Molecular Discrimination of Perna (Mollusca: Bivalvia) Species Using the Polymerase Chain Reaction and Species-Specific Mitochondrial Primers

This work was prompted by the need to be able to identify the invasive mussel species, Perna viridis, in tropical Australian seas using techniques that do not rely solely on morphology. DNA-based molecular methods utilizing a polymerase chain reaction (PCR) approach were developed to distinguish unambiguously between the three species in the genus Perna. Target regions were portions of two mitochondrial genes, cox1 and nad4, and the intergenic spacer between these that occurs in at least two Perna species. Based on interspecific sequence comparisons of the nad4 gene, a conserved primer has been designed that can act as a forward primer in PCRs for any Perna species. Four reverse primers have also been designed, based on nad4 and intergenic spacer sequences, which yield species-specific products of different lengths when paired with the conserved forward primer. A further pair of primers has been designed that will amplify part of the cox1 gene of any Perna species, and possibly other molluscs, as a positive control to demonstrate that the PCR is working.     

Morphological and Genetic Diversity of the Wood-Boring Xylophaga (Mollusca,Bivalvia): New Species and Records from Deep-Sea Iberian Canyons

Deep-sea bivalves of the Xylophagaidae, a poorly known group, are obligate wood-borers. Deployment of wood in three submarine canyons off the Iberian coast, the Blanes and La Fonera Canyons (Mediterranean Sea) and the Avilés Canyon (Cantabric Sea, Bay of Biscay), lead to the discovery of four xylophagaid species in our samples. Xylophaga dorsalis (the dominant species), X. atlantica, X. cf. anselli and the new species X. brava, were identified on the basis of morphological data, and supported by a phylogenetic reconstruction based on the nuclear genes 18S rDNA and 28S rDNA and including several genus of Xylophagaidae. Genetic divergence between species of Xylophaga varied between genes, ranging from 0.5 to 4.0% for the 18SrDNA and from 4.1 to 16.6% for the 28SrDNA. Xylophaga brava sp. nov. appeared to be restricted to the Mediterranean and morphologically resembled the closely related X. cf. anselli from the Cantabrian Sea. However, they clearly diverged in two well-supported clades. Low levels of intraspecific variability and higher interspecific divergence between species also supported the existence of these two different species. Morphologically they differ in the number of cirri at the siphon openings, in the shape of the posterior shell and in the size of prodissoconch II. The new species is characterized by having weak, poorly mineralized mesoplax and siphons united throughout, covered by a periostracal, non-calcified tube; distinct proximal and distal siphons, the former translucent and soft, the latter muscular, with concentric rings. Xylophaga atlantica, previously known only from the western Atlantic, is reported for the first time in the Mediterranean Sea. Whether its presence in the Mediterranean indicates its natural distribution or reflects its recent introduction is unknown. Although xylophagaids have been previously reported to recruit heavily to wood deposited on the seabed, these four species colonized wood suspended 30 m above the seafloor.     

用SSR研究栲树群体遗传结构

利用微卫星（SSR）分子标记对福建省内4个栲树（Castanopsis fargesii Franch.）群体遗传结构进行了研究。SSR标记揭示了栲树群体丰富的遗传变异：平均等位基因数A＝9.0,平均有效等位基因数Ne=4.8,平均期望杂合度He=0.65,而群 具有较低的Fst值（Fst=0.031）。SSR每个位点的等位基因频率分布在栲树群体间都存在显或极显差异,表明根据SSR等位基因频率分布亦能了解各体的分化。SSR标记使栲树群体中一些稀有等位基因得以表现,54个SSR等位基因中有15个等位基因仅出现在1个或2个群体中,且频率较低,在遗传多样性保护中更应注重保护这些稀有的等位变异。     

Study on Population Genetic Structure in Castanopsis fargesii with Microsatellite Markers

Genetic structure of four populations in Castanopsis fargesii Franch. in Fujian Province was studied with microsatellite (SSR) markers. A high level of genetic variation was detected in the populations of C. fargesii by using SSR with A=9.0, Ne=4.8, He=0.65 and the population differentiation coefficient ( Fst ) was only 0.031. The distributions of alleles of all loci were significantly different among the populations of C. fargesii , and the population differentiation could be found according to the distributions of SSR alleles. Some rare alleles in the populations of C. fargesii were revealed by SSR: Fifteen of 54 alleles appeared in one or two populations with lower frequencies; conservation of these rare alleles is of great importance.     

Population Genetic Structure and Demographic History of Atrina pectinata Based on Mitochondrial DNA and Microsatellite Markers

The pen shell, Atrina pectinata, is one of the commercial bivalves in East Asia and thought to be recently affected by anthropogenic pressure (habitat destruction and/or fishing pressure). Information on its population genetic structure is crucial for the conservation of A. pectinata. Considering its long pelagic larval duration and iteroparity with high fecundity, the genetic structure for A. pectinata could be expected to be weak at a fine scale. However, the unusual oceanography in the coasts of China and Korea suggests potential for restricted dispersal of pelagic larvae and geographical differentiation. In addition, environmental changes associated with Pleistocene sea level fluctuations on the East China Sea continental shelf may also have strongly influenced historical population demography and genetic diversity of marine organisms. Here, partial sequences of the mitochondrial Cytochrome c oxidase subunit I (COI) gene and seven microsatellite loci were used to estimate population genetic structure and demographic history of seven samples from Northern China coast and one sample from North Korea coast. Despite high levels of genetic diversity within samples, there was no genetic differentiation among samples from Northern China coast and low but significant genetic differentiation between some of the Chinese samples and the North Korean sample. A late Pleistocene population expansion, probably after the Last Glacial Maximum, was also demonstrated for A. pectinata samples. No recent genetic bottleneck was detected in any of the eight samples. We concluded that both historical recolonization (through population range expansion and demographic expansion in the late Pleistocene) and current gene flow (through larval dispersal) were responsible for the weak level of genetic structure detected in A. pectinata.     

Modulation of Mytilus trossulus (Bivalvia: Mollusca) larval survival and growth in culture. Short communication

Commercial importance and ability to live in a wide range of salinities have made the common mussel, Mytilus trossulus, a relevant model to study modulation of larval growth and development. We investigated the effects of various salinities combined with neomycin and ampicillin application on Mytilus larvae survival and growth. Both neomycin and ampicillin enhanced trochophore and veliger survival under condition of low salinity. The average veliger size was increasing in accordance with the increase of salinity. In case of neomycin treatment 3.6% of the larvae reached the pediveliger stage. No abnormalities of larval morphology of the FMRFamide and 5-HT systems occurred after 7 days of culturing with both antibiotics.     

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.     

Genetic Markers and Quantitative Genetic Variation in Medicago Truncatula (Leguminosae): A Comparative Analysis of Population Structure

Two populations of the selfing annual Medicago truncatula Gaertn. (Leguminoseae), each subdivided into three subpopulations, were studied for both metric traits (quantitative characters) and genetic markers (random amplified polymorphic DNA and one morphological, single-locus marker). Hierarchical analyses of variance components show that (1) populations are more differentiated for quantitative characters than for marker loci, (2) the contribution of both within and among subpopulations components of variance to overall genetic variance of these characters is reduced as compared to markers, and (3) at the population level, within population structure is slightly but not significantly larger for markers than for quantitative traits. Under the hypothesis that most markers are neutral, such comparisons may be used to make hypotheses about the strength and heterogeneity of natural selection in the face of genetic drift and gene flow. We thus suggest that in these populations, quantitative characters are under strong divergent selection among populations, and that gene flow is restricted among populations and subpopulations.     

The genus Neilo in New Zealand (Mollusca: Bivalvia)

Abstract

The phylogenetic history, paleontological implications, and ecology of larger New Zealand Recent species of Neilo (sensu stricto) are discussed. N. wairoana delli, N. blacki, and N. (Pseudomalletia) aoteana are described as new. The following taxa are reduced to chronosubspecies: N. jugifera Marwick - of N. australis (Quoy & Gaimard); N. annectens Powell and N. rugata Dell - of N. sublaevis Marwick; N. sinangula Finlay - of N. awamoana Finlay.     

The Arcoidea (Mollusca: Bivalvia): a review of the current phenetic-based systematics

The diversity and adaptive radiations of modern Arcoidea, here considered to contain the families Arcidae, Noetiidae, Cucullaeidae, and Glycymerididae, are reviewed. Most fall into either epibyssate or endobyssate life habits with only the Glycymerididae living as free burrowers. The phenetic characters of the families within the Arcoida are reviewed and the families are shown to be supported by very few synapomorphic characters. Homoplasy is shown to be widespread and is illustrated in a series of discussions on the ligament, epibyssate–endobyssate radiations, and possible parallelism within genera, and in a review of arcoid anatomical characters. Previously published molecular data are reviewed and these support the inclusion of the Glycymerididae in the Arcoidea. They also indicate, however, that polyphyly is probably widespread at the subfamily level.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 148 , 237–251.     

Mitochondrial DNA Sequence-Based Population Genetic Structure of the Firefly, Pyrocoelia rufa (Coleoptera: Lampyridae)

The genetic divergence, population genetic structure, and possible speciation of the Korean firefly, Pyrocoelia rufa, were investigated on the midsouthern Korean mainland, coastal islets, a remote offshore island, Jedu-do, and Tsushima Island in Japan. Analysis of DNA sequences from the mitochondrial COI protein-coding gene revealed 20 mtDNA-sequence-based haplotypes with a maximum divergence of 5.5%. Phylogenetic analyses using PAUP, PHYLIP, and networks subdivided the P. rufa into two clades (termed clade A and B) and the minimum nucleotide divergence between them was 3.7%. Clade A occurred throughout the Korean mainland and the coastal islets and Tsushima Island in Japan, whereas clade B was exclusively found on Jeju-do Island. In the analysis of the population genetic structure, clade B formed an independent phylogeographic group, but clade A was further subdivided into three groups: two covering western and eastern parts of the Korean peninsula, respectively, and the other occupying one eastern coastal islet and Japanese Tsushima Island. Considering both phylogeny and population structure of P. rufa, the Jeju-do Island population is obviously differentiated from other P. rufa populations, but the Tsushima Island population was a subset of the Korean coastal islet, Geoje. We interpreted the isolation of the Jeju-do population and the grouping of Tsushima Island with Korean coastal islets in terms of Late Pleistocene-Holocene events. The eastern-western subdivision on the Korean mainland was interpreted partially by the presence of a large major mountain range, which bisects the midpart of the Korean peninsula into western and eastern parts.     

通过RAPD分析揭示五种淡水无齿蚌（软体动物门：双壳类）的遗传多样性

Unionidae(Bivalvia)are distributed infreshwaters,and represent a significanttaxonof benthic community[1].In China,freshwater mussels are abundant resources[2].Since1949,substantial investigations onthe unionidfau-na had been undertakenin China[3—8].Withreference tooverseas research[9,10],a preliminary reorganization onthe Unionidae was performed accordingtosome classifica-tion characteristics such as shell shape,larvae character-istics,and breeding habit[11].Due tothe serious conver-gence o…     

基于COI序列的DNA条形码在中国沿海缀锦蛤亚科贝类中的应用分析

该研究探讨了将COI序列应用于中国沿海缀锦蛤亚科贝类物种鉴定的可行性,获得了该亚科5属11种贝类51个个体的43个单倍型序列.碱幕替换饱和性分析表明,颠换未出现饱和现象,而转换在序列分化达到10%至15%时即到达饱和.单倍犁Hap33可能是由杂交引起的,排除此瞥倍型,种内个体间遗传距离在0%到2.02%之间,平均为0.46%,属内不同种个体间遗传距离在17.21%～32.24%之间,平均为24.96%,存在条形码问隙:11种缀锦蛤哑科贝类在邻接树和贝叶斯树上都独立的单系群.该研究表明,基于COI的DNA条形码技术能够将研究所涉及的约98%的缀锦蛤亚科贝类鉴定剑种的水平,因此,利用DNA条形码技术可以对缀锦蛤亚科贝类进行有效地分类鉴定.     

Microsatellite Markers Reveal Strong Genetic Structure in the Endemic Chilean Dolphin

Understanding genetic differentiation and speciation processes in marine species with high dispersal capabilities is challenging. The Chilean dolphin, Cephalorhynchus eutropia, is the only endemic cetacean of Chile and is found in two different coastal habitats: a northern habitat with exposed coastlines, bays and estuaries from Valparaíso (33°02′S) to Chiloé (42°00′S), and a southern habitat with highly fragmented inshore coastline, channels and fjords between Chiloé and Navarino Island (55°14′S). With the aim of evaluating the potential existence of conservation units for this species, we analyzed the genetic diversity and population structure of the Chilean dolphin along its entire range. We genotyped 21 dinucleotide microsatellites for 53 skin samples collected between 1998 and 2012 (swab: n = 8, biopsy: n = 38, entanglement n = 7). Bayesian clustering and spatial model analyses identified two genetically distinct populations corresponding to the northern and southern habitats. Genetic diversity levels were similar in the two populations (He: 0.42 v/s 0.45 for southern and northern populations, respectively), while effective size population was higher in the southern area (Ne: 101 v/s 39). Genetic differentiation between these two populations was high and significant (F_ST = 0.15 and R_ST = 0.19), indicating little or no current gene flow. Because of the absence of evident geographical barriers between the northern and southern populations, we propose that genetic differentiation may reflect ecological adaptation to the different habitat conditions and resource uses. Therefore, the two genetic populations of this endemic and Near Threatened species should be considered as different conservation units with independent management strategies.     

Mytilus galloprovincialis (Mollusca: Bivalvia) in a warm-temperate South African estuarine embayment

The distribution, population structure, condition and gonad indices, and the attachment strengths of the invasive Mediterranean mussel Mytilus galloprovincialis are described from the Knysna Estuary, South Africa. Mussels were found in the rocky intertidal at the mouth of the estuary and on all man-made hard substrata as far as 12?km from the mouth in 2013. However, mussel beds were found only in the lower reach of the estuary, where mussel densities were as high as 120 per 0.01?m². When compared to mussels from the embayment regions of the estuary, those at the estuary mouth, where wave action was high, were generally smaller, had significantly lower condition and gonad indices, and greater attachment strength. This suggests that mussels within the sheltered regions of the estuary invest more energy in growth and reproduction, and that this is one reason for their success as an invasive species in the Knysna estuarine embayment.     

Effects of photoperiod on sodium flux in Corbicula fluminea (Mollusca:Bivalvia)

• 1.1. A significant diurnal rhythm of net sodium flux was demonstrated in the freshwater clam Corbicula fluminea entrained to either a 12L:12D or 24L photoperiod.
• 2.2. Highest net flux occurred during the dark hours on 12L: 12D. The overall mean net flux over 24 hr was not significantly different from a steady state condition.
• 3.3. Net flux values of clams on a 24L photoperiod were negative and significantly lower than the net flux on a 12L:12D photoperiod.
• 4.4. The 12L: 12D net sodium flux rhythm pattern is similar to rhythmic patterns of other physiological processes in another freshwater clam.

     

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.     

Mitochondrial phylogenomics of the Bivalvia (Mollusca): searching for the origin and mitogenomic correlates of doubly uniparental inheritance of mtDNA

Background  

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).     

Species distributions and shell characteristics of Pisidium (Mollusca: Bivalvia) in the Colorado Front Range: the role of abiotic factors

SUMMARY.

• 1 Forty lakes in the Colorado Front Range were sampled to examine the relationship between water chemistry and the distributions and shell characteristics of Pisidium species. Alkalinity, pH, and dissolved organic carbon contributed most to the classification of lakes according to the dominant Pisidium species. Alkalinity was also strongly correlated with mean clam weight for populations of P. casertanum, the most common of the five species collected.
• 2 Historical evidence shows a reduction in the number of lakes occupied by clams and a constriction in the distributions of certain species. These changes have occurred mainly in lakes that now have low alkalinity.
• 3 A role for acidification is suggested because the recorded changes in distributions have occurred during the last 20 years, coincident with a general decline in alkalinity in waters of the Front Range.