Comparative morphometry and phenetics of the genera of esocoid fishes (Salmoniformes)

Using shape data derived from the externa] body morphometry of esocoid fishes in which the effects of size were standardized, a close relationship of Umbra and Novumbra is supported. Dallia is provisionally associated with these but some data contradicted this. Esox is distantly associated with all of these. Thus the appropriate systematic classification for this group is: suborder Esocoidei; family Esocidae (five species in one genus— Esox ), family Umbridae (four species in two genera— Umbra and Novumbra ), and, incertae sedis Dallia (one or perhaps two species).     

Comparative study on the surface ultrastructures of fertilized eggs of three Sebastes species

Fertilized eggs of Sebastes schlegelii, Sebastes pachycephalus and Sebastes hubbsi are morphologically similar under stereomicroscope. However, under the scanning electron microscope, significant differences in the ultrastructures of the egg surface among the three species were observed, and herein, a taxonomic key was proposed for future applications. A clustering analysis based on the ultrastructures of the egg surface and the diameter of the oil globule suggested that among the three species, S. hubbsi and S. pachycephalus were more genetically similar, while S. schlegelii had diverged earlier. The results agree with the conclusions drawn from morphological and molecular analyses on adult samples of the same species.     

Life History Variation in Female Gambusia hubbsi

Gambusia hubbsi populations occur in a variety of fresh and brackish-water habitats on Andros, Bahamas. These include shallow water sites (tidal creeks, lakes, roadside ditches), and blueholes (vertical solution caves). In some blueholes G. hubbsi is the only species present, in others it co-occurs with other species, principal among these is a predator, Eleotris pisonis. By contrast to blueholes, shallow water sites have highly variable temperature and depth. In addition, they are frequented by avian piscivores and may be occasionally occupied by piscivores such as Eleotris. We sampled 10 shallow water sites, 14 blueholes where Eleotris is absent and 12 blueholes where Eleotris co-occurs with G. hubbsi. We measured and compared variation in female body size, fecundity, and reproductive investment among these three habitats. The observed patterns of life history variation are only partially in accord with expectations from theory regarding the effects of predation and seasonality on life history variation. Samples from populations that colonized a series of man-made trenches (Well Fields), a set of introductions into that habitat, and changes in life history traits of lab-raised females from three blueholes, suggest that the observed pattern of life history variation in other habitats also reflects differences in food availability among habitats, and imperfectly reflects the potential phenotypic variability of this species.     

New tools (DNA barcoding), old hypothesis: the case of the taxonomic identity of the Argentine hakes (Actinopterygii: Merluccius)

The present study evaluated the possible occurrence of cryptic species among Merluccidae from Argentina by examining sequences of cytochrome c oxidase subunit I (coI) mtDNA. This approach can discriminate Merluccius hubbsi and Merluccius australis; specimens with morphological diagnostic characters of Merluccius patagonicus formed a cohesive cluster with M. hubbsi specimens. BIN analysis confirmed the effectiveness of barcoding within a global context.     

Evolution of ZZ/ZW and XX/XY sex-determination systems in the closely related medaka species, <Emphasis Type="Italic">Oryzias hubbsi</Emphasis> and <Emphasis Type="Italic">O. dancena</Emphasis>

A DM-domain gene on the Y chromosome was identified as the sex-determining gene in the medaka, Oryzias latipes, and named DMY (also known as dmrt1bY). However, this gene is absent in most Oryzias fishes, suggesting that closely related species have another sex-determining gene. In fact, it has been demonstrated that the Y chromosome in O. dancena is not homologous to that in O. latipes, whereas both species have an XX/XY sex-determination system. Through a progeny test of sex-reversed fish and a linkage analysis of isolated sex-linked DNA markers, we show that O. hubbsi, which is one of the most closely related species to O. dancena, has a ZZ/ZW system. In addition, genetic and fluorescence in situ hybridization mapping of the sex-linked markers revealed that sex chromosomes in O. hubbsi and O. dancena are not homologous, indicating different origins of these ZW and XY sex chromosomes. Furthermore, we found that O. hubbsi has morphologically heteromorphic sex chromosomes, in which the W chromosome has 4,6-diamidino-2-phenylindole (DAPI)-positive heterochromatin blocks and is larger than the Z chromosome, although such differentiated sex chromosomes have not been observed in other Oryzias species. These findings suggest that a variety of sex-determining mechanisms and sex chromosomes have evolved in Oryzias.     

Litter Overlap in Gambusia hubbsi: Superfetation Revisited

The frequency of litter overlap, the simultaneous presence of two litters at different stages of development within a single female, varies among populations of Gambusia hubbsi in different habitats on Andros, Bahamas. In freshwater bluehole and shallow water populations, less than 2% of the females carried two litters, independent of the difference in developmental stage between the litters. In well field populations, 2% of the females carried two litters composed of immature and mature oocytes, whereas 10% carried developing oocytes and late stage embryos, and 16% carried mature oocytes (or older) and late stage embryos. Among females from populations that we introduced into unoccupied well fields 2% carried two litters composed of immature and mature oocytes, about 14% carried developing oocytes and late stage embryos, and less than 6% carried mature oocytes (or older) and late stage embryos. When two litters composed developing oocytes and late stage embryos were present, the two litters were of equal size, and the total number of offspring was 1.5 times larger than expected on the basis of female body length. When two litters composed mature oocytes (or older stages) and late stage embryos were present, the two litters were also of equal size, and the total number of offspring was as expected on the basis of female body length. Litter overlap was independent of female size. A comparison of the consequences of litter overlap for strictly lecithotrophic and strictly matrotrophic modes of reproduction with the patterns of litter overlap observed in G. hubbsi, suggests that litter overlap in G. hubbsi reduces the cost of reproduction, but does not increase the rate of offspring production.     

Temperature-sensitive mutations in Drosophila melanogaster. XIV. A selection of immobile adults

Summary Improved methods for rearing and screening large numbers of flies permitted the recovery of 10 mutations exhibiting a reversible temperature-dependent adult paralysis among 1.1×10⁶ flies tested. Of the 10 mutations, two were allelic to para ^ts,two were alleles in a new locus, stoned (stn), and six fell into a third area, the shibire (shi) locus. Several of the shi alleles cause embryonic, larval and adult paralysis at 29° C as well as structural anomalies of various tissues. In addition to the ts mutations, several non-conditional mutations affecting adult movement were recovered.This work was supported by the National Research Council of Canada, grant A-1764, National Cancer Institute of Canada, grant 6051.Medical Research Council of Canada Postdoctoral Fellow.     

Male mating success,sexual size dimorphism,and site fidelity in two species of Malacoctenus (Labrisomidae)

Synopsis In both Malacoctenus hubbsi and Malacoctenus macropus, males defended preferred oviposition sites from both other males and potential egg predators. In M. hubbsi, adult females were larger than adult males. Larger M. hubbsi males were not associated with territory parameters that were correlated with higher mating success, and male size was not correlated with mating success. Male size did affect mating success when territory parameters were statistically controlled for, but the failure of large males to associate with better territories eliminated any mating advantage for larger males. In M. macropus, males are larger than females. Larger males defended preferred oviposition sites, and had higher mating success than did smaller males. Male M. macropus also had much higher site fidelity than male M. hubbsi. These results suggest that the evolution of the differences in site fidelity and sexual size dimorphism between these two species may be due to sexual selection acting differentially in these two species.     

A new clade of Dickeya spp. plays a major role in potato blackleg outbreaks in North Finland

Until recently Dickeya was regarded as a pathogen not established in Finland. As a result the blackleg symptom observed on potato was often associated with Pectobacterium atrosepticum. The occurrence of Dickeya spp. on potato in Finland was first reported in 2004. Since then the prevalence of Dickeya has been monitored through surveys and routine test of seed lots produced in the country. The results of monitoring of Dickeya spp. in seed lots produced in Finland between the years 2004 and 2008 indicated a steady increase in the incidence of Dickeya spp. The highest incidence was observed in samples from the 2006 growing season where about 37% were positive for Dickeya spp. The summer in 2006 was one of the warmest summers recorded in 100 years in Finland. The majority of infected lots were imported varieties. Since recently heavy blackleg outbreaks have occurred in production fields in the High Grade (HG) zone. A detailed study of these incidents of blackleg outbreaks in North Finland during the years 2008 and 2010 indicated that Dickeya spp. was the major component in the observed blackleg complex. It was detected and isolated from almost all symptomatic plants investigated. Repetitive sequences PCR (REP‐PCR) and Pulsed Field Gel Electrophoresis (PFGE) analysis of strains isolated in Finland showed identical pattern with those isolated recently in other European countries with a proposed name ‘Dickeya solani’. Moreover, the dnaX gene sequence of the representative strains isolated in Finland indicated 100% similarity to the dnaX sequences of ‘D. solani’. The study presents the first report of a detailed analysis of bacteria involved in potato blackleg complex from natural field outbreaks in North Finland HG zone and characterisation of the ‘D. solani’ strains playing the major role in the disease complex.     

Characterization of bacterial communities from activated sludge: Culture-dependent numerical identification versus in situ identification using group- and genus-specific rRNA-targeted oligonucleotide probes

The structures of bacterial communities were studied in activated sludge samples obtained from the aerobic and anaerobic zones of a wastewater treatment plant showing enhanced phosphorous removal. Samples were analyzed by in situ hybridization with oligonucleotide probes complementary to selected regions of the 16S and 23S ribosomal RNA (rRNA) characteristic for defined phylogenetic entities (genera and larger groups). The microbial community structures revealed by molecular techniques were compared with the compositions of culturable bacterial communities, obtained from the characterization of 255 isolates from tryptone-soy (TS) agar and R2A agar. These isolates were characterized by 89 physiological tests and their cellular fatty acid patterns, and identified. Culture-dependent techniques indicated the following distribution: different Aeromonas spp. (2.7–8.3% on R2A agar; 45.0–63.7% on TS agar), Acinetobacter spp. (5.4–9.0% on R2A agar; 5.0–9.1% on TS agar), Pseudomonas spp. (up to 10% on R2A agar) and Shewanella putrefaciens (up to 3.0% on R2A agar), all members of the gamma subclass of Proteobacteria, were isolated most frequently. The relatively rare isolates of the beta subclass were identified as Acidovorax spp., Alcaligenes spp., and Comamonas spp., The Gram-positive bacteria (high DNA G+C) were assigned mainly to Arthrobacter spp., Microbacterium spp., and Mycobacterium phlei. In order to assess the in situ abundance of the most frequently isolated genus, Aeromonas, two rRNA-targeted oligonucleotide probes were developed. The two gamma proteobacterial genera Aeromonas and Acinetobacter constituted less than 5% of all bacteria. In situ, Proteobacteria belonging to the beta subclass and high G+C Gram-positive bacteria were dominant. From filamentous bacteria, Sphaerotilus spp. and Leptothrix spp. could be detected occasionally. In addition, one sample contained a high proportion of the morphologically distinct filaments of Microthrix parvicella.As for the genus Acinetobacter, the relative abundance of the most frequently gamma-proteobacterial genus Aeromonas was overestimated by the intrinsic selectivity of cultivation. Cultivation on nutrient-rich medium (TS-agar) especially supported an enhanced isolation of bacteria belonging to these two genera. Correspondence to: P. Kämpfer.     

Mitochondrial haplotypes in populations of the plant-infecting fungus Sclerotinia sclerotiorum: wide distribution in agriculture, local distribution in the wild

Analysis of mitochondrial DNA (mtDNA) haplotypes of Sclerotinia sclerotiorum points to a common origin of some genotypes from agricultural populations, especially when compared with two wild populations that are sharply distinguished from the agricultural sample and from each other. Five agricultural population samples from canola (Alberta, Canada and Norway), cabbage (North Carolina, USA), sunflower (Manitoba, Canada and Queensland, Australia) and two Norwegian populations from a wild plant, Ranunculus ficaria were compared. Haplotypes were determined by Southern hybridization of purified organelle DNA from S. sclerotiorum and Neurospora crassa to total genomic DNA of S. sclerotiorum. Each isolate had one haplotype. Haplotypes of S. sclerotiorum from R. ficaria were different between the two wild populations and also from all haplotypes observed in the agricultural populations. Among the wild isolates, DNA fingerprint, mtDNA haplotype and location in the sampling transect were all associated. Among the agricultural isolates, four haplotypes were observed in at least two agricultural populations and one haplotype was observed in all agricultural populations. In the Canadian canola sample some clones had one mtDNA haplotype, indicating association with DNA fingerprint, some clones had more than one haplotype, and some groups of clones shared haplotypes. Some of the haplotype diversity may be due to the presence of extra-chromosomal elements associated with the mitochondria of S. sclerotiorum.     

Structural Alteration of Humic Acids by Pseudomonas spp. from Deep Terrestrial Subsurface Diatomite Formations in Northernmost Japan

Bacterial utilization of humic acids (HAs) was examined under aerobic conditions using Pseudomonas spp. from diatomite from a depth of 250 m below ground level in the Horonobe Underground Research Laboratory. HA decolorization and bacterial aggregation were observed during cultivation when an auxiliary carbon source was added. High-performance size-exclusion chromatography showed that high-molecular-weight HAs were produced. Fourier transform infrared spectroscopy indicated that carboxyl groups and polysaccharide-related substances in HAs were eliminated, while aliphatic structural units and amide groups were added to HAs. These results suggested that Pseudomonas spp. utilize and alter the molecular structure of HAs under aerobic conditions caused by the construction of underground facilities.     

The ever increasing diversity of begomoviruses infecting non‐cultivated hosts: new species from Sida spp. and Leonurus sibiricus,plus two New World alphasatellites

Begomoviruses (whitefly‐transmitted, single‐stranded DNA plant viruses) are among the most damaging pathogens causing epidemics in economically important crops worldwide. Besides cultivated plants, many weed and wild hosts act as virus reservoirs where recombination may occur, resulting in new species. The aim of this study was to further characterise the diversity of begomoviruses infecting two major weed genera, Sida and Leonurus. Total DNA was extracted from samples collected in the states of Rio Grande do Sul, Paraná and Mato Grosso do Sul during the years 2009–2011. Viral genomes were enriched by rolling circle amplification (RCA), linearised into unit length genomes using various restriction enzymes, cloned and sequenced. A total of 78 clones were obtained: 37 clones from Sida spp. plants and 41 clones from Leonurus sibiricus plants. Sequence analysis indicated the presence of six bipartite begomovirus species and two alphasatellites. In Sida spp. plants we found Sida micrantha mosaic virus (SiMMV), Euphorbia yellow mosaic virus (EuYMV), and three isolates that represent new species, for which the following names are proposed: Sida chlorotic mottle virus (SiCMoV), Sida bright yellow mosaic virus (SiBYMV) and Sida golden yellow spot virus (SiGYSV), an Old World‐like begomovirus. L. sibiricus plants had a lower diversity of begomoviruses compared to Sida spp., with only Tomato yellow spot virus (ToYSV) and EuYMV (for the first time detected infecting plants of the genus Leonurus) detected. Two satellite DNA molecules were found: Euphorbia yellow mosaic alphasatellite, for the first time detected infecting plants of the genus Sida, and a new alphasatellite associated with ToYSV in L. sibiricus. These results constitute further evidence of the high species diversity of begomoviruses in non‐cultivated hosts, particularly Sida spp.     

橡胶树体细胞胚发生过程中DNA甲基化分析

为探讨巴西橡胶树(Hevea brasiliensis)自根幼态无性系与供体间差异产生的原因,应用甲基化敏感扩增多态性扩增技术,对巴西橡胶树体细胞胚发生过程中基因组DNA 胞嘧啶甲基化程度和模式进行了分析。结果表明,在巴西橡胶树体细胞胚发生过程中不同阶段的DNA 甲基化程度不同,以花药的DNA 甲基化程度最高,体细胞胚的DNA 甲基化水平最低。在体细胞胚发生过程中出现了I、Ⅱ和Ⅲ 3 种类型的甲基化多态性带型的改变,包括他们的出现与消失。因此,橡胶树体细胞胚发生过程中可能通过DNA 甲基化甲基化和去甲基化来调控基因的表达。     

Identification of rhizobacteria from maize and determination of their plant-growth promoting potential

During the growing season of 1986, the rhizobacteria (including organisms from the ectorhizosphere, the rhizoplane and endorhizosphere) of 20 different maize hybrids sampled from different locations in the Province of Quebec were inventoried by use of seven different selective media. Isolates were characterized by morphological and biochemical tests and identified using the API20E and API20B diagnostic strips.Pseudomonas spp. were the prominent bacteria found in the rhizoplane and in the ectorhizosphere.Bacillus spp. andSerratia spp. were also detected, but in smaller numbers. In the endorhizosphere,Bacillus spp. andPseudomonas spp. were detected in order of importance. Screening for plant growth-promoting rhizobacteria was carried out in three soils with different physical and chemical characteristics. The results depended on the soil used, but two isolates (Serratia liquefaciens andPseudomonas sp.) consistently caused a promotion of plant growth.Contribution no. 350 of the Research Station, Agriculture Canada, Sainte-Foy, Quebec.     

The cover of living and dead corals from airborne remote sensing

Trends in coral cover are widely used to indicate the health of coral reefs but are costly to obtain from field survey over large areas. In situ studies of reflected spectra at the coral surface show that living and recently dead colonies can be distinguished. Here, we investigate whether such spectral differences can be detected using an airborne remote sensing instrument. The Compact Airborne Spectrographic Imager (Itres Research Ltd, Canada) was flown in two configurations: 10 spectral bands with 1-m² pixels and 6 spectral bands with 0.25-m² pixels. First, we show that an instrument with 10 spectral bands possesses adequate spectral resolution to distinguish living Porites, living Pocillopora spp., partially dead Porites, recently dead Porites (total colony mortality within 6 months), old dead (>6 months) Porites, Halimeda spp., and coralline red algae when there is no water column to confuse spectra. All substrata were distinguished using fourth-order spectral derivatives around 538 nm and 562 nm. Then, at a shallow site (Tivaru) at Rangiroa Atoll, Tuamotu Archipelago (French Polynesia), we show that live and dead coral can be distinguished from the air to a depth of at least 4 m using first- and fourth-order spectral derivatives between 562–580 nm. However, partially dead and recently dead Porites colonies could not be distinguished from an airborne platform. Spectral differences among substrata are then exploited to predict the cover of reef substrata in ten 25-m² plots at nearby Motu Nuhi (max depth 8 m). The actual cover in these plots was determined in situ using quadrats with a 0.01-m² grid. Considerable disparity occurred between field and image-based measures of substrate cover within individual 25-m² quadrats. At this small scale, disparity, measured as the absolute difference in cover between field and remote-sensing methods, reached 25% in some substrata but was always less than 10% for living coral (99% of which consisted of Porites spp.). At the scale of the reef (all ten 25-m² quadrats), however, disparities in percent cover between imagery and field data were less than 10% for all substrata and extremely low for some classes (e.g. <3% for living Porites, recently dead Porites and Halimeda). The least accurately estimated substrata were sand and coralline red algae, which were overestimated by absolute values 7.9% and 6.6%, respectively. The precision of sampling was similar for field and remote-sensing methods: field methods required 19 plots to detect a 10% difference in coral cover among three reefs with a statistical power of 95%. Remote-sensing methods required 21 plots. However, it took 1 h to acquire imagery over 92,500 m² of reef, which represents 3,700 plots of 25 m² each, compared with 3 days to survey 10 such plots underwater. There were no significant differences in accuracy between 1-m² and 0.25-m² image resolutions, suggesting that the advantage of using smaller pixels is offset by reduced spectral information and an increase in noise (noise was observed to be 1.6–1.8 times greater in 0.25-m² pixels). We show that airborne remote sensing can be used to monitor coral and algal cover over large areas, providing that water is shallow and clear, and that brown fleshy macroalgae are scarce, that depth is known independently (e.g. from sonar survey).     

Identification of Yersinia enterocolitica using a random genomic DNA microarray chip

Aims: To fabricate a DNA chip containing random fragments of genomic DNA of Yersinia enterocolitica and to verify its diagnostic ability. Methods and Results: A DNA microarray chip was fabricated using randomly fragmented DNA of Y. enterocolitica. Chips were hybridized with genomic DNA extracted from other Y. enterocolitica strains, other Yersinia spp. and bacteria in different genera. Genomic DNA extracted from Y. enterocolitica showed a significantly higher hybridization rate compared with DNA of other Yersinia spp. or bacterial genera, thereby distinguishing it from other bacteria. Conclusions: A DNA chip containing randomly fragmented genomic DNA from Y. enterocolitica can detect Y. enterocolitica and clearly distinguish it from other Yersinia spp. and bacteria in different genera. Significance and Impact of the Study: A microarray chip containing randomly fragmented genomic DNA of Y. enterocolitica was fabricated without sequence information, and its diagnostic ability to identify Y. enterocolitica was verified.     

Spring “bleaching” among <Emphasis Type="Italic">Pocillopora</Emphasis> in the Sea of Cortez,Eastern Pacific

A mild bleaching event was observed among Pocillopora spp. in the southern Gulf of California in the spring of 2006. Uniform bleaching occurred in numerous colonies on the upper portions of their branches. Most (∼90%) colonies that exhibited bleaching contained a species of endosymbiotic dinoflagellate, Symbiodinium C1b-c, which differed from the Symbiodinium D1 found inhabiting most unbleached colonies. Analysis of chlorophyll fluorescence, indicated a decline in photosystem II photochemical activity, especially among colonies populated with C1b-c. By early August, most affected colonies had recovered their normal pigmentation and fluorescence values were once again high for all colonies. No mortality was observed among tagged bleached colonies nor did symbiont species composition change during recovery. This unusual episode of bleaching did not appear to be a response to thermal stress, but may have been triggered by high levels of solar radiation during a period of unseasonally high water clarity in the early spring.     

Alternative approach for consistent yields of total genomic DNA from cotton (Gossypium hirsutum L.)

A persistent limitation to molecular biological research on cotton (Gossypium spp.) has been the difficulty in isolation of total genomic DNA from the plant tissue. This report describes a reliable strategy for isolation of genomic DNA from cotton. The mini-preparation procedure involves use of lyophilized, etiolated cotyledons and an anion exchange column kit. The isolated DNA had a molecular weight in excess of 50 kb with minimal degradation or shearing. Routine yields ranged from 5 to 7 μg DNA per etiolated cotyledon pair (corresponding to 100 ng/mg dry weight), in contrast to little or no DNA from equivalent amounts of either green cotyledons or mature leaf tissue. The decreased yields from the latter tissues appeared to be correlated with increased afmounts of flavonoid. The DNA was amenable to routine molecular applications as demonstrated by: digestibility with a number of restriction enzymes (Eco RI,HindIII,Sau 3A), and hybridization of a tomato genomic clone containing the gene for S-adenosylmethionine synthetase to a 13.3-kbEco RI fragment of cotton. Using DNA from an isoline immune to root-knot nematodes, we observed no impediment to genomic cloning.     

Geographic and Demographic Variation in the Prevalence of Overweight Canadian Children

Objective : To examine the geographic and demographic variation in the prevalence of overweight Canadian children. Research Methods and Procedures : Using BMI data from the 1981 Canada Fitness Survey and the 1996 National Longitudinal Survey of Children and Youth, this study assessed: 1) the prevalence of overweight and obesity among Canadian boys and girls ages 7 to 13 years; 2) secular trends in the prevalence of overweight from 1981 to 1996, by province and adjusted for age and sex; and 3) provincial variation in the prevalence of overweight, before and after adjusting for socioeconomic and demographic characteristics. Results : The prevalence of boys and girls classified as overweight in 1996 was 33% and 26%, respectively. The corresponding figures for obesity were 10% for boys and 9% for girls. Provincial variation was observed with a trend of increasing risk of being overweight from west to east. Socioeconomic status was inversely related to the prevalence of overweight regardless of geographic region. The risk of being overweight was more related to geography (province) than demographic variables (income and family background); however, the effect of secular trends (1981 to 1996) exceeded the effect of geographic or demographic variables. Discussion : The prevalence of childhood overweight and obesity is increasing in all areas of Canada and can be explained only partially by geographic or demographic characteristics.