of linked units of 5S ribosomal DNA (5S rDNA) and U1 small nuclear DNA (U1 snDNA) in 10 razor shell species (Mollusca: Bivalvia: Pharidae) from four different genera. We obtained several clones containing partial or complete repeats of both multigene families in which both types of genes displayed the same orientation. We provide a comprehensive collection of razor shell 5S rDNA clones, both with linked and nonlinked organisation, and the first bivalve U1 snDNA sequences. We predicted the secondary structures and characterised the upstream and downstream conserved elements, including a region at −25 nucleotides from both 5S rDNA and U1 snDNA transcription start sites. The analysis of 5S rDNA showed that some nontranscribed spacers (NTSs) are more closely related to NTSs from other species (and genera) than to NTSs from the species they were retrieved from, suggesting birth-and-death evolution and ancestral polymorphism. Nucleotide conservation within the functional regions suggests the involvement of purifying selection, unequal crossing-overs and gene conversions. Taking into account this and other studies, we discuss the possible mechanisms by which both multigene families could have become linked in the Pharidae lineage. The reason why 5S rDNA is often found linked to other multigene families seems to be the result of stochastic processes within genomes in which its high copy number is determinant.
birth-and-death evolution; regulatory regions; 5S ribosomal RNA; U1 small nuclear RNA; linkage; Ensis
Marine bivalves of the family Teredinidae (shipworms) are voracious consumers of wood in marine environments. In several shipworm species, dense communities of intracellular bacterial endosymbionts have been observed within specialized cells (bacteriocytes) of the gills (ctenidia). These bacteria are proposed to contribute to digestion of wood by the host. While the microbes of shipworm gills have been studied extensively in several species, the abundance and distribution of microbes in the digestive system have not been adequately addressed. Here we use Fluorescence In-Situ Hybridization (FISH) and laser scanning confocal microscopy with 16S rRNA directed oligonucleotide probes targeting all domains, domains Bacteria and Archaea, and other taxonomic groups to examine the digestive microbiota of 17 specimens from 5 shipworm species (Bankia setacea, Lyrodus pedicellatus, Lyrodus massa, Lyrodus sp. and Teredo aff. triangularis). These data reveal that the caecum, a large sac-like appendage of the stomach that typically contains large quantities of wood particles and is considered the primary site of wood digestion, harbors only very sparse microbial populations. However, a significant number of bacterial cells were observed in fecal pellets within the intestines. These results suggest that due to low abundance, bacteria in the caecum may contribute little to lignocellulose degradation. In contrast, the comparatively high population density of bacteria in the intestine suggests a possible role for intestinal bacteria in the degradation of lignocellulose.
Our objective was to identify the distribution of the endangered golden-cheeked warbler (Setophaga chrysoparia) in fragmented oak–juniper woodlands by applying a geoadditive semiparametric occupancy model to better assist decision-makers in identifying suitable habitat across the species breeding range on which conservation or mitigation activities can be focused and thus prioritize management and conservation planning.
We used repeated double-observer detection/non-detection surveys of randomly selected (n = 287) patches of potential habitat to evaluate warbler patch-scale presence across the species breeding range. We used a geoadditive semiparametric occupancy model with remotely sensed habitat metrics (patch size and landscape composition) to predict patch-scale occupancy of golden-cheeked warblers in the fragmented oak–juniper woodlands of central Texas, USA.
Our spatially explicit model indicated that golden-cheeked warbler patch occupancy declined from south to north within the breeding range concomitant with reductions in the availability of large habitat patches. We found that 59% of woodland patches, primarily in the northern and central portions of the warbler’s range, were predicted to have occupancy probabilities ≤0.10 with only 3% of patches predicted to have occupancy probabilities >0.90. Our model exhibited high prediction accuracy (area under curve = 0.91) when validated using independently collected warbler occurrence data.
We have identified a distinct spatial occurrence gradient for golden-cheeked warblers as well as a relationship between two measurable landscape characteristics. Because habitat-occupancy relationships were key drivers of our model, our results can be used to identify potential areas where conservation actions supporting habitat mitigation can occur and identify areas where conservation of future potential habitat is possible. Additionally, our results can be used to focus resources on maintenance and creation of patches that are more likely to harbour viable local warbler populations.
Bayesian inference; golden-cheeked warbler; habitat conservation; occupancy; semiparametric regression; Setophaga chrysoparia
North American Agalinis Raf. species represent a taxonomically challenging group and there have been extensive historical revisions at the species, section, and subsection levels of classification. The genus contains many rare species, including the federally listed endangered species Agalinis acuta. In addition to evaluating the degree to which historical classifications at the section and subsection levels are supported by molecular data sampled from 79 individuals representing 29 Agalinis species, we assessed the monophyly of 27 species by sampling multiple individuals representing different populations of those species. Twenty-one of these species are of conservation concern in at least some part of their range.
Phylogenetic relationships estimated using maximum likelihood analyses of seven chloroplast DNA loci (aligned length = 11 076 base pairs (bp) and the nuclear ribosomal DNA ITS (internal transcribed spacer) locus (733 bp); indicated no support for the historically recognized sections except for Section Erectae. Our results suggest that North American members of the genus comprise six major lineages, however we were not able to resolve branching order among many of these lineages. Monophyly of 24 of the 29 sampled species was supported based on significant branch lengths of and high bootstrap support for subtending branches. However, there was no statistical support for the monophyly of A. acuta with respect to Agalinis tenella and Agalinis decemloba. Although most species were supported, deeper relationships among many species remain ambiguous.
The North American Agalinis species sampled form a well supported, monophyletic group within the family Orobanchaceae relative to the outgroups sampled. Most hypotheses regarding section- and subsection-level relationships based on morphology were not supported and taxonomic revisions are warranted. Lack of support for monophyly of Agalinis acuta leaves the important question regarding its taxonomic status unanswered. Lack of resolution is potentially due to incomplete lineage sorting of ancestral polymorphisms among recently diverged species; however the gene regions examined did distinguish among almost all other species in the genus. Due to the important policy implications of this finding we are further evaluating the evolutionary distinctiveness of A. acuta using morphological data and loci with higher mutation rates.
A galeommatid bivalve mollusk, representing a new species, is described from off the coasts of California and Vancouver Island, British Columbia. The new bivalve has a commensal relationship with the heart urchin, Brisaster latifrons. It has been observed crawling between the oral spines of this urchin, frequently near the peristome. The bivalve has been recorded from 80 (Vancouver Island) to 444 (southern California) meters depth, in muddy sediments.
In common with other galeommatoideans, the new species broods its young; however it differs from the large majority of commensal members in lacking planktotrophic larval development.
Waldo arthuri, new species, has multiple morphological, ecological and developmental similarities to other members of the genus Waldo Nicol, 1966, from the southern Atlantic and Antarctic Oceans. This is most pronounced for the Argentine species, Waldo paucitentaculatus Zelaya & Ituarte, 2013, Waldo arthuri’s sister speciesin nuclear and mitochondrial gene trees. Despite this close relationship, Waldo arthuri is phylogentically distinct and possesses several hinge, shell sculpture, foot, and mantle tentacle characteristics that merit its description as new.
Commensal relationships; Bivalvia; Galeommatidae; Waldo; Echinodea; urchin; taxonomy
Bivalve mitochondrial genomes exhibit a wide array of uncommon features, like extensive gene rearrangements, large sizes, and unusual ways of inheritance. Species pertaining to the order Solemyida (subclass Opponobranchia) show many peculiar evolutionary adaptations, f.i. extensive symbiosis with chemoautotrophic bacteria. Despite Opponobranchia are central in bivalve phylogeny, being considered the sister group of all Autobranchia, a complete mitochondrial genome has not been sequenced yet.
In this paper, we characterized the complete mitochondrial genome of the Atlantic awning clam Solemya velum: A-T content, gene arrangement and other features are more similar to putative ancestral mollusks than to other bivalves. Two supranumerary open reading frames are present in a large, otherwise unassigned, region, while the origin of replication could be located in a region upstream to the cox3 gene.
We show that S. velum mitogenome retains most of the ancestral conchiferan features, which is unusual among bivalve mollusks, and we discuss main peculiarities of this first example of an organellar genome coming from the subclass Opponobranchia. Mitochondrial genomes of Solemya (for bivalves) and Haliotis (for gastropods) seem to retain the original condition of mollusks, as most probably exemplified by Katharina.
Solemya velum; Mitochondrial genome; Gene arrangement; Origin of replication; Mitogenomics
Wood-boring bivalves of the family Teredinidae (commonly called shipworms) are known to harbor dense populations of gram-negative bacteria within specialized cells (bacteriocytes) in their gills. These symbionts are thought to provide enzymes, e.g., cellulase and dinitrogenase, which assist the host in utilizing wood as a primary food source. A cellulolytic, dinitrogen-fixing bacterium, Teredinibacter turnerae, has been isolated from the gill tissues of numerous teredinid bivalves and has been proposed to constitute the sole or predominant symbiont of this bivalve family. Here we demonstrate that one teredinid species, Lyrodus pedicellatus, contains at least four distinct bacterial 16S rRNA types within its gill bacteriocytes, one of which is identical to that of T. turnerae. Phylogenetic analyses indicate that the three newly detected ribotypes are derived from gamma proteobacteria that are related to but distinct (>6.5% sequence divergence) from T. turnerae. In situ hybridizations with 16S rRNA-directed probes demonstrated that the pattern of occurrence of symbiont ribotypes within bacteriocytes was predictable and specific, with some bacteriocytes containing two symbiont ribotypes. However, only two of the six possible pairwise combinations of the four ribotypes were observed to cooccur within the same host cells. The results presented here are consistent with the existence of a complex multiple symbiosis in this shipworm species.
More than 1,500 clams of Corbicula fluminea, the most favorable food source of freshwater bivalves in Korea, were collected from 5 localities to examine cercarial and metacercarial infection with Echinostoma cinetorchis. Although 3 clams infected with suspicious E. cinetorchis metacercariae out of 200 specimens collected at Kangjin, Chollanam-do were detected, no cercarial and metacercarial infections with E. cinetorchis were observed in field-collected Corbicula specimens. In the susceptibility experiments with laboratory-reared clams, those infected with miracidia of E. cinetorchis did not release their cercariae up to 60 days after infection. To confirm the identity of second intermediate host of E. cinetorchis experimentally, a total of 30 clams were exposed to the cercariae from Segmentina hemisphaerula that had been infected with miracidia of E. cinetorchis. The clams were susceptible to cercariae of E. cinetorchis with an infection rate of 93.3%. Metacercariae from clams taken more than 7 days after cercarial exposure were fed to rats (S/D strain), and adult worms of E. cinetorchis, characterized by 37-38 collar spines on the head crown, were recovered from the ileocecal regions. This is the first report of C. fluminea as a possible second intermediate host of E. cinetorchis.
Corbicula fluminea; Echinostoma cinetorchis; susceptibility; metacercaria
Four new species and a new genus of lucinid bivalves are described from shallow and deeper waters in the Indian and West Pacific Oceans. The new genus Scabrilucina (subfamily Lucininae) includes the little-known Scabrilucina victorialis (Melvill, 1899) from the Arabian Sea and Scabrilucina vitrea (Deshayes, 1844) from the Andaman Sea as well as a new species Scabrilucina melvilli from the Torres Strait off northeastern Australia. Ferrocina brunei new species (Lucininae) was recovered from 60 m near oil drilling activities off Borneo; its anatomy confirmed the presence of symbiotic bacteria. Two unusual deeper water species of Leucosphaerinae are described, both species included in on-going molecular analyses; Gonimyrtea ferruginea from 400–650 m in the southwest Pacific and Myrtina reflexa from 200–825 m off Zanzibar and Madagascar.
Bivalvia; Lucinidae; chemosymbiosis; taxonomy; new species; deep water; Indo-West Pacific
The eye has evolved across 13 separate lineages of molluscs. Yet, there have been very few studies examining the molecular machinary underlying eye function of this group, which is due, in part, to a lack of genomic resources. The scallop (Bivalvia: Pectinidae) represents a compeling molluscan model to study photoreception due to its morphologically novel and separately evolved mirror-type eye. We sequenced the adult eye transcriptome of two scallop species to: 1) identify the phototransduction pathway components; 2) identify any additional light detection functions; and 3) test the hypothesis that molluscs possess genes not found in other animal lineages.
A total of 3,039 contigs from the bay scallop, Argopecten irradians and 26,395 contigs from the sea scallop, Placopecten magellanicus were produced by 454 sequencing. Targeted BLAST searches and functional annotation using Gene Ontology (GO) terms and KEGG pathways identified transcripts from three light detection systems: two phototransduction pathways and the circadian clock, a previously unrecognized function of the scallop eye. By comparing the scallop transcriptomes to molluscan and non-molluscan genomes, we discovered that a large proportion of the transcripts (7,776 sequences) may be specific to the scallop lineage. Nearly one-third of these contain transmembrane protein domains, suggesting these unannotated transcripts may be sensory receptors.
Our data provide the most comprehensive transcriptomic resource currently available from a single molluscan eye type. Candidate genes potentially involved in sensory reception were identified, and are worthy of further investigation. This resource, combined with recent phylogenetic and genomic data, provides a strong foundation for future investigations of the function and evolution of molluscan photosensory systems in this morphologically and taxonomically diverse phylum.
The shell of the bivalve Montacuta ferruginosa, a symbiont living in the burrow of an echinoid, is covered with a rust-colored biofilm. This biofilm includes different morphotypes of bacteria that are encrusted with a mineral rich in ferric ion and phosphate. The aim of this research was to determine the genetic diversity and phylogenetic affiliation of the biofilm bacteria. Also, the possible roles of the microorganisms in the processes of mineral deposition within the biofilm, as well as their impact on the biology of the bivalve, were assessed by phenotypic inference. The genetic diversity was determined by denaturing gradient gel electrophoresis (DGGE) analysis of short (193-bp) 16S ribosomal DNA PCR products obtained with primers specific for the domain Bacteria. This analysis revealed a diverse consortium; 11 to 25 sequence types were detected depending on the method of DNA extraction used. Individual biofilms analyzed by using the same DNA extraction protocol did not produce identical DGGE profiles. However, different biofilms shared common bands, suggesting that similar bacteria can be found in different biofilms. The phylogenetic affiliations of the sequence types were determined by cloning and sequencing the 16S rRNA genes. Close relatives of the genera Pseudoalteromonas, Colwellia, and Oceanospirillum (members of the γ-Proteobacteria lineage), as well as Flexibacter maritimus (a member of the Cytophaga-Flavobacter-Bacteroides lineage), were found in the biofilms. We inferred from the results that some of the biofilm bacteria could play a role in the mineral formation processes.
The European eel (Anguilla anguilla L.) is distributed in coastal and inland habitats all over Europe, but spawns in the Sargasso Sea and is thus affected by both continental and oceanic factors. Since the 1980s a steady decline has been observed in the recruitment of glass eels to freshwater and in total eel landings. The eel is considered as critically endangered on the International Union for the Conservation of Nature and Natural Resources Red List of species. The Skagerrak beach seine survey from Norway constitutes the longest fishery-independent dataset on yellow/silver eels (starting in 1904). The Skagerrak coastal region receives larvae born in the Sargasso Sea spawning areas that have followed the Gulf Stream/North Atlantic Drift before they penetrate far into the North Sea. The Skagerrak coastal time series is therefore particularly valuable for exploring the impacts of oceanic factors on fluctuations in eel recruitment abundance. Analyses showed that Sargasso Sea surface temperature was negatively correlated with eel abundance, with a lag of 12 years revealing a cyclic and detrimental effect of high temperatures on the newly hatched larvae. The North Atlantic Oscillation index and inflow of North Atlantic water into the North Sea were negatively correlated with eel abundance, with a lag of 11 years. Increased currents towards the North Atlantic during high North Atlantic Oscillation years may send larvae into the subpolar gyre before they are ready to metamorphose and settle, resulting in low recruitment in the northern part of the distribution area for these years. The Skagerrak time series was compared with glass eel recruitment to freshwater in the Netherlands (Den Oever glass eel time series), and similar patterns were found revealing a cycle linked to changes in oceanic factors affecting glass eel recruitment. The recent decline of eels in the Skagerrak also coincided with previously documented shifts in environmental conditions of the North Sea ecosystem.
European eel; Anguilla anguilla; time series; oceanic factors; population decline
Doubly Uniparental Inheritance (DUI) is a fascinating exception to matrilinear inheritance of mitochondrial DNA (mtDNA). Species with DUI are characterized by two distinct mtDNAs that are inherited either through females (F-mtDNA) or through males (M-mtDNA). DUI sex-linked mitochondrial genomes share several unusual features, such as additional protein coding genes and unusual gene duplications/structures, which have been related to the functionality of DUI. Recently, new evidence for DUI was found in the mytilid bivalve Musculista senhousia. This paper describes the complete sex-linked mitochondrial genomes of this species.
Our analysis highlights that both M and F mtDNAs share roughly the same gene content and order, but with some remarkable differences. The Musculista sex-linked mtDNAs have differently organized putative control regions (CR), which include repeats and palindromic motifs, thought to provide sites for DNA-binding proteins involved in the transcriptional machinery. Moreover, in male mtDNA, two cox2 genes were found, one (M-cox2b) 123bp longer.
The complete mtDNA genome characterization of DUI bivalves is the first step to unravel the complex genetic signals allowing Doubly Uniparental Inheritance, and the evolutionary implications of such an unusual transmission route in mitochondrial genome evolution in Bivalvia. The observed redundancy of the palindromic motifs in Musculista M-mtDNA may have a role on the process by which sperm mtDNA becomes dominant or exclusive of the male germline of DUI species. Moreover, the duplicated M-COX2b gene may have a different, still unknown, function related to DUI, in accordance to what has been already proposed for other DUI species in which a similar cox2 extension has been hypothesized to be a tag for male mitochondria.
Shipworms (wood-boring bivalves of the family Teredinidae) harbor in their gills intracellular bacterial symbionts thought to produce enzymes that enable the host to consume cellulose as its primary carbon source. Recently, it was demonstrated that multiple genetically distinct symbiont populations coexist within one shipworm species, Lyrodus pedicellatus. Here we explore the extent to which symbiont communities vary among individuals of this species by quantitatively examining the diversity, abundance, and pattern of occurrence of symbiont ribotypes (unique 16S rRNA sequence types) among specimens drawn from a single laboratory-reared population. A total of 18 ribotypes were identified in two clone libraries generated from gill tissue of (i) a single specimen and (ii) four pooled specimens. Phylogenetic analysis assigned all of the ribotypes to a unique clade within the γ subgroup of proteobacteria which contained at least five well-supported internal clades (phylotypes). By competitive quantitative PCR and constant denaturant capillary electrophoresis, we estimated the number and abundance of symbiont phylotypes in gill samples of 13 individual shipworm specimens. Phylotype composition varied greatly; however, in all specimens the numerically dominant symbiont belonged to one of two nearly mutually exclusive phylotypes, each of which was detected with similar frequencies among specimens. A third phylotype, containing the culturable symbiont Teredinibacter turnerae, was identified in nearly all specimens, and two additional phylotypes were observed more sporadically. Such extensive variation in ribotype and phylotype composition among host specimens adds to a growing body of evidence that microbial endosymbiont populations may be both complex and dynamic and suggests that such genetic variation should be evaluated with regard to physiological and ecological differentiation.
The protobranch bivalve Solemya velum Say (Mollusca: Bivalvia) houses chemoautotrophic symbionts intracellularly within its gills. These symbionts were characterized through sequencing of polymerase chain reaction-amplified 16S rRNA coding regions and hybridization of an Escherichia coli gene probe to S. velum genomic DNA restriction fragments. The symbionts appeared to have only one copy of the 16S rRNA gene. The lack of variability in the 16S sequence and hybridization patterns within and between individual S. velum organisms suggested that one species of symbiont is dominant within and specific for this host species. Phylogenetic analysis of the 16S sequences of the symbionts indicates that they lie within the chemoautotrophic cluster of the gamma subdivision of the eubacterial group Proteobacteria.