The fish populations of inshore waters of the west coast of Scotland. The unusual occurrence of the blue whiting (Micromesistius poutassou) and some notes on its biology

This paper records the unusual occurrence of the blue whiting ( Micromesistius poutassou ) from inshore waters of the west coast of Scotland from 1971 to 1974. The fish were O and I-group and appeared to migrate into the area during the autumn and winter months. Data on growth, length for weight relationships and feeding are described.     

Endoparasites of the blue whiting, Micromesistius poutassou from north-west Spain

The communities of metazoan endoparasites of blue whiting, Micromesistius poutassou, in waters of north-west Spain were analysed and a geographical comparison made with other localities. Four hundred blue whiting collected in July 1999 and September 2000 were examined for parasites, excluding the head and gills. Six species were found: Anisakis simplex s.l. (L3), A. physeteris (L3), Hysterothylacium aduncum (L2 and L3), Stephanostomum lophii (metacercaria), S. pristis (adult), and Prosorhynchus crucibulum (metacercaria). The latter is a new host record, and A. physeteris is reported for the first time in blue whiting from the north-east Atlantic. Host gender was not a significant predictor of abundance of any helminth species, and host length was only weakly and positively related to the abundance of A. simplex. Infracommunities were species-poor, with 56% of fish harbouring only one parasite species, and 92% up to two species. Infracommunities were strongly dominated by A. simplex (389 fish) or S. lophii (6 fish). Fish length or gender, and the year of capture, did not affect species richness nor the degree of dominance. There were no significant pair-wise associations between species. Infracommunities were basically composed of several allogenic parasites with different life histories that converge in the blue whiting through the local food web. The parasite fauna of blue whiting in the study area was poor and distinctive compared with that of other localities in the north-east North Atlantic. These peculiarities might primarily be related to the composition of the local community of definitive hosts, although there might also be some influence of the geographical distribution of parasites.     

Larval anisakids parasitizing the blue whiting, Micromesistius poutassou, from Motril Bay in the Mediterranean region of southern Spain

A total of 301 blue whiting, Micromesistius poutassou Risso, 1826, ranging in length from 17 to 28 cm, from Motril Bay (Mediterranean coast, south Spain) were examined for anisakid nematodes, as these fish are common items in the Spanish Mediterranean diet. Three anisakid species were morphologically identified with a total prevalence of 10.63%. Anisakis simplex s.l. Rudolphi, 1809 had a prevalence value of 6.65%, compared with 2.66% for A. physeteris Baylis, 1923 and 2.33% for Hysterothylacium aduncum Rudolphi, 1802. Variations in prevalence values with season and host size are discussed. Allozyme markers (leucine aminopeptidase-1) were used to identify anisakid nematodes assigned to the A. simplex complex and all examined larvae were found to correspond genetically to A. pegreffii Nascetti et al., 1986.     

Population genetic substructure in blue whiting based on allozyme data

The genetic population structure of the pelagic gadoid blue whiting Micromesistius poutassou throughout its east Atlantic distribution range was explored using polymorphisms at the tissue enzyme loci IDHP-2 * and PGM-1 *. The study included 5025 individuals from 65 locations in the east Atlantic and the Mediterranean. Significant geographic heterogeneity in allele frequencies was demonstrated at both loci ( IDHP-2 *: P=0·030, PGM-1 *: P=0·005). The degree of genetic differentiation ( F _ST= 1·1%) in blue whiting appears to be at the same level as for the demersal gadoids cod and haddock. Several separate reproductive units were indicated at the fringes of the distribution range, i.e. in the Barents Sea, and in one Norwegian fjord (Romsdalsfjord).     

Tempo of hybrid inviability in centrarchid fishes (Teleostei: Centrarchidae)

Hybrid viability decreases with divergence time, a pattern consistent with a so-called speciation clock. However, the actual rate at which this clock ticks is poorly known. Most speciation-clock studies have used genetic divergence as a proxy for time, adopting a molecular clock and often far-distant calibration points to convert genetic distances into age. Because molecular clock assumptions are violated for most genetic datasets and distant calibrations are of questionable utility, the actual rate at which reproductive isolation evolves may be substantially different than current estimates suggest. We provide a robust measure of the tempo at which hybrid viability declines with divergence time in a clade of freshwater fishes (Centrarchidae). This incompatibility clock is distinct from a speciation clock because speciation events in centrarchids appear to be driven largely by prezygotic isolation. Our analyses used divergence times estimated with penalized likelihood applied to a phylogeny derived from seven gene regions and calibrated with six centrarchid fossils. We found that hybrid embryo viability declined at mean rate of 3.13% per million years, slower than in most other taxa investigated to date. Despite measurement error in both molecular estimated ages and hatching success of hybrid crosses, divergence time explained between 73% and 90% of the variation in hybrid viability among nodes. This high correlation is consistent with the gradual accumulation of many genetic incompatibilities of small effect. Hybrid viability declined with the square of time, consistent with an increasing rate of accumulation of incompatibilities between divergent genomes (the snowball effect). However, the quadratic slope is due to a lag phase resulting from heterosis among young species pairs, a phenomenon rarely considered in predictions of hybrid fitness. Finally, we found that reciprocal crosses often show asymmetrical hybrid viabilities. We discuss several alternative explanations for this result including possible deleterious cytonuclear interactions. Speciation-clock studies have been a small cottage industry recently, but there are still novel insights to be gained from analyses of more taxonomic groups. However, between-group comparisons require more careful molecular-clock calibration than has been the norm.     

Genetic variation at isozyme loci in blue whiting from the north-east Atlantic

Genetic variation in blue whiting Micromesistius poutassou was investigated by starch gel electrophoresis of enzymes in tissue extracts. A total of 130 specimens from the spawning areas west of the British Isles were collected from trawl catches in 1990 ( n = 30) and 1992 ( n = 100). In 25 tissue enzyme loci screened for genetic variants in the 1990 sample, polymorphisms (0.95 criterion) were found at IDDH-2 *, IDHP-2 * and PGM-1 *, giving a frequency of polymorphic loci of P _0.95= 0.12. In pooled samples the average heterozygosity per locus was estimated at H _e =0.043 and the effective number of alleles per locus at 2.20, 1.45 and 1.53, respectively, for IDDH-2 *, IDHP-2 * and PGM-1 *.     

Dating the time of viral subtype divergence

Precise dating of viral subtype divergence enables researchers to correlate divergence with geographic and demographic occurrences. When historical data are absent (that is, the overwhelming majority), viral sequence sampling on a time scale commensurate with the rate of substitution permits the inference of the times of subtype divergence. Currently, researchers use two strategies to approach this task, both requiring strong conditions on the molecular clock assumption of substitution rate. As the underlying structure of the substitution rate process at the time of subtype divergence is not understood and likely highly variable, we present a simple method that estimates rates of substitution, and from there, times of divergence, without use of an assumed molecular clock. We accomplish this by blending estimates of the substitution rate for triplets of dated sequences where each sequence draws from a distinct viral subtype, providing a zeroth-order approximation for the rate between subtypes. As an example, we calculate the time of divergence for three genes among influenza subtypes A-H3N2 and B using subtype C as an outgroup. We show a time of divergence approximately 100 years ago, substantially more recent than previous estimates which range from 250 to 3800 years ago.     

Observations on the food and diel feeding behaviour of pelagic O-group gadoids in the northern North Sea

The diets and diel feeding behaviour of six O-group gadoid species are described, the cod Gadus morhua (L.), the haddock Melanogramus aeglefinus (L.), whiting Merlangius merlangus (L.), saithe Pollachius virens (L.), Norway pout Trisopterus esmarkii (L.) and the blue whiting Micromesistius poutassou (R.). There were differences, in the main food groups selected by each species with respect to the type, size and number. The main prey consumed did not vary with depth. Cod, saithe and Norway pout had only one period of feeding activity whereas haddock and whiting apparently had two. The diets of haddock and whiting varied in association with these two periods. It is suggested that the differences between the diets were the result of each species having a different feeding behaviour which reflects that adopted in adult life.     

Data partitioning and correction for ascertainment bias reduce the uncertainty of placental mammal divergence times inferred from the morphological clock

Bayesian estimates of divergence times based on the molecular clock yield uncertainty of parameter estimates measured by the width of posterior distributions of node ages. For the relaxed molecular clock, previous works have reported that some of the uncertainty inherent to the variation of rates among lineages may be reduced by partitioning data. Here we test this effect for the purely morphological clock, using placental mammals as a case study. We applied the uncorrelated lognormal relaxed clock to morphological data of 40 extant mammalian taxa and 4,533 characters, taken from the largest published matrix of discrete phenotypic characters. The morphologically derived timescale was compared to divergence times inferred from molecular and combined data. We show that partitioning data into anatomical units significantly reduced the uncertainty of divergence time estimates for morphological data. For the first time, we demonstrate that ascertainment bias has an impact on the precision of morphological clock estimates. While analyses including molecular data suggested most divergences between placental orders occurred near the K‐Pg boundary, the partitioned morphological clock recovered older interordinal splits and some younger intraordinal ones, including significantly later dates for the radiation of bats and rodents, which accord to the short‐fuse hypothesis.     

牛分枝杆菌Mb0950c的免疫特性及其血清学检测方法的建立

【目的】利用原核表达系统对牛分枝杆菌Mb0950c蛋白进行表达和纯化,通过小鼠模型评价其免疫原性,建立血清学间接ELISA方法用于牛结核病的临床检测。【方法】构建pET32a-Mb0950c原核表达质粒,并转化至BL21(DE3)中诱导蛋白的表达,对蛋白进行纯化。使用流式细胞术(flow cytometry,FCM)、ELISA等对该蛋白在小鼠中的免疫原性进行分析。建立基于Mb0950c的间接ELISA方法,评价该方法的临床检测潜力。【结果】SDS-PAGE和Western blotting结果显示,成功获得了可溶性Mb0950c蛋白,且具有良好免疫反应性;FCM结果显示,Mb0950c蛋白上调了T细胞表面CD69分子的表达。细胞因子和抗体结果表明,该蛋白能够诱导特异性的IFN-γ和IL-4的分泌,同时能诱导机体分泌特异性的抗体,且以IgG1型为主。建立了ELISA检测方法应用于牛结核临床检测,结果显示,该方法与牛结核外周血IFN-γ外释放试验和皮试试验结果的阳性符合率、阴性符合率和总符合率分别为65.7%、97.9%和72.4%。【结论】在原核表达系统中可溶性表达Mb0950c蛋白,...     

Rates of Molecular Evolution in RNA Viruses: A Quantitative Phylogenetic Analysis

The study of rates of nucleotide substitution in RNA viruses is central to our understanding of their evolution. Herein we report a comprehensive analysis of substitution rates in 50 RNA viruses using a recently developed maximum likelihood phylogenetic method. This analysis revealed a significant relationship between genetic divergence and isolation time for an extensive array of RNA viruses, although more rate variation was usually present among lineages than would be expected under the constraints of a molecular clock. Despite the lack of a molecular clock, the range of statistically significant variation in overall substitution rates was surprisingly narrow for those viruses where a significant relationship between genetic divergence and time was found, as was the case when synonymous sites were considered alone, where the molecular clock was rejected less frequently. An analysis of the ecological and genetic factors that might explain this rate variation revealed some evidence of significantly lower substitution rates in vector-borne viruses, as well as a weak correlation between rate and genome length. Finally, a simulation study revealed that our maximum likelihood estimates of substitution rates are valid, even if the molecular clock is rejected, provided that sufficiently large data sets are analyzed. Received: 23 February 2001 / Accepted: 3 July 2001     

Testing the molecular clock: molecular and paleontological estimates of divergence times in the Echinoidea (Echinodermata)

The phylogenetic relationships of 46 echinoids, with representatives from 13 of the 14 ordinal-level clades and about 70% of extant families commonly recognized, have been established from 3 genes (3,226 alignable bases) and 119 morphological characters. Morphological and molecular estimates are similar enough to be considered suboptimal estimates of one another, and the combined data provide a tree that, when calibrated against the fossil record, provides paleontological estimates of divergence times and completeness of their fossil record. The order of branching on the cladogram largely agrees with the stratigraphic order of first occurrences and implies that their fossil record is more than 85% complete at family level and at a resolution of 5-Myr time intervals. Molecular estimates of divergence times derived from applying both molecular clock and relaxed molecular clock models are concordant with estimates based on the fossil record in up to 70% of cases, with most concordant results obtained using Sanderson's semiparametric penalized likelihood method and a logarithmic-penalty function. There are 3 regions of the tree where molecular and fossil estimates of divergence time consistently disagree. Comparison with results obtained when molecular divergence dates are estimated from the combined (morphology + gene) tree suggests that errors in phylogenetic reconstruction explain only one of these. In another region the error most likely lies with the paleontological estimates because taxa in this region are demonstrated to have a very poor fossil record. In the third case, morphological and paleontological evidence is much stronger, and the topology for this part of the molecular tree differs from that derived from the combined data. Here the cause of the mismatch is unclear but could be methodological, arising from marked inequality of molecular rates. Overall, the level of agreement reached between these different data and methodological approaches leads us to believe that careful application of likelihood and Bayesian methods to molecular data provides realistic divergence time estimates in the majority of cases (almost 80% in this specific example), thus providing a remarkably well-calibrated phylogeny of a character-rich clade of ubiquitous marine benthic invertebrates.     

Evolutionary divergence of AP-PCR (RAPD) patterns

Rates at which AP-PCR patterns diverge among isolated taxa were examined to test whether they exhibit clocklike regularity. The results showed that rates of divergence differed significantly among the groups examined (primates, antelopes, and Hawaiian Drosophila grimshawi). Therefore, AP-PCR divergence rates cannot be used as a "universal clock" with an invariant rate in all animals. Nevertheless, within each group, a strong relationship existed between degree of AP-PCR pattern divergence and time since separation of isolated taxa. Thus, AP-PCR divergence may prove useful for dating evolutionary events if calibrated within a more limited taxon.      

Molecular phylogenetic relationships of pangasiid and schilbid catfishes in Thailand

In this study, the phylogenetic relationships among 13 pangasiids and six schilbids of Thailand were reconstructed based on the almost complete mitochondrial cytochrome b (cyt b), 12S rRNA, tRNA-Val and 16S rRNA, as well as the partial nuclear recombination-activating gene 1 (rag1) sequences by using the maximum likelihood and the Bayesian inference methods of phylogenetic reconstruction. The reconstructed phylogeny based on the concatenated sequence data set recovered Pangasiidae and Schilbidae as reciprocally monophyletic groups. Within Pangasiidae, four major clades were recovered, which according to the cyt b genetic distances can be categorized into four genera: Pangasius, Pseudolais, Helicophagus and Pangasianodon. The genus Pangasianodon was strongly supported as the most basal taxon within pangasiids, whereas Pseudolais + Helicophagus were recovered as a sister group of Pangasius. Within the latter, the giant pangasius Pangasius sanitwongsei was recovered as a sister group of the spot pangasius Pangasius larnaudii, Pangasius krempfi as a sister group of Pangasius nasutus + Pangasius conchophilus and Pangasius polyuranodon as a sister species of Pangasius macronema. Other internal phylogenetic relationships, however, were unresolved. Within Schilbidae, Pseudeutropius was supported as the most basal lineage. Eutropiichthys was recovered as a sister group of Clupisoma. The enigmatic Clupisoma sinense was recognized as more closely related to Laides longibarbis than to Clupisoma prateri. Thus, based on the cyt b genetic distances, a recategorization of C. sinense to the genus Laides is suggested. On the basis of a relaxed clock fossil calibration, the divergence of pangasiids and schilbids was estimated to have occurred 14·93 million years before present (b.p.) during the Miocene epoch. The separation between Pangasiidae and Schilbidae took place c. 13·12 Mb.p. during the early middle Miocene. The estimated divergence time of pangasiids is similar to the age of the calibrated fossil, Cetopangasius chaetobranchus, which was discovered in north-central Thailand. This suggests that the oldest pangasiid ancestor diverged into diverse genera in the area.     

Intercontinental and intracontinental biogeography patterns and methods

The study of biogeography has benefited from the exponential increase of DNA sequence data from recent molecular systematic studies, the development of analytical methods in the last decade concerning divergence time estimation and geographic area analyses, and the availability of large-scale distributiofi data of species in many groups of organisms. The underlying principle of divergence time estimation from DNA and protein data is that sequence divergence depends on the product of evolutionary rate and time. With their molecular clock hypothesis, Zuckerkandl and Pauling （1965） separated rates of molecular evolution from time by incorporating fossil evidence. Originally,     

Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability

Since divergence ∼50 Ma ago from their terrestrial ancestors, cetaceans underwent a series of adaptations such as a ∼10–20 fold increase in myoglobin (Mb) concentration in skeletal muscle, critical for increasing oxygen storage capacity and prolonging dive time. Whereas the O₂-binding affinity of Mbs is not significantly different among mammals (with typical oxygenation constants of ∼0.8–1.2 µM⁻¹), folding stabilities of cetacean Mbs are ∼2–4 kcal/mol higher than for terrestrial Mbs. Using ancestral sequence reconstruction, maximum likelihood and Bayesian tests to describe the evolution of cetacean Mbs, and experimentally calibrated computation of stability effects of mutations, we observe accelerated evolution in cetaceans and identify seven positively selected sites in Mb. Overall, these sites contribute to Mb stabilization with a conditional probability of 0.8. We observe a correlation between Mb folding stability and protein abundance, suggesting that a selection pressure for stability acts proportionally to higher expression. We also identify a major divergence event leading to the common ancestor of whales, during which major stabilization occurred. Most of the positively selected sites that occur later act against other destabilizing mutations to maintain stability across the clade, except for the shallow divers, where late stability relaxation occurs, probably due to the shorter aerobic dive limits of these species. The three main positively selected sites 66, 5, and 35 undergo changes that favor hydrophobic folding, structural integrity, and intra-helical hydrogen bonds.     

Effects of density dependence,zooplankton and temperature on blue whiting Micromesistius poutassou growth

Blue whiting Micromesistius poutassou mean total length at age in the north‐east Atlantic Ocean was found to vary by around ±6% during the period 2004–2011 and mean mass at age by ±22% during the years 1981–2013. Linear modelling provided strong evidence that these phenotypic growth variations can be explained by trophic conditions, mainly negative density dependence and also food availability, and a negative long‐term temperature effect on asymptotic size.     

Estimation of primate speciation dates using local molecular clocks

Protein-coding genes of the mitochondrial genomes from 31 mammalian species were analyzed to estimate the speciation dates within primates and also between rats and mice. Three calibration points were used based on paleontological data: one at 20-25 MYA for the hominoid/cercopithecoid divergence, one at 53-57 MYA for the cetacean/artiodactyl divergence, and the third at 110-130 MYA for the metatherian/eutherian divergence. Both the nucleotide and the amino acid sequences were analyzed, producing conflicting results. The global molecular clock was clearly violated for both the nucleotide and the amino acid data. Models of local clocks were implemented using maximum likelihood, allowing different evolutionary rates for some lineages while assuming rate constancy in others. Surprisingly, the highly divergent third codon positions appeared to contain phylogenetic information and produced more sensible estimates of primate divergence dates than did the amino acid sequences. Estimated dates varied considerably depending on the data type, the calibration point, and the substitution model but differed little among the four tree topologies used. We conclude that the calibration derived from the primate fossil record is too recent to be reliable; we also point out a number of problems in date estimation when the molecular clock does not hold. Despite these obstacles, we derived estimates of primate divergence dates that were well supported by the data and were generally consistent with the paleontological record. Estimation of the mouse-rat divergence date, however, was problematic.     

Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events

A comprehensive dataset of 62 beta globin gene sequences from various vertebrates was compiled to test the molecular clock and to estimate dates of gene duplications. We found that evolution of the beta globin family of genes is not clock-like, a result that is at odds with the common use of this family as an example of a constant rate of evolution over time. Divergence dates were estimated either with or without assuming the molecular clock, and both analyses produced similar date estimates, which are also in general agreement with estimates reported previously. In addition we report date estimates for seven previously unexamined duplication events within the beta globin family. Despite multiple sources of rate variation, the average rate across the beta globin phylogeny yielded reasonable estimates of divergence dates in most cases. Exceptions were cases of gene conversion, where it appears to have led to underestimates of divergence dates. Our results suggest (i) the major duplications giving rise to the paralogous beta globin genes are associated with significant evolutionary rate variation among gene lineages; and (ii) genes arising from more recent gene duplications (e.g., tandem duplications within lineages) do not appear to differ greatly in rate. We believe this pattern reflects a complex interplay of evolutionary forces where natural selection for diversifying paralogous functions and lineage-specific effects contribute to rate variation on a long-term basis, while gene conversion tends to increase sequence similarity. Gene conversion effects appear to be stronger on recent gene duplicates, as their sequences are highly similar. Lastly, phylogenetic analyses do not support a previous report that avian globins are members of a relic lineage of omega globins.