Assessment of Genetic Diversities of Selected Laminaria （Laminariales, Phaeophyta） Gametophytes by Inter-Simple Sequence Repeat Analysis

Inter-simple sequence repeat (ISSR) analysis was used to assess genetic diversity among 10 pairs of male and female Laminaria gametophytes. A total of 58 amplification loci was obtained from 10 selected ISSR primers, of which 34 revealed polymorphism among the gametophytes. Genetic distances were calculated with the Dice coefficient ranging from 0.006 to 0.223. A dendrogram based on the unweighted pair-group method arithmetic (UPGMA) average showed that most male and female gametophytes of the same species were clustered together and that 10 pairs of gametophytes were divided into four groups. This was generally consistent with the taxonomic categories. The main group consisted of six pairs of gametophytes, which were selected from Laminaria japonica Aresch. by intensive inbreeding through artificial hybridization. One specific marker was cloned, but was not converted successfully into a sequence characterized amplified region (SCAR) marker. Our results demonstrate the feasibility.of applying ISSR markers to evaluate Laminaria germplasm diversities.     

The roles of the Chantransia phase of Lemanea (Lemaneaceae,Batrachospermales, Rhodophyta) and of the ‘Mushroom’ phase of Himanthalia (Himanthaliaceae,Fucales, Phaeophyta)

Summary

The life cycle of the Batrachospermales (freshwater florideophyte red such as Batrachospermum, Lemanea) is a shortened variant of the ‘normal’ marine florideophyte life cycle. The perennial Chantransia diploid phase is microscopic and encrusting. Each winter it produces one or more semi-erect haploid gametophytes by vegetative meiosis. Gamete production and fertilization is followed by production of diploid carposporophytes; these produce diploid carpospores which disperse, and regenerate the Chantransia phase. The question of the extent to which the Chantransia phase contributes resources to the gametophyte was approached by physiological-hydrodynamic modelling. These computations suggest that the photosynthetic rates in situ on an area basis are 20 times greater for the gametophyte than the Chantransia phase; this agrees with the observed ratios of peak biomass. The conclusion is that the Chantransia phase has a negligible role in provisioning the growing gametophyte, and that the role of the Chantransia phase is to occupy space with living biomass throughout the year, including exposure at summer drawdown, and (perhaps) by dispersal via production of monospores. A similar conclusion is arrived at on the basis of biomass data for the role of the perennial ‘mushroom’ phase of the semelparous marine Fucalean brown alga Himanthalia elongata in relation to the short-lived but much larger reproductive receptacles.     

Spawning aggregations of squid (Sepioteuthis australis) populations: a continuum of ‘microcohorts’

The aim of this study was to determine how size, age, somatic and reproductive condition, abundance and egg production of southern calamary spawning aggregations changed during the spawning season in each of 2 years. During the spawning period in at least one of the years there was a decline as much as 20% in average size, 50% in somatic condition, 28–34% in size-at-age, 26–29% in reproductive status, as well as abundance and reproductive output of the stock declining during the spawning season. However, this change was not a function of the population becoming reproductively exhausted, as the aggregation was composed of different individuals with different biological characteristics. In each month the average age of individuals was ca. 6 mo, indicating that squid that had hatched at different times had entered the spawning aggregations, suggesting that the aggregation was made-up of a succession of microcohorts. Currently, management of many squid populations assumes that there is a single cohort in the aggregation. Therefore, estimating stock biomass at the start of the spawning season cannot be used as the population is constantly changing as micro-cohorts move into the aggregation. An instantaneous estimate of the spawning biomass, independent of fishing activity may be obtained by quantifying the density of deposited eggs. The strategy of individuals with a diversity of life history characteristics coming together in a single spawning aggregation may ensure the phenotypic and genetic diversity required to guarantee successful recruitment of this short-lived species. Therefore, temporally structured protection from harvest throughout the spawning season will ensure maintenance of this population diversity.     

Population genetics of wild Hizikia fusiformis (Sargassaceae, Phaeophyta) along China’s coast

Hizikia fusiformis is one of the important commercially cultivated seaweeds in China. Inter-simple sequence repeats (ISSR) and sequence-related amplified polymorphism (SRAP) markers were used to assess genetic structure of nine wild H. fusiformis populations collected along the coast of China. Of the 255 bands generated by 21 ISSR primers, 99.61% were polymorphic and 99.71% of 344 bands amplified by 30 SRAP primers were polymorphic. The tested high genetic diversities show that the average Nei’s genetic diversity (H) were 0.1519 and 0.1624, and average Shannon’s information index (I) were 0.2248 and 0.2400 in ISSR and SRAP analyses, respectively. Unweighted pair group method with arithmetic mean (UPGMA) dendrograms of the nine populations were divided into two main groups. The ISSR and SRAP analyses values of gene differentiation (G _ST, 0.5955, 0.5486, respectively) indicate that high variation exists among the nine populations, likely due to external interferences and limitation of gene flow (N _m?=?0.3397, 0.4114). Our study indicated that human activities and herbivore overgrazing had influenced the natural Hizikia populations and that the understanding of population genetics would be helpful in sustainable utilization and biomass conservation of Sargassaceae resources.     

On the correct use of ‘data’

Acknowledgement  Thanks are due to Drs. Paul Johnston (P.Johnston@ exeter.ac.uk) and E. William Beese (ebeese@t-online.de) for kindly providing dictionary definitions and for sharing their thoughts about the correct use of ‘data’.     

Analysis of bacterial community shifts in the gastrointestinal tract of pigs fed diets supplemented with β-glucan from Laminaria digitata,Laminaria hyperborea and Saccharomyces cerevisiae

This study was designed to evaluate the effects of algal and yeast β-glucans on the porcine gastrointestinal microbiota, specifically the community of Lactobacillus, Bifidobacterium and coliforms. A total of 48 pigs were fed four diets over a 28-day period to determine the effect that each had on these communities. The control diet consisted of wheat and soya bean meal. The remaining three diets contained wheat and soya bean meal supplemented with β-glucan at 250 g/tonne from Laminaria digitata, Laminaria hyperborea or Saccharomyces cerevisiae. Faecal samples were collected from animals before feeding each diet and after the feeding period. The animals were slaughtered the following day and samples were collected from the stomach, ileum, caecum, proximal colon and distal colon. Alterations in Lactobacillus in the gastrointestinal tract (GIT) were analysed using denaturing gradient gel electrophoresis (DGGE) profiles generated by group-specific 16S rRNA gene PCR amplicons. Plate count analysis was also performed to quantify total coliforms. DGGE profiles indicated that all β-glucan diets provoked the emergence of a richer community of Lactobacillus. The richest community of lactobacilli emerged after feeding L. digitata (LD β-glucan). Plate count analysis revealed that the L. hyperborea (LH β-glucan) diet had a statistically significant effect on the coliform counts in the proximal colon in comparison with the control diet. β-glucan from L. digitata and S. cerevisiae also generally reduced coliforms but to a lesser extent. Nevertheless, the β-glucan diets did not significantly reduce levels of Lactobacillus or Bifidobacterium. DGGE analysis of GIT samples indicated that the three β-glucan diets generally promoted the establishment of a more varied range of Lactobacillus species in the caecum, proximal and distal colon. The LH β-glucan had the most profound reducing effect on coliform counts when compared with the control diet and diets supplemented with L. digitata and S. cerevisiae β-glucans.     

Sur la disparition progressive de Laminaria digitata sur les côtes du Calvados (France)

In comparison with results from 1983–1988, when a cartographic study was made on the distribution of the Laminariales and of Sargassum muticum in Lower Normandy (France), we note, on the Calvados coast, a regression of Laminaria digitata which has almost disappeared on the Grandcamp rocks. On the contrary, the growth of the populations of Sargassum muticum is very spectacular at Grandcamp; in summer, 80 % of the substratum in the lower parts of the intertidal zone and in the subtidal are covered by this species.     

Molecular genetic diversity and differentiation of populations of ‘somnus’ passion fruit trees (Passiflora setacea DC): Implications for conservation and pre-breeding

The ‘somnus’ passion fruit tree (Passiflora setacea) is native to the ‘Cerrado’ and ‘Caatinga’ biomes in Brazil and possesses agrobiological and commercial traits of interest. Studies examining the nature of genetic variability in natural populations are important for the utilization of these traits in conservation and breeding programs. In this study, we analyzed 12 populations of P. setacea from different locations distributed in three agro-ecological zones within the Bahia state of Brazil. Eleven ISSR primers and four pairs of RGA primers were used to assay 109 and 49 unique and reproducible loci, of which 108 (99%) and 49 (100%) were polymorphic. Although the level of genetic diversity in ‘somnus’ passion fruit trees was greater than that observed for other species of the same genus, preferential collection of certain populations, such as those located in the cities of Vitória da Conquista and Licinio de Almeida, is important when considering the fact that ‘somnus’ passion fruit trees occur in areas that are highly disturbed. This disturbance is primarily due to the deployment of pasture, predatory extraction and accelerated urban expansion. An analysis of molecular variance revealed a balance between the estimated genetic variation within and among populations. These data may be useful for developing strategies for preservation of this species in the Cerrado.     

Cross-breeding experiments among different populations of the ‘cosmopolitan’ species Phyllognathopus viguieri (Copepoda: Harpacticoida)

Populations of harpacticoid copepods belonging to the family Phyllognathopodidae found on most continents are usually assignable to the taxon of Phyllognathopus viguieri, as it is presently diagnosed, on the basis of their morphological characters. This taxon has been considered as cosmopolitan since the unifying revision of Lang in 1948. Here we reveal that Phyllognathopus viguieri is not a single biological species. Cross-breeding experiments with individuals from five different populations of Phyllognathopus viguieri obtained from Germany, Maryland and Florida in the USA, Jamaica, and Brazil indicated that two of these mutually distant populations were reproductively isolated from each other but crossed easily with others, whereas the other populations did not interbreed, with the exception of the two populations from the USA. From these results we conclude that Phyllognathopus viguieri is not a single cosmopolitan biological species. The high proportion of mutually non-reproducing populations identified in the five populations examined in this study indicate that further analysis of the micromorphology and genetic composition of populations over the entire putative range of Phyllognathopus viguieri will be necessary to clarify their interrelationships.     

Genetic analysis of two wheat cultivars, ‘Sonalika’ and ‘WL 711’ for reaction to leaf rust (Puccinia recondita)

Summary Genetic analysis for leaf rust reaction of two widely adapted cultivars, Sonalika and WL 711, has been done using 21 near isogenic Lr lines and rust culture IL004 — avirulent on the two cultivars and all the Lr lines used. The segregation pattern in the F₂ generation indicated the presence of a recessive gene in Sonalika and of a dominant gene in WL 711. These genes in cultivars Sonalika and WL 711 have been identified as Lr 11 and Lr 13, respectively. Gene Lr 13 is no longer effective in WL 711 but it continues to give field resistance in the backgrounds of Chris, Prelude and Thatcher. There has been no significant change in the virulence spectrum of the leaf rust pathogen in India with the release of WL 711. High susceptibility of WL 711 seems to be due to the evolution of more aggressive forms of the pathogen to this cultivar. The gene Lr 11, which behaves as a recessive in Sonalika, was effective against leaf rust when this cultivar was released. The high susceptibility of Sonalika is probably due to an increase in the frequency of race 77 virulent on Lr 11. Lr 11 has shown a dominance reversal in the background of Sonalika. Present results suggest that interaction of resistance genes with the background genotype must be studied for their effective use in breeding programme.     

Lost in space? Searching for directions in the spatial modelling of individuals,populations and species ranges

The workshop ‘Spatial models in animal ecology, management and conservation’ held at Silwood Park (UK), 9–11 March 2010, aimed to synthesize recent progress in modelling the spatial dynamics of individuals, populations and species ranges and to provide directions for research. It brought together marine and terrestrial researchers working on spatial models at different levels of organization, using empirical as well as theory-driven approaches. Different approaches, temporal and spatial scales, and practical constraints predominate at different levels of organization and in different environments. However, there are theoretical concepts and specific methods that can fruitfully be transferred across levels and systems, including: habitat suitability characterization, movement rules, and ways of estimating uncertainty.     

Microbiological characterization of yam fermentation for ‘Elubo’ (yam flour) production

Yams (Dioscorea rotundata) were processed and fermented to the traditional West African dried yam flour Elubo. Yam slices were blanched at 60°C for 10min and then fermented at 30°C for 24h. The microbial population increased with fermentation time during the first 24h of natural fermentation with a fall in the pH from 6.2 to 5.4. The dominant aerobic mesophilic bacteria consisted of Lactobacillus plantarum, Lactobacillus brevis, Lactobacillus delbrueckii and Bacillus subtilis. Significant contributions were also made by Lactococcus lactis, Klebsiella pneumoniae, Citrobacter freundii and the yeasts Pichia burtonii and Candida krusei. Accelerated natural lactic fermentation was achieved by repetitive use of the previous fermentation batch as an inoculum through back-slopping at a rate of 10% (w/v). After three consecutive fermentation cycles, the microflora was dominated by L. plantarum and L. brevis. Fermentation of blanched samples with pure cultures of the isolates showed L. plantarum L. brevis and B. subtilis to be the main species responsible for pH reduction and in changes in the browning levels of the reconstituted flour paste (amala). The typical colour of amala is disliked by many individuals and it seems possible that amala with a lighter colour which will be more acceptable can be produced by fermentation.     

Taxamatch,an Algorithm for Near (‘Fuzzy’) Matching of Scientific Names in Taxonomic Databases

Misspellings of organism scientific names create barriers to optimal storage and organization of biological data, reconciliation of data stored under different spelling variants of the same name, and appropriate responses from user queries to taxonomic data systems. This study presents an analysis of the nature of the problem from first principles, reviews some available algorithmic approaches, and describes Taxamatch, an improved name matching solution for this information domain. Taxamatch employs a custom Modified Damerau-Levenshtein Distance algorithm in tandem with a phonetic algorithm, together with a rule-based approach incorporating a suite of heuristic filters, to produce improved levels of recall, precision and execution time over the existing dynamic programming algorithms n-grams (as bigrams and trigrams) and standard edit distance. Although entirely phonetic methods are faster than Taxamatch, they are inferior in the area of recall since many real-world errors are non-phonetic in nature. Excellent performance of Taxamatch (as recall, precision and execution time) is demonstrated against a reference database of over 465,000 genus names and 1.6 million species names, as well as against a range of error types as present at both genus and species levels in three sets of sample data for species and four for genera alone. An ancillary authority matching component is included which can be used both for misspelled names and for otherwise matching names where the associated cited authorities are not identical.     

Genetic differentiation between three ecological variants (‘type’, ‘mysorensis’ and ‘intermediate’) of malaria vector Anopheles stephensi (Diptera: Culicidae)

Abstract Anopheles stephensi is the main vector of urban malaria in South Asia. Three ecological variants (‘type’, ‘mysorensis’and‘intermediate’) of An. stephensi have been reported on the basis of ecology and egg morphology. However, it is unclear if there is any genetic isolation between the three variants. We analyzed the three variants of An. stephensi using eight microsatellite loci and found that large and significant genetic differentiation exists between them (mean F_ST= 0.393 and mean R_ST= 0.422). Pairwise estimates of genetic differentiation between the variants were ‘type’ versus ‘mysorensis’ (mean F_ST= 0.411 and mean R_ST= 0.308), ‘type’ versus ‘intermediate’ (mean F_ST= 0.388 and mean R_ST= 0.518) and ‘intermediate’ versus ‘mysorensis’ (mean F_ST= 0.387 and mean R_ST= 0.398) and all were statistically significant (P < 0.05). The greater sensitivity of R_ST in differentiation indicated that mutations and not genetic drift had generated the differences between three variants of An. stephensi. The present study indicated large genetic differentiation and presence of non-significant low level of gene flow between the three variants (‘type’, ‘mysorensis’and‘intermediate’) of An. stephensi.     

Structural and Narrative Reconstruction of Rural Residents’ Representations of ‘Nature’, ‘Wildlife’, and ‘Landscape’

The objective of this paper is the structural and narrative reconstruction of representations of ‘nature’, ‘wildlife’ and ‘landscape’, held by rural residents of the Dadia Forest Reserve. Data collection involved in-depth interviews. Employing a social representations’ approach, we recovered representational elements that are expected in the case of rural belief systems, such as negative dispositions towards wolves and foxes, as well as elements of an urban adherence, such as nature’s independence. Representational elements refer to visual aspects of the countryside, which seem compatible with the figurative nucleus of the rural idyll. Concerning ‘wildlife’, residents focused on vultures, which comprise the main tourist attraction of the reserve. Scientific knowledge adds to the complexity of the narrative schema, which corresponds to the representation of ‘wildlife’. Interviewees perceived the rural landscape as an interface between the natural and the human-conditioned environment. Our study shows that interviewees make no reference to environmental conservation or quality of life issues, as it could be expected according to relatively wide definitions of the term ‘environmentalism’. Environmental messages reinforced by ecotourism development seem to be recalled primarily in terms of their compatibility with the perceived economic benefit of local people. Despite ecotourism development, representational elements that diverge from a tourist version of ‘nature’, ‘wildlife’ and ‘landscape’ were not pronounced within rural belief-systems. Further interventions within the study area are needed, in order to address a variety of topics under the environmental conservation discourse and raise the environmental awareness of rural residents.     

A submerged culture system for rapid micropropagation of the commercially important aquarium plant, ‘Amazon sword’ (Echinodorus ‘Indian Red’)

Echinodorus ‘Indian Red’ is an underwater plant, used worldwide for aquarium ornamentation. An efficient method for in vitro propagation and plantlet acclimatization of this popular aquarium plant was standardized. Surface-disinfected shoot-tips were cultured in submerged conditions in a solid–liquid bilayer medium, consisting of an upper, liquid layer (sterile distilled water) and a lower, solid layer Murashige and Skoog (MS) basal medium supplemented with 3.0% (w/v) sucrose, 0.8% (w/v) agar-agar, and plant growth regulators (PGRs) in different combinations and concentrations. The combination of 2.5 mg L⁻¹ 6-benzylaminopurine and 1.0 mg L⁻¹ α-naphthaleneacetic acid improved the multiplication rate to a maximum of 26.8 ± 0.51 shoots per explant after 60 d of culture. The number of multiplied shoots increased with each regeneration cycle, thus from only 26.8 ± 0.51 shoots per explant (first regeneration cycle), this number increased to 33.5 ± 0.58 (second regeneration cycle), and to 38.3 ± 0.62 for the third regeneration cycle with the same medium composition. The highest number of roots (8.3 ± 0.28) per shoot was induced in the presence of 1.0 mg L⁻¹ indole-3-butyric acid, but further growth of these roots was stunted. The best rooting was achieved on PGR-free ½-strength MS medium, where 6.1 ± 0.21 roots per shoot were induced with 5.8 ± 0.35 cm length after 30 d of culture. The regenerated plantlets were successfully acclimatized to submerged underwater conditions, with 100% survival rate. The present protocol is suitable for the commercial propagation of Echinodorus ‘Indian Red’ for aquarium-industries.

     

Support for the ‘out-of-Southeast Asia’ hypothesis for the origin of Australian populations of <Emphasis Type="Italic">Radopholus similis</Emphasis> (Cobb, 1893) (Nematoda: Pratylenchidae)

Radopholus similis is one of the world’s ten most economically important plant-parasitic nematodes. It is especially a problem in banana cultivation, where the nematodes’ feeding reduces yields and causes toppling disease. It has been suggested that the genus Radopholus Thorne, 1949 might have an Australian origin, but the native range of R. similis (Cobb, 1893) is not well known. Here we undertake a phylogeographical study of samples of R. similis from banana plantations down the eastern seaboard of Australia, with additional samples from Costa Rica and accessions from GenBank, to examine the origin of pest populations of R. similis. The lack of genetic diversity of R. similis within Australia, and its sharing of a worldwide pest haplotype, suggest that populations of R. similis in Australia were introduced from a single source population, most likely from the Southeast Asian region. This might not be the case in Africa, where extensive genetic diversity has been found.     

A program for handling data obtained by ‘blind’ histopathological evaluations

An interactive data input, storage, retrieval and treatment system (LAMES) is described for use in histophatological studies where pathologists evaluate tissues without any identification (termed evaluations which are ‘blind’). The system produces the mean values of individual groups within an experiment, and results of statistical comparisons between the groups. The system was implemented on a Hewlett-Packard (HP) 1000-F minicomputer operating under RTE-6/VM, and was written using FORTRAN IV.