Origin, diversification, and historical biogeography of the genus Trachurus (Perciformes: Carangidae)

We addressed phylogenetic relationships in the genus Trachurus using cytochrome b gene and D-loop sequences. The trees showed five groups: (1) the Southwest Pacific species (T. japonicus, T. novaezelandiae, and T. declivis); (2) The Mediterranean Sea and Eastern Atlantic species (T. mediterraneus); (3) The Atlantic Ocean species (T. lathami and T. trecae); (4) Eastern Atlantic species (T. trachurus and T. capensis); and (5) a group of highly mobile pelagic species, two from the Eastern Pacific (T. symmetricus and T. murphyi) and one from the Eastern Atlantic (T. picturatus). The phylogeny based on Cyt b, supports the molecular clock hypothesis and our results agree with the reported fossil indicating that the origin of this genus occur when the Thetys Sea closed (around 18.4 MYA). In addition, a very slow neutral substitution rate is reported identified only two periods of maximum diversification: the first occurring between 18.4 and 15.0 MYA and the second between 8.4 MYA and present day.     

Molecular phylogeny of Turkish Trachurus species (Perciformes: Carangidae) inferred from mitochondrial DNA analyses

Genetic variation among three species of Trachurus (T. trachurus, T. mediterraneus and T. picturatus) from Turkey was investigated by phylogenetic analysis of the entire mtDNA control region (CR) (862 bp, n = 182) and partial cytochrome (cyt) b (239 bp, n = 174) sequences. Individuals were collected at nine stations in four geographic locations: North‐eastern Mediterranean Sea, Aegean Sea, Sea of Marmara and Black Sea. Polymerase chain reaction‐direct sequencing of the CR and the partial cyt b genes produced 28 and 131 distinct haplotypes, respectively. Maximum likelihood, neighbour‐joining and maximum parsimony methods produced similar tree topologies. The results of both CR and cyt b sequence analyses revealed the existence of several species‐specific nucleotide sites that can be used to discriminate between the three species. Genetic distances indicated that T. mediterraneus and T. picturatus are more closely related to each other than either is to T. trachurus. Inter‐nucleotide and intra‐nucleotide diversities of T. picturatus were larger than those of T. mediterraneus and T. trachurus. There was no evidence of a geographical difference in haplotype frequencies of these two mtDNA regions to be clustered.     

Evolutionary analysis of cytochrome b sequences in some perciformes: Evidence for a slower rate of evolution than in mammals

To obtain information relative to the phylogenesis and microevolutionary rate of fish mitochondrial DNA, the nucleotide sequence of cytochrome b gene in seven fish species belonging to the order of Perciformes was determined. Sequence analysis showed that fish mitochondrial DNA has a nucleotide compositional bias similar to that of sharks but lower compared to mammals and birds. Quantitative evolutionary analysis, carried out by using a markovian stochastic model, clarifies some phylogenetic relationships within the Perciformes order, particularly in the Scombridae family, and between Perciformes, Gadiformes, Cypriniformes, and Acipenseriformes. The molecular clock of mitochondrial DNA was calibrated with the nucleotide substitution rate of cytochrome b gene in five shark species having divergence times inferred from paleontological estimates. The results of such analysis showed that Acipenseriformes diverged from Perciformes by about 200 MY, that the Perciformes common ancestor dates back to 150 MY, and that fish mitochondrial DNA has a nucleotide substitution rate three to five times lower than that of mammals.Correspondence to: C. SacconeThe nucleotide sequences reported in this paper have been submitted to the GenBank/EMBL Data Library with accession numbers X81562 (Sarda sarda), X81563 (Thunnus thynnus), X81564 (Scomber scombrus), X81565 (Oreochromis mossambicus), X81566 (Dicentrarchus labrax), X81567 (Boops hoops), X81568 (Trachurus trachurus)     

Molecular characterization of larval anisakid nematodes from marine fishes of Madeira by a PCR-based approach, with evidence for a new species

One-hundred and fifteen anisakid larvae from 3 different fish hosts, Aphanopus carbo, Scomber japonicus, and Trachurus picturatus, caught in Madeiran waters, were identified by PCR-RFLP. Three distinct species were identified in A. carbo, namely Anisakis simplex sensu srricto, Anisakis pegreffii, and Anisakis ziphidarum; 5 in S. japonicus, i.e., A. simplex s.s., A. pegreffii, Anisakis physeteris, Anisakis typica, and A. ziphidarum; and 3 in T. picturatus, i.e., A. simplex s.s., A. pegreffii, and A. typica. Anisakis simplex s.s. was the most frequent species in both A. carbo and S. japonicus (54% and 23.5%, respectively). Anisakis pegreffii and A. physeteris occurred with a frequency of 20.6% in S. japonicus, whereas in T. picturatus the most frequent species was A. typica (41.9%), followed by A. simplex s.s. (32.3%). Furthermore, A. carbo and S. japonicus were infected by an apparently undescribed taxon, provisionally named Anisakis sp. A. Based on estimations of the genetic distance, this new taxon seems to be more similar to A. ziphidarum (0.0335) than to other species of the genus.     

Lipid composition of the muscles and liver of Mediterranean fish

Studies have been made on lipid composition of the liver, white and red skeletal muscles in 9 species of Mediterranean fishes (Scomber scomber, Scomberesox saurus, Trachurus trachurus, T. mediteraneus. Sprattus sprattus, Engraulis engrasicholus, Diplodus annularis, Gadus merlangus, Scorpaena porcus). Lipids were fractionated by means of thin layer chromatography. It was shown that the content of lipids in red muscles is significantly higher than in white ones. Muscles of highly active species are richer in lipids as compared with those in species which are characterized by lower functional activity. In fishes with high muscle activity, lipids exhibit a higher triglyceride content. Tissue concentration of lipids is closely related to the degree of maturity of gonads. Ecological and physiological peculiarities of fishes significantly affect lipid characteristics of their tissues.     

Parasites as biological tags in population studies of demersal and pelagic fish species

Among the different techniques applied in a holistic approach for fish stock identification, the use of parasites as "biological tags" is becoming increasingly important. In this presentation, our recent studies on the use of some parasite species, identified by genetic markers, and the parasite/fauna composition, in stock identification of demersal (Merluccius merluccius), small pelagic (Trachurus trachurus), and large pelagic fish species (Xiphias gladius) are reviewed. Different species of Anisakis and Hysterothylacium were genetically identified by the application of genetic (allozyme) markers. Statistically significant differences in the spatial distribution of distinct species of Anisakis were found in the fish considered. As to the species of Hysterothylacium genetically detected, different relative proportions were detected in several Mediterranean and Atlantic samples of swordfish (X. gladius). This study demonstrates the potential value of these anisakid nematodes, at both larval and adult stages, as "biological tags" for these fish species in European waters.     

New data on Myxosporidia of Black Sea fishes

A new species of myxosporidians Alatospora solomoni from Trachurus mediterraneus is described. Two more species Sphaeromyxa balbiani from Blennius sanguinolentus and Ortholinea divergens from Symphodus roissali are found in the Black Sea for the first time.     

Integrating genetic and parasitological approaches in the frame of multidisciplinary fish stock analysis

To assess fish stocks boundaries and state, the tools of population genetics have been widely used, contributing to the evaluation of relevant parameters such as the identification of stock boundaries, the assessment of gene flow and the estimation of effective population size. Also, increasing evidences show that the monitoring of the genetic diversity level is a reliable method to check the status of fish stocks. However, genetics cannot answer all the questions. For example, in high gene flow species the genetic approach could have not enough resolution to identify stock limits, while the use of parasites as biological tags could provide insights into stock structure. Even better, the so-called holistic approach, applying simultaneously a wide range of complementary techniques, is the only one considered able to provide a reliable and complete picture of fish stocks and to address a sustainable exploitation of marine resources. The work will present some examples from multidisciplinary studies concerning commercially relevant species with different biological features: the demersal European hake (Merluccius merluccius), the small pelagic horse mackerel (Trachurus trachurus) and the large pelagic swordfish (Xiphias gladius). In all these case studies merging genetic, parasitological and environmental data helped to reveal the real patterns of stocks structure.     

Chloroplast genome sequences from total DNA for plant identification

Chloroplast DNA sequence data are a versatile tool for plant identification or barcoding and establishing genetic relationships among plant species. Different chloroplast loci have been utilized for use at close and distant evolutionary distances in plants, and no single locus has been identified that can distinguish between all plant species. Advances in DNA sequencing technology are providing new cost‐effective options for genome comparisons on a much larger scale. Universal PCR amplification of chloroplast sequences or isolation of pure chloroplast fractions, however, are non‐trivial. We now propose the analysis of chloroplast genome sequences from massively parallel sequencing (MPS) of total DNA as a simple and cost‐effective option for plant barcoding, and analysis of plant relationships to guide gene discovery for biotechnology. We present chloroplast genome sequences of five grass species derived from MPS of total DNA. These data accurately established the phylogenetic relationships between the species, correcting an apparent error in the published rice sequence. The chloroplast genome may be the elusive single‐locus DNA barcode for plants.     

Larval trypanorhynchs (Platyhelminthes: Eucestoda: Trypanorhyncha) from black-scabbard fish, Aphanopus carbo and oceanic horse mackerel, Trachurus picturatus in Madeira (Portugal)

Four different types of trypanorhynch postlarvae were found attached to the stomach mucosa, external stomach wall or free in the body cavity of two marine fishes from Madeira, namely blackscabbard fish, Aphanopus carbo and oceanic horse mackerel, Trachurus picturatus. Morphological features shown by SEM indicated that the postlarvae belonged to the species Tentacularia coryphaenae, Sphyriocephalus tergestinus, Nybelinia lingualis and possibly N. yamaguitii. Prevalence [mean intensity (range)] of T. coryphaenae, S. tergestinus and Nybelinia spp. in A. carbo (n = 135) was 12.6% [1.65 +/- 1.27(1-6)], 5.9% [1.57 +/- 0.79 (1-3)] and 2.2% [1.33 +/- 0.58 (1-2)] respectively. The prevalence of T. coryphaenae and S. tergestinus showed some seasonality, with a rise in prevalence of T. coryphaenae corresponding to a decrease in prevalence of S. tergestinus. However these differences were not significant. In T. picturatus (n = 304) only N. lingualis was found at a prevalence of 9.6%. Both S. tergestinus and N. lingualis were recovered only from the stomach mucosa or external stomach wall, while T. coryphaenae was observed either attached to the stomach mucosa or free in the visceral cavity of the fish. The paper presents the first scanning electron micrographs (SEM) of Sphyriocephalus tergestinus and a new geographical record of N. lingualis in T. picturatus.     

The Taxonomic Status and Intraspecific Differentiation of the Black Sea Horse Mackerel, <Emphasis Type="Italic">Trachurus mediterraneus ponticus</Emphasis> (Aleev, 1956) (Carangidae)

The taxonomic status of the horse mackerel, Trachurus mediterraneus ponticus (Aleev, 1956), which inhabits the Black Sea, has been clarified based on the analysis of variation in the nucleotide sequence of the mtDNA cytochrome b (Cyt-b) locus. A comparison of this species with the horse mackerel from the Mediterranean basin and the World Ocean has shown that the Black Sea horse mackerel is neither an independent species nor a subspecies and can only be qualified as the species Trachurus mediterraneus (Steindachner, 1868) distributed throughout the Mediterranean Sea basin. A hypothesis has been made about the possible cause of the origin and existence of two forms, “large” and “small”, of the horse mackerel. By using the technique of calculating ontogenetic trajectories, it has been found that these are two morpho-ecological forms, whose differentiation is most likely determined by the type of feeding.     

Causes of Size Homoplasy Among Chloroplast Microsatellites in Closely Related <Emphasis Type="Italic">Clusia</Emphasis> Species

Chloroplast DNA sequences and microsatellites are useful tools for phylogenetic as well as population genetic analyses of plants. Chloroplast microsatellites tend to be less variable than nuclear microsatellites and therefore they may not be as powerful as nuclear microsatellites for within-species population analysis. However, chloroplast microsatellites may be useful for phylogenetic analysis between closely related taxa when more conventional loci, such as ITS or chloroplast sequence data, are not variable enough to resolve phylogenetic relationships in all clades. To determine the limits of chloroplast microsatellites as tools in phylogenetic analyses, we need to understand their evolution. Thus, we examined and compared phylogenetic relationships of species within the genus Clusia, using both chloroplast sequence data and variation at seven chloroplast microsatellite loci. Neither ITS nor chloroplast sequences were variable enough to resolve relationships within some sections of the genus, yet chloroplast microsatellite loci were too variable to provide any useful phylogenetic information. Size homoplasy was apparent, caused by base substitutions within the microsatellite, base substitutions in the flanking regions, indels in the flanking regions, multiple microsatellites within a fragment, and forward/reverse mutations of repeat length resulting in microsatellites of identical base composition that were not identical by descent.     

Characterization of human-specific DNA sequences obtained by genome subtraction

Recent studies on molecular evolution using nucleotide sequence data to clarify phylogenetic relationships among humans and the African great apes, have revealed that humans are more closely related to chimpanzees than to gorillas. However, the genetic basis of human uniqueness remains unclear. This is because phylogenetic studies have merely evaluated the degree of similarity by calculating the accumulation of nucleotide substitutions that have occurred in neutral DNA regions commonly present in all the species examined. In contrast, the genome subtraction method recently developed by us has revealed dissimilarity even among the genomes of the most closely related species. Here we describe the characteristics of the DNA sequences obtained by genome subtraction between humans and chimpanzees.     

Close relatedness between mitochondrial DNA from seven Anser goose species

The phylogenetic relationships of seven goose species and two of the subspecies representing the genus Anser were studied by approximately 1180 bp of mitochondrial DNA tRNAglu, control region and tRNAphe sequences. Despite obvious morphological and behavioural affinities among the species, their evolutionary relationships have not been studied previously. The small amount of genetic differentiation observed in the mitochondrial DNA indicates an extremely close evolutionary relationship between the Anser species. The sequence divergences between the species (0.9–5.5%) are among the lowest reported for avian species with speciation events of Anser geese dating to late Pliocene and Pleistocene. The species grouped into four mtDNA lineages: (1) snow and Ross’ goose, (2) greylag goose, (3) white‐fronted goose, and (4) bean, pink‐footed and lesser white‐fronted goose. The phylogenetic relationships of the most closely related species, bean, pink‐footed and lesser white‐fronted goose, indicate a period of rapid cladogenesis. The poor agreement between morphological relationships and the phylogenetic relationships indicated by mtDNA sequences implies that either ancestral polymorphism and lineage sorting, hybridization and introgression or convergent evolution has been involved.     

Molecular data reveal high taxonomic diversity of allogromiid Foraminifera in Explorers Cove (McMurdo Sound,Antarctica)

Allogromiids are organic-walled or agglutinated, single-chambered Foraminifera, common in deep-sea and polar benthic communities. The simple forms and paucity of distinctive features make allogromiid identification difficult by traditional means. Molecular phylogenetic methods offer alternative tools for species identification and are used here to investigate allogromiid diversity. We obtained 135 partial small-subunit ribosomal DNA sequences of allogromiids collected in Explorers Cove, McMurdo Sound, Antarctica. In contrast to the 27 morphotypes identified, phylogenetic analysis revealed 49 molecular types (considered separate species) that differ by more than 5% of sequence divergence. The 49 genetic types form 28 molecular supra-groups that differ by more than 20% and probably represent distinct genera or families. Large genetic distances separating the molecular types indicate unexpectedly high taxonomic diversity. Comparison of our data with sequences of non-Antarctic allogromiids suggests that Explorers Cove species might be endemic and only distantly related to comparable northern hemisphere fauna.     

Evolutionary Origin of Nonuniversal Cug(ser) Codon in Some Candida Species as Inferred from a Molecular Phylogeny

CUG, a universal leucine codon, has been reported to be read as serine in various yeast species belonging to the genus Candida. To gain a deeper insight into the origin of this deviation from the universal genetic code, we carried out a phylogenetic analysis based on the small-subunit ribosomal RNA genes from some Candida and other related Hemiascomycetes. Furthermore, we determined the phylogenetic relationships between the tRNA(Ser)CAG, responsible for the translation of CUG, from some Candida species and the other serine and leucine isoacceptor tRNAs in C. cylindracea. We demonstrate that the group of Candida showing the genetic code deviation is monophiletic and that this deviation could have been originated more than 150 million years ago. We also describe how phylogenetic analysis can be used for genetic code predictions.     

The occurrence and infection dynamics of Anisakis larvae in the black-scabbard fish,Aphanopus carbo,chub mackerel,Scomber japonicus,and oceanic horse mackerel,Trachurus picturatus from Madeira,Portugal

Larval stages of Anisakis spp. (Nematoda: Anisakidae) were found encapsulated or free in the viscera and abdominal cavity of the black-scabbard fish, Aphanopus carbo, chub mackerel, Scomber japonicus and oceanic horse mackerel, Trachurus picturatus in Madeiran waters. The prevalence of infection reached 97.2% for A. carbo, 69.5% for S. japonicus and 62.5% for T. picturatus. Considerable differences in parasite intensities between A. carbo and both S. japonicus and T. picturatus were found, with mean intensities up to 69.6 in A. carbo, while in the other two fish hosts the intensity reached only a maximum of 2.6. These differences were probably due to different feeding behaviours of the hosts. Intensities of Anisakis sp. in A. carbo were high irrespective of sex and season. No relationship between host length and prevalence of infection was observed for A. carbo, while for S. japonicus a weak positive significant relationship was found.     

Molecular evolution of insertions and deletion in the chloroplast genome of silene

Insertions, deletions, and inversions in the chloroplast genome of higher plants have been shown to be extremely useful for resolving phylogenetic relationships both between closely related taxa and among more basal lineages. Introns and intergenic spacers from the chloroplast genome are now increasingly used for phylogenetic and population genetic studies of populations from a single species, and it is therefore interesting to know whether indels can provide useful data and hence increase the power of intraspecific studies. Here, we show that indels in three cpDNA intergenic spacers and one cpDNA intron for two species of Silene evolve at slightly higher rates than base pair substitutions. Repeat indels appear to have the highest rate of evolution and are thus more prone to homoplasy. We show that coded indel data have high information content for phylogenetic analysis, and indels thus provide useful information to infer phylogenetic relationships at the intraspecific level.     

Continuous culture of Perkinsus mediterraneus, a parasite of the European flat oyster Ostrea edulis, and characterization of its morphology, propagation, and extracellular proteins in vitro

Continuous in vitro cultures of Perkinsus mediterraneus were established from tissues of infected European flat oysters, Ostrea edulis. The parasite proliferated in protein-free medium and divided by schizogony in vitro. Cell morphology was similar to that observed for P. mediterraneus in tissues of naturally infected O. edulis and for other Perkinsus spp. cultured in vitro. Parasite cells enlarged approximately 8-fold when placed in alternative Ray's fluid thioglycollate medium, and stained black with Lugol's iodine solution, a response characteristic of Perkinsus spp. DNA sequences matched those determined previously for P. mediterraneus, and phylogenetic analyses on three different data sets indicated that this was a Perkinsus species with a close relationship to another recently described species, Perkinsus honshuensis. Parasite viability was high (>90%) in vitro, but the proliferation rate was low, with densities generally increasing 2-to-6-fold between subcultures at 6-wk intervals. Enzyme analysis of cell-free culture supernatants revealed protease-, esterase-, glycosidase-, lipase-, and phosphatase-like activities. Incubation with class-specific protease inhibitors showed that P. mediterraneus produced serine proteases, and eight proteolytic bands with molecular weights ranging from 34 to 79 kDa were detected in the supernatants by gelatin sodium dodecylsulfate-polyacrylamide gel electrophoresis.