Unveiling the unknown phylogenetic position of the scallop Austrochlamys natans and its implications for marine stewardship in the Magallanes Province.

Two species of scallop, Austrochlamys natans ("Ostión del Sur") and Zygochlamys patagonica ("Ostión patagonico") are presently exploited in the southern part of the Magallanes Province (MP). The lack of clarity in taxonomic identification and ecological aspects is generating both erroneous extraction statistics and an unperceived harvesting pressure on A. natans and Z. patagonica. We aim to discriminate these Magallanes scallops accurately, improve our understanding of their complex natural history and discuss possible implications for their management and conservation status, given the current fisheries statistics. To achieve these goals, we present a complete review of the historical identification of the Magallanes scallop and a multi-locus molecular phylogeny which allowed us to recover the phylogenetic position of A. natans. We sampled 54 individuals from five localities across the southern Pacific coast of the MP. We calculated the depth of the byssal notch (BND) and shell height (VH) ratio from morphological characters and conducted phylogenetic reconstructions with mitochondrial (12S and 16S) and nuclear markers (28S) using Bayesian and maximum likelihood analyses. Both morphology and molecular phylogeny identified two distinct entities, Z. patagonica and a distinct, highly divergent lineage that corresponds to A. natans. Our study provides integrative evidence to alert the current fishery management and the need for further conservation studies.

Histological and Expression Differences Among Different Mantle Regions of the Yesso Scallop (Patinopecten yessoensis) Provide Insights into the Molecular Mechanisms of Biomineralization and Pigmentation.

The molecular mechanisms of shell formation and pigmentation are issues of great interest in molluscan studies due to the unique physical and biological properties of shells. The Yesso scallop, Patinopecten yessoensis, is one of the most important maricultural bivalves in Asian countries, and its shell color shows polymorphism. To gain more information about the underlying mechanisms of shell formation and pigmentation, this study presents the first analyses of histological and transcriptional differences between different mantle regions of the Yesso scallop, which are thought to be responsible for the formation of different shell layers. The results showed major microstructural differences between the edge and central mantles, which were closely associated with their functions. Different biomineralization-related GO functions, which might participate in the formation of different shell layers, were significantly enriched in the different mantle regions, indicating the different molecular functions of the two mantle regions in shell formation. The melanogenesis pathway, which controls melanin biosynthesis, was the most significantly enriched pathway in the DEGs between the two mantle regions, indicating its important role in shell pigmentation. Tyr, the key and rate-limiting gene in melanogenesis, was expressed at a remarkably high level in the central mantle, while the upstream regulatory genes included in melanogenesis were mainly upregulated in the edge mantle, suggesting the different molecular functions of the two mantle regions in shell pigmentation.

Molecular phylogeny of the Pectinoidea (Bivalvia) indicates Propeamussiidae to be a non-monophyletic family with one clade sister to the scallops (Pectinidae).

Scallops (Pectinidae) are one of the most diverse families of bivalves and have been a model system in evolutionary biology. However, in order to understand phenotypic evolution, the Pectinidae needs to be placed in a deeper phylogenetic framework within the superfamily Pectinoidea. We reconstructed a molecular phylogeny for 60 species from four of the five extant families within the Pectinoidea using a five gene dataset (12S, 16S, 18S, 28S rRNAs and histone H3). Our analyses give consistent support for the non-monophyly of the Propeamussiidae, with a subset of species as the sister group to the Pectinidae, the Propeamussiidae type species as sister to the Spondylidae, and the majority of propeamussiid taxa sister to the Spondylidae + Pr. dalli. This topology represents a previously undescribed relationship of pectinoidean families. Our results suggest a single origin for eyes within the superfamily and likely multiple instances of loss for these characters. However, it is now evident that reconstructing the evolutionary relationships of Pectinoidea will require a more comprehensive taxonomic sampling of the Propeamussiidae sensu lato.

Mitochondrial genome of Argopecten irradians reveals higher-level phylogenetic relationships in Anisomyaria.

The complete mitochondrial genome of Argopecten irradians strain Zhongkehong was sequenced and annotated: it is 16,212 bp in length and contains twelve protein-coding genes (atp8 is absent, as in most species in Anisomyaria), two ribosomal RNA genes, and 21 transfer RNA genes (trnS is absent and there are two copies of trnF). The heavy strand has an overall A + T content of 57.3%; GC and AT skews are 0.249 and -0.262, respectively, indicating more Gs and more Ts than Cs and As. Phylogenetic analysis based on Bayesian Inference and Maximum Likelihood of the twelve protein-coding genes shows that A. irradians has close relationships with A. purpuratus and A. ventricosus; this indicated that A. irradians belongs to the Pectinidae family. The Pectinidae was sister to (Ostreidae + Mytilidae). This work provides general information on the evolution of cultured scallops.

First data on three bivalve species exposed to an intra-harbour polymetallic contamination (La Rochelle, France).

Evaluating diffuse sediment contamination in the environment is a major concern with the aim of reaching a good chemical and ecological state of the littoral zone. In this study the risks of chronic chemical contamination and consequences in the bivalves Crassostrea gigas, Mytilus sp. and Mimachlamys varia were evaluated in coastal environments. The objective here was to understand the anthropological phenomena that affect the functioning of the marina of La Rochelle (semi-closed environment). Harbours seeking ecomanagement accreditations (such as the international reference ISO 14001) constitute zones of interest to implement biomonitoring studies. The biological effects of chemical pollution in the Marina of La Rochelle were studied to develop a multi-biomarker biomonitoring approach on specific marine species of this site. Moreover, a genetic (DNA barcoding) approach was applied to validate the species identity of collected bivalves. Of the three species tested the scallop, M. varia, was the most sensitive to metal exposure.

The immunomodulation of a maternal translationally controlled tumor protein (TCTP) in Zhikong scallop Chlamys farreri.

Translationally controlled tumor protein (TCTP) is initially described as a highly conserved protein implicated in cell growth, and it is subsequently confirmed to play important roles in mediating the innate immune response, especially the inflammatory. In the present study, the full-length cDNA sequence of a TCTP from Zhikong scallop Chlamys farreri (designed as CfTCTP) was cloned by rapid amplification of cDNA ends (RACE) technique based on the expression sequence tag (EST) analysis. It was of 1230 bp with an open reading frame (ORF) of 543 bp encoding a polypeptide of 180 amino acids. The deduced amino acid sequence contained a conserved TCTP signature sequence (from I47 to E58) and it shared 26.1%-48.9% similarities with previously identified TCTPs. CfTCTP was clustered with the TCTP from Argopectehs irradias in the phylogenetic tree and was designated into a single branch of mollusk with TCTP from Ruditapes philippinarum. The mRNA transcripts of CfTCTP were constitutively expressed in all the tested tissues, including haemocytes, muscle, mantle, gill, hepatopancreas, kidney and gonad, with the highest expression level in hepatopancreas. The mRNA expression level of CfTCTP in oocytes and fertilized eggs kept at a higher level, and was down-regulated from 2-cell embryos to the lowest level in gastrula. Then it was up-regulated in trochophore and dropped down in the late veliger larvae to the similar level as that in oocytes. After pathogen-associated molecular patterns (PAMPs) stimulation, the expression of CfTCTP mRNA in haemocytes was increased at 3 or 6 h, and fall down to the normal level at 24 h. The recombinant protein of CfTCTP could induce the release of histamine from BT-549 cells. All these results indicated that CfTCTP was a pro-inflammatory factor and it could be maternally transferred from female gonad to oocytes and offspring, and play pivotal role in the embryonic development and immune protection of scallops.

Hsp70 gene expansions in the scallop Patinopecten yessoensis and their expression regulation after exposure to the toxic dinoflagellate Alexandrium catenella.

Heat shock protein 70 (Hsp70s) family members are present in virtually all living organisms and perform a fundamental role against different types of environmental stressors and pathogenic organisms. Marine bivalves live in highly dynamic environments and may accumulate paralytic shellfish toxins (PSTs), a class of well-known neurotoxins closely associated with harmful algal blooms (HABs). Here, we provide a systematic analysis of Hsp70 genes (PyHsp70s) in the genome of Yesso scallop (Patinopecten yessoensis), an important aquaculture species in China, through in silico analysis using transcriptome and genome databases. Phylogenetic analyses indicated extensive expansion of Hsp70 genes from the Hspa12 sub-family in the Yesso scallop and also the bivalve lineages, with gene duplication events before or after the split between the Yesso scallop and the Pacific oyster. In addition, we determined the expression patterns of PyHsp70s after exposure to Alexandrium catenella, the dinoflagellate producing PSTs. Our results confirmed the inducible expression patterns of PyHsp70s under PSTs stress, and the responses to the toxic stress may have arisen through the adaptive recruitment of tandem duplication of Hsp70 genes. These findings provide a thorough overview of the evolution and modification of the Hsp70 family, which will gain insights into the functional characteristics of scallop Hsp70 genes in response to different stresses.

Trends in the sand: Directional evolution in the shell shape of recessing scallops (Bivalvia: Pectinidae).

Directional evolution is one of the most compelling evolutionary patterns observed in macroevolution. Yet, despite its importance, detecting such trends in multivariate data remains a challenge. In this study, we evaluate multivariate evolution of shell shape in 93 bivalved scallop species, combining geometric morphometrics and phylogenetic comparative methods. Phylomorphospace visualization described the history of morphological diversification in the group; revealing that taxa with a recessing life habit were the most distinctive in shell shape, and appeared to display a directional trend. To evaluate this hypothesis empirically, we extended existing methods by characterizing the mean directional evolution in phylomorphospace for recessing scallops. We then compared this pattern to what was expected under several alternative evolutionary scenarios using phylogenetic simulations. The observed pattern did not fall within the distribution obtained under multivariate Brownian motion, enabling us to reject this evolutionary scenario. By contrast, the observed pattern was more similar to, and fell within, the distribution obtained from simulations using Brownian motion combined with a directional trend. Thus, the observed data are consistent with a pattern of directional evolution for this lineage of recessing scallops. We discuss this putative directional evolutionary trend in terms of its potential adaptive role in exploiting novel habitats.

Genome-wide identification, characterization and expression analyses of two TNFRs in Yesso scallop (Patinopecten yessoensis) provide insight into the disparity of responses to bacterial infections and heat stress in bivalves.

Tumor necrosis factors receptors (TNFRs) comprise a superfamily of proteins characterized by a unique cysteine-rich domain (CRD) and play important roles in diverse physiological and pathological processes in the innate immune system, including inflammation, apoptosis, autoimmunity and organogenesis. Although significant effects of TNFRs on immunity have been reported in most vertebrates as well as some invertebrates, the complete TNFR superfamily has not been systematically characterized in scallops. In this study, two different types of TNFR-like genes, including PyTNFR1 and PyTNFR2 genes were identified from Yesso scallop (Patinopecten yessoensis, Jay, 1857) through whole-genome scanning. Phylogenetic and protein structural analyses were carried out to determine the identities and evolutionary relationships of the two genes. The expression profiling of PyTNFRs was performed at different development stages, in healthy adult tissues and in hemocytes after bacterial infection and heat stress. Expression analysis revealed that both PyTNFRs were significantly induced during the acute phase (3 h) after infection with Gram-positive (Micrococcus luteus) and Gram-negative (Vibrio anguillarum) bacteria, though much more dramatic chronic-phase (24 h) changes were observed after V. anguillarum challenge. For heat stress, only PyTNFR2 displayed significant elevation at 12 h and 24 h, which suggests a functional difference in the two PyTNFRs. Collectively, this study provides novel insight into the PyTNFRs and the specific role and response of TNFR-involved pathways in host immune responses against different bacterial pathogens and heat stress in bivalves.

Molecular genetic analysis of heterosis in interspecific hybrids of Argopecten purpuratus x A. irradians irradians.

Argopecten purpuratus and Argopecten irradians irradians hybridization was successfully performed and the hybrid offspring displayed apparent heterosis in growth traits. To better understand the genetic basis of heterosis, the genomic composition and genetic variation of the hybrids were analyzed with amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers. Seven of eight universal SSR primers displayed polymorphism in the hybrids and their parental groups, and hybrids inherited both parental geno-types at each locus. Using five primer combinations in AFLP analysis, 433 loci were amplified in the hybrids and their parental groups. The frequency of polymorphisms was 88.22%. F1 hybrids inherited 88.11 and 92.88% of AFLP bands from their parents. Some loci did not follow Mendelian Law, including 48 loci in parents that were lost, and 11 new loci that were amplified in the hybrids. The parameters of Nei's gene diversity, Shannon's Information index, genetic distance, and molecular variance between groups were calculated. The genetic differentiation between two hybrid groups (0.253) was smaller than that between hybrids and their parents (0.554 to 0.645), and was especially smaller than that between two parental groups (0.769). The high genetic similarity (0.9347) and low genetic differentiation (0.2531) between two hybrid groups suggests that these hybrid groups were genetically very close. Heterozygosities of hybrid groups were higher than those of parental groups, indicating that the hybrids had increased genetic diversity.

PUFA biosynthesis pathway in marine scallop Chlamys nobilis Reeve.

Long-chain polyunsaturated fatty acids (LC-PUFAs) are essential in important physiological processes. However, the endogenous PUFA biosynthesis pathway is poorly understood in marine bivalves. Previously, a fatty acyl desaturase (Fad) with Δ5 activity was functionally characterized and an elongase termed Elovl2/5 was reported to efficiently elongate 18:2n-6 and 18:3n-3 to 20:2n-6 and 20:3n-3 respectively in Chlamys nobilis. In this study, another elongase and another Fad were identified. Functional characterization in recombinant yeast showed that the newly cloned elongase can elongate 20:4n-6 and 20:5n-3 to C22 and C24, while the newly cloned scallop Fad exhibited a Δ8-desaturation activity, and could desaturate exogenously added PUFA 20:3n-3 and 20:2n-6 to 20:4n-3 and 20:3n-6 respectively, providing the first compelling evidence that noble scallop could de novo biosynthesize 20:5n-3 and 20:4n-6 from PUFA precursors though the "Δ8 pathway". No Δ6 or Δ4 activity was detected for this Fad. Searching against our scallop transcriptome database failed to find any other Fad-like genes, indicating that noble scallop might have limited ability to biosynthesize 22:6n-3. Interestingly, like previously characterized Elovl2/5, the two newly cloned genes showed less efficient activity toward n-3 PUFA substrates than their homologous n-6 substrates, resulting in a relatively low efficiency to biosynthesize n-3 PUFA, implying an adaption to marine environment.

A high mobility group box 1 (HMGB1) gene from Chlamys farreri and the DNA-binding ability and pro-inflammatory activity of its recombinant protein.

High-mobility group box 1 (HMGB1) protein, a highly conserved DNA binding protein, plays an important role in maintaining nucleosome structures, transcription, and inflammation. In the present research, a cDNA of 1268 bp for the Zhikong scallop Chlamys farreri HMGB1 (designed as CfHMGB1) was cloned via rapid amplification of cDNA ends (RACE) technique and expression sequence tag (EST) analysis. The complete cDNA sequence of CfHMGB1 contained an open reading frame (ORF) of 648 bp, which encoded a protein of 215 amino acids. The amino acid sequence of CfHMGB1 shared 53-57% similarity with other identified HMGB1s. There were two HMG domains, two low complexity regions and a conserved acidic tail in the amino acid sequence of CfHMGB1. The mRNA transcripts of CfHMGB1 were constitutively expressed in all the tested tissues, including haemocytes, muscle, mantle, gill, hepatopancreas, kidney and gonad, with the highest expression level in hepatopancreas. The mRNA expression profiles of CfHMGB1 in haemocytes after the stimulation with different pathogen-associated molecular patterns (PAMPs), including lipopolysaccharide (LPS), peptidoglycan (PGN) and glucan (Glu), were similar with an up-regulation in the early stage and then recovered to the original level. The recombinant CfHMGB1 protein could bind double-stranded DNA and induce the release of TNF-α activity in mixed primary culture of scallop haemocytes. These results collectively indicated that CfHMGB1, with DNA-binding ability and pro-inflammatory activity, could play an important role in the immune response of scallops.

A low-density lipoprotein receptor-related protein (LRP)-like molecule identified from Chlamys farreri participated in immune response against bacterial infection.

Low-density lipoprotein receptor-related protein (LRP) is a group of important endocytic receptors contributing to binding ligands and maintaining internal environment. In the present study, an LRP-like molecule was identified from Zhikong scallop Chlamys farreri (CfLPR), and its mRNA expression profiles, tissue location, and immunology activities were analyzed to explore its possible function in the innate immune system. The ORF of CfLRP was of 1971 bp encoding a polypeptide of 656 amino acids with ten low-density lipoprotein-receptor YWTD (LY) domains and one scavenger receptor cysteine-rich (SRCR) domain. It shared similar structure with out-membrane domains of LRP family members in mammalian. The mRNA transcripts of CfLRP were dominantly expressed in hepatopancreas and mantle (P < 0.01), and its mRNA level in hemocytes was up-regulated (P < 0.01) significantly after the stimulations of lipopolysaccharides (LPS), peptidoglycan (PGN) and ß-glucan. Western blotting assay using polyclonal antibody specific for CfLRP revealed that CfLRP was localized in the plasma. The recombinant protein of CfLRP (rCfLRP) could bind acetylated low density lipoprotein (Ac-LDL), metalloprotease SPF1 of Vibrio splendidus and mannan, but could not bind other typical PAMPs such as LPS, PGN, ß-glucan and zymosan. Meanwhile, rCfLRP also exhibited strong bacteriostatic activity to Gram-negative bacteria Vibrio anguillarum and V. splendidus. These results indicated that CfLRP could serve as a receptor to recognize and eliminate the invading pathogens, which provided a new implication in the function of LRP-like molecules in invertebrate immunity.

Identification of a CYP3A-like gene and CYPs mRNA expression modulation following exposure to benzo[a]pyrene in the bivalve mollusk Chlamys farreri.

In this study, we isolated a CYP3A-like gene from ovary of the scallop (Chlamys farreri). High levels of CYP3A-like gene expression occur in the digestive gland and gonad, which suggested their role in the metabolism of steroids and xenobiotics. Scallops were exposed to a polycyclic aromatic hydrocarbons (PAHs), benzo[a]pyrene (B[a]P) for 10 days. The CYP4 and CYP3A-like gene can be up-regulated by B[a]P in a dose-dependent manner after 10 days exposure. But no induction of the CYP3A-like was observed in 10 µg/L B[a]P group. The CYP1A-like expression can only be induced by 0.025 µg/L B[a]P. 0.5 and 10 µg/L B[a]P caused significant DNA damage and 10 µg/L B[a]P can also lead to oxidative damage. These results demonstrate that the mollusk CYPs can be modulated by environmental pollutant, and the blocked induction of CYP3A-like and CYP1A-like expression probably results from the high genotoxicity and oxidative damage partly.

Análise bacteriológica de músculo e gônadas de vieira, Nodipecten nodosus (Mollusca: Bivalvia), congelados e irradiados / Bacteriological analysis of frozen and irradiated scallops’ muscle and gonads Nodipecten nodosus (Mollusca: Bivalvia)

No presente trabalho foram analisadas amostras de músculo e gônadas de vieira crus e congelados, oriunda de maricultura de Angra dos Reis, Rio de Janeiro, Brasil. Esta pesquisa teve como finalidade a verificação da eficiência da irradiação, utilizando-se doses de 2kGy e 5kGy. Na Contagem de Bactérias Heterotróficas Aeróbias Mesófilas (CBHAM) observou-se diferença estatisticamente significativa do grupo controle em relação ao grupo irradiado a 5kGy; enquanto que para a Contagem de Bactérias Heterotróficas Aeróbias Psicrotróficas (CBHAP) não se observou nenhuma diferença estatisticamente significativa entre os grupos avaliados. O Número Mais Provável (NMP) de Enterococcus spp. não teve sua presença evidenciada em nenhuma das amostras analisadas. Conclui-se que a irradiação, nesta pesquisa, foi eficiente somente para bactérias mesófilas na dose de 5kGy.

The present article investigated the effectiveness of irradiation process to conservate frozen raw scallops’ muscle and gonads. Samples of this animal were collected from cultivated areas at Angra dos Reis, Rio de Janeiro state, Brazil. The samples were submitted to treatment of 2 and 5 kGy doses. Mesophilic Aerobic Heterotrophic Bacteria Count showed a statistically significant difference from the control group related to the 5kGy one, while for the Heterotrophic Bacteria Aerobic Psychrotrophic Count were not observed any statistically significant difference among the analysed groups. The Most Probable Number of Enterococcus spp. was not evident in any of the samples. It was concluded that irradiation was effective only for mesophilic bacteria using the 5kGy dose in this research.

A novel C-type lectin from bay scallop Argopecten irradians (AiCTL-7) agglutinating fungi with mannose specificity.

C-type lectins are a superfamily of proteins that can bind pathogen-associated molecular patterns (PAMPs) and microorganisms through the recognition of carbohydrates, thus they are directly involved in innate defense mechanisms as part of the acute-phase response to infection. In this study, the cDNA of a novel C-type lectin (designated as AiCTL-7) was cloned from bay scallop Argopecten irradians by expression sequence tag (EST) analysis and rapid amplification of cDNA ends (RACE) approach. The full-length cDNA of AiCTL-7 was of 651 bp containing a 525 bp open reading frame which encoded a signal peptide of 15 residues and a conserved carbohydrate-recognition domain (CRD) of 174 residues with the EPD and WSD motifs instead of the invariant EPN and WND motifs for determining the carbohydrate-binding specificity and constructing Ca(2+)-binding site 2 in vertebrates. The deduced amino acid sequence of AiCTL-7 CRD shared homology not only with the CRDs of C-type lectins in mollusks, but also with the fish lectin CRDs. The mRNA transcripts of AiCTL-7 were mainly detected in the tissue of hepatopancreas and also marginally detectable in kidney, gonad, hemocytes, heart and adductor of health scallop. After challenge with fungi Pichia pastoris GS115 and Gram-negative bacteria Listonella anguillarum, the relative expression level of AiCTL-7 was up-regulated significantly in hepatopancreas and hemocytes. The CRD of AiCTL-7 was recombined and expressed in Escherichia coli, and the recombinant protein (rAiCTL-7) aggregated P. pastoris remarkably in a Ca(2+)-dependent manner, and this agglutination could be inhibited by d-mannose, but not by d-galactose or ß-1,3-glucan. However, rAiCTL-7 displayed no obvious agglutinating activity against L. anguillarum. These results collectively indicated that AiCTL-7 was involved in the primitive acute-phase response to microbial invasion as an important pattern recognition receptor (PRR) in the innate immune system of scallops.

A macrophage migration inhibitory factor like gene from scallop Chlamys farreri: Involvement in immune response and wound healing.

Macrophage migration inhibitory factor (MIF) is an evolutionarily ancient and highly conserved cytokine with multiple functions. In the present study, a MIF-like gene was cloned from Zhikong scallop Chlamys farreri (designated as CfMIF) based on expressed sequence tag (EST) analysis and rapid amplification of cDNA ends (RACE) approach. The full-length cDNA of CfMIF was of 2296bp, consisting of a 5' untranslated region (UTR) of 60bp, a 3' UTR of 1903bp with a poly(A) tail and an open reading frame (ORF) of 333bp encoded 111 amino acid residues with a calculated molecular mass of 12.6kDa and a theoretical isoelectric point of 5.63. The deduced amino acid sequence of CfMIF shared 27-50.5% similarity with those of other known MIFs. A conserved MIF domain was identified in the deduced amino acid sequence of CfMIF, and conserved proline(2) and lysine(33) were also found to be present in CfMIF. Phylogenetic analysis revealed that CfMIF is one of MIF members. The tissue distribution and temporal expression of CfMIF in hemocytes of scallop after lipopolysaccharide (LPS), peptidoglycan (PGN) and ß-glucan stimulation were detected by real-time RT-PCR. CfMIF gene was ubiquitously expressed in six selected tissues of healthy scallops, with the higher expression levels in hepatopancreas, mantle and gill. In comparison with the control group, the expression of CfMIF mRNA in hemocytes was up-regulated significantly at 6h, 24h and 48h after LPS treatment, and at all time points after PGN and glucan treatment. The cDNA fragment encoding mature peptide of CfMIF was recombined and expressed in Escherichia coli BL21 (DE3) pLysS. The recombinant protein of CfMIF (rCfMIF) promoted sheep fibroblast migration into scraped spaces in vitro. These results generated from the present study encourage us to suggest that CfMIF was a novel member of MIF family, and it was involved in immune response and wound healing by promoting fibroblast migration.

Complete mitochondrial DNA sequence and phylogenetic analysis of Zhikong scallop Chlamys farreri (Bivalvia: Pectinidae).

The complete mitochondrial genome of Zhikong scallop Chlamys farreri is 21,695 bp in length and contains 12 protein-coding genes (the atp8 gene is absent, as in most bivalves), 2 ribosomal RNA genes, and 22 transfer RNA genes. The heavy strand has an overall A+T content of 58.7%. GC and AT skews for the mt genome of C. farreri are 0.337 and -0.184, respectively, indicating the nucleotide bias against C and A. The mitochondrial gene order of C. farreri differs drastically from the scallops Argopecten irradians, Mimachlamys nobilis and Placopecten magellanicus, which belong to the same family Pectinidae. 6623 bp non-coding nucleotides exist intergenically in the mitogenome of C. farreri, with a large continuous sequence (4763 bp) between tRNA ( Val ) and tRNA ( Asn ). Two repeat families are found in the large continuous sequence, which seems to be a common feature of scallops. Phylogenetic analysis based on 12 concatenated amino acid sequences of protein-coding genes supports the monophyly of Pectinidae and paraphyletic Pteriomorphia with respect to Heteroconchia.

Inferring the demographic history of the Adriatic Flexopecten complex.

Phylogenetic analysis of DNA sequences can be a useful tool in taxonomical studies, which has important implications in terms of species traceability. The aim of our study is to solve the controversy regarding the taxonomical status of the Flexopecten group, which includes two putative sister species (F. glaber and F. proteus) that co-occur in the Adriatic Sea and are clearly distinguishable on the basis of morphometric characters. Our molecular analysis using three mitochondrial genes (COI, 12S rRNA and 16S rRNA) and one nuclear gene (Histone H3) suggest that F. glaber and F. proteus are the same species, as evidenced by both putative species appearing mixed in all genetic trees with no clustering according to species. Using a Bayesian approach, we inferred the demographic history of the Flexopecten group, which suggests that first F. glaber occurred in the Mediterranean, then F. glaber colonized the Adriatic sometime in the last 18,000 years, and finally the F. proteus morph appeared only recently in the Adriatic Sea. We propose F. proteus to be synonymized with F. glaber, which should have priority and be used in the future.