The role of exotic plants in the invasion of Seychelles by the polyphagous insect Aleurodicus disperses: a phylogenetically controlled analysis

The accidental introduction of the spiralling whitefly, Aleurodicus dispersus Russell (Homoptera: Aleyrodidae) to Seychelles in late 2003 is exploited during early 2005 to study interactions between A. dispersus, native and exotic host plants and their associated arthropod fauna. The numbers of A. dispersus egg spirals and pupae, predator and herbivore taxa were recorded for eight related native/exotic pairs of host plants found on Mahe, the largest island in Seychelles. Our data revealed no significant difference in herbivore density (excluding A. dispersus) between related native and exotic plants, which suggests that the exotic plants do not benefit from 'enemy release'. There were also no differences in predator density, or combined species richness between native and exotic plants. Together these data suggest that 'biotic resistance' to invasion is also unlikely. Despite the apparent lack of differences in community structure significantly fewer A. dispersus egg spirals and pupae were found on the native plants than on the exotic plants. Additional data on A. dispersus density were collected on Cousin Island, a managed nature reserve in which exotic plants are carefully controlled. Significantly higher densities of A. dispersus were observed on Mahe, where exotic plants are abundant, than on Cousin. These data suggest that the rapid invasion of Seychelles by A. dispersus may largely be due to the high proportion of plant species that are both exotic and hosts of A. dispersus; no support was found for either the 'enemy release' or the 'biotic resistance' hypotheses.

A note on the accuracy of PAC-likelihood inference with microsatellite data

Stephens and Donnelly have introduced a simple yet powerful importance sampling scheme for computing the likelihood in population genetic models. Fundamental to the method is an approximation to the conditional probability of the allelic type of an additional gene, given those currently in the sample. As noted by Li and Stephens, the product of these conditional probabilities for a sequence of draws that gives the frequency of allelic types in a sample is an approximation to the likelihood, and can be used directly in inference. The aim of this note is to demonstrate the high level of accuracy of "product of approximate conditionals" (PAC) likelihood when used with microsatellite data. Results obtained on simulated microsatellite data show that this strategy leads to a negligible bias over a wide range of the scaled mutation parameter theta. Furthermore, the sampling variance of likelihood estimates as well as the computation time are lower than that obtained with importance sampling on the whole range of theta. It follows that this approach represents an efficient substitute to IS algorithms in computer intensive (e.g. MCMC) inference methods in population genetics. (c) 2006 Elsevier Inc. All rights reserved.

The tagged microarray marker (TAM) method for high-throughput detection of single nucleotide and indel polymorphisms

The tagged microarray marker (TAM) method allows high-throughput differentiation between predicted alternative PCR products. Typically, the method is used as a molecular marker approach to determining the allelic states of single nucleotide polymorphisms (SNPs) or insertion-deletion (indel) alleles at genomic loci in multiple individuals. Biotin-labeled PCR products are spotted, unpurified, onto a streptavidin-coated glass slide and the alternative products are differentiated by hybridization to fluorescent detector oligonucleotides that recognize corresponding allele-specific tags on the PCR primers. The main attractions of this method are its high throughput (thousands of PCRs are analyzed per slide), flexibility of scoring (any combination, from a single marker in thousands of samples to thousands of markers in a single sample, can be analyzed) and flexibility of scale (any experimental scale, from a small lab setting up to a large project). This protocol describes an experiment involving 3,072 PCRs scored on a slide. The whole process from the start of PCR setup to receiving the data spreadsheet takes 2 d.

Using phylogeny to investigate the origins of the Cape flora: the importance of taxonomic, gene and genome sampling strategies

Phylogenetic methods hold great promise for the reconstruction of the transition from precursor to modern flora and the identification of underlying factors which drive the process. The phylogenetic methods presently used to address the question of the origin of the Cape flora of South Africa are considered here. The sampling requirements of each of these methods, which include dating of diversifications using calibrated molecular trees, sister pair comparisons, lineage through time plots and biogeographical optimizations are reviewed. Sampling of genes, genomes and species are considered. Although increased higher-level studies and increased sampling are required for robust interpretation, it is clear that much progress is already made. It is argued that despite the remarkable richness of the flora, the Cape flora is a valuable model system to demonstrate the utility of phylogenetic methods in determining the history of a modern flora.

Detecting non-multiplicative genotype relative risks from transmissions of parental alleles to affected children

The differential transmission of alleles from parents to affected children indicates that the locus under investigation is either directly involved in the occurrence of the disease or that there are allelic associations with other loci that are directly involved. Conditional logistic regression applied to a diallelic locus leads to a test with two degrees of freedom. The power of a single degree of freedom test to detect non-multiplicative allelic effects is discussed here.

Influence of occupant microhabitat on the composition of encrusting communities on gastropod shells

The exploitation of microhabitats is widely considered to increase biodiversity in marine ecosystems. Although intertidal hermit crabs and gastropods may inhabit the same shell type and shore level, their microhabitat may differ depending on the state of the tide. On the south coast of Wales the hermit crab Pagurus bernhardus mainly inhabits the shells of Nucella lapillus (84%). Hermit crab shells had a significantly different encrusting community compared with live N. lapillus shells. At low tide the live gastropods were found on exposed rock surfaces whereas hermit crabs were restricted to tidal pools. Communities encrusting live gastropod shells were characterised by lower species richness and abundance compared with shells inhabited by hermit crabs (12 species found in total). A greater abundance and richness of epibionts was recorded from both shell types during the summer compared with winter. Differences in community composition between shell occupant types were attributed to microhabitats used by gastropods and hermit crabs and the associated desiccation pressures, rather than competitive interactions or shell characteristics. This contradicts earlier studies of subtidal shells where biological processes were considered more important than physical factors in controlling species abundance and richness patterns. The use of rockpool microhabitats by hermit crabs increases the biodiversity of rocky shores, as some species commonly found on hermit-crab-inhabited shells were rare in other local habitats.

High throughput, high resolution selection of polymorphic microsatellite loci for multiplex analysis

Background Large-scale genetic profiling, mapping and genetic association studies require access to a series of well-characterised and polymorphic microsatellite markers with distinct and broad allele ranges. Selection of complementary microsatellite markers with non-overlapping allele ranges has historically proved to be a bottleneck in the development of multiplex microsatellite assays. The characterisation process for each microsatellite locus can be laborious and costly given the need for numerous, locus-specific fluorescent primers. Results Here, we describe a simple and inexpensive approach to select useful microsatellite markers. The system is based on the pooling of multiple unlabelled PCR amplicons and their subsequent ligation into a standard cloning vector. A second round of amplification utilising generic labelled primers targeting the vector and unlabelled locus-specific primers targeting the microsatellite flanking region yield allelic profiles that are representative of all individuals contained within the pool. Suitability of various DNA pool sizes was then tested for this purpose. DNA template pools containing between 8 and 96 individuals were assessed for the determination of allele ranges of individual microsatellite markers across a broad population. This helped resolve the balance between using pools that are large enough to allow the detection of many alleles against the risk of including too many individuals in a pool such that rare alleles are over-diluted and so do not appear in the pooled microsatellite profile. Pools of DNA from 12 individuals allowed the reliable detection of all alleles present in the pool. Conclusion The use of generic vector-specific fluorescent primers and unlabelled locus-specific primers provides a high resolution, rapid and inexpensive approach for the selection of highly polymorphic microsatellite loci that possess non-overlapping allele ranges for use in large-scale multiplex assays.

Monitoring growth of hard corals as performance indicators for coral reefs

Digital videophotography, computer image analysis and physical measurements have been used to monitor sedimentation rates, coral cover, genera richness, rugosity and estimated recruitment dates of massive corals at three different sites in the Wakatobi Marine National Park, Indonesia, and on the reefs around Discovery Bay, Jamaica. Semi-structured interviews with key stakeholders in the Wakatobi Marine National Park indicated that coral mining was extensively practised, and is responsible for the absence of large non-branching corals on the Sampela reef Blast fishing is also practised in the Wakatobi Marine Park, and the authors, together with students, showed that blast fishing resulted in coral bleaching and not mortality of two Porites lutea colonies. In addition, we showed that monitoring of bleaching in Porites colonies induced by blast fishing could be a useful way of monitoring blast fishing practices in susceptible areas in the Indo-Pacific. The techniques used in this study are appropriate for use by volunteers with sufficient training, and provide excellent projects for dissertation students reading undergraduate degrees.

Biodiversity of Collembola in urban soils and the use of Folsomia candida to assess soil 'quality'

The effects of metal contamination on natural populations of Collembola in soils from five sites in the Wolverhampton area ( West Midlands, England) were examined. Analysis revealed that metal concentrations were elevated above background levels at all sites. One location in particular (Ladymoor, a former smelting site) was highly contaminated with Cd, Cu, Pb and Zn at more than 20 times background levels. Biodiversity indices ( Shannon - Weiner, Simpson index, Margalef index, alpha index, species richness, Shaneven ( evenness) and Berger - Parker dominance) were calculated. Of these indices, estimates of species richness and evenness were most effective at highlighting the differences between the Collembola communities. Indeed, the highest number of species were found at the most contaminated site, although the Collembola population also had a comparatively low evenness value, with just two species dominating. The number of individuals per species were allocated into geometric classes and plotted against the cumulative number of species as a percentage. At Ladymoor, there were more geometric classes, and the slope of the line was shallower than at the other four sites. This characteristic is a feature of polluted sites, where a few species are dominant and most species are rare. The Ladymoor soil also had a dominance of Isotomurus palustris, and was the only site in which Ceratophysella denticulata was found. Previous studies have shown that these two species are often found in sites subject to high metal contamination. Survival and reproduction of the "standard'' test springtail, Folsomia candida (Willem), were determined in a 4 week exposure test to soils from all five sites. Mortality was significantly increased in adults and reproduction significantly lower in the Ladymoor soil in comparison to the other four sites. This study has shown that severe metal contamination can be related to the population structure of Collembola in the field, and performance of F. candida ( in soils from such sites) in the laboratory.

Cross-species amplification and phylogenetic reconstruction using fragaria microsatellite primers

Twenty-eight microsatellite primer pairs developed from Fragaria vesca ‘Rügen’ were applied to sixteen accessions representing eight diploid Fragaria species. The number of alleles generated, the power of discrimination and the percentage of accessions where no PCR product could be amplified were calculated for each locus for the thirteen non-F. vesca accessions. A phylogeny was then generated for the species accessions sampled, using the presence or absence of alleles at the polymorphic loci as character states. Despite the problems inherent in phylogeny reconstruction from microsatellite data, the phylogeny showed some congruence with a previously published phylogeny of Fragaria, based on nucleotide sequence data. However, relationships inferred from microsatellite allele data were relatively unresolved and poorly supported. The genetic basis of allelic polymorphisms at specific loci was investigated through direct sequencing of the PCR products amplified by three primer pairs. The potential utility of sequence data generated from microsatellite loci in evolutionary studies of closely related species groups is briefly explored.

Temporal and spatial variability of mobile fauna on a submarine cliff and boulder scree complex: a community in flux

The mobile component of a community inhabiting a submarine boulder scree/cliff was investigated at Lough Hyne, Ireland at dawn, midday, dusk and night over a 1-week period. Line transects (50 m) were placed in the infralittoral (6 m) and circumlittoral (18 m) zones and also the interface between these two zones (12 m). The dominant mobile fauna of this cliff consisted of echinoderms (6 species), crustaceans (10 species) and fish (23 species). A different component community was identified at each time/depth interval using Multi-Dimensional Scaling (MDS) even though both species diversity (Shannon-Wiener indices) and richness (number of species) remained constant. These changes in community composition provided indirect evidence for migration by these mobile organisms. However, little evidence was found for migration between different zones with the exception of the several wrasse species. These species were observed to spend the daytime foraging in the deeper zone, but returned to the upper zone at night presumably for protection from predators. For the majority of species, migration was considered to occur to cryptic habitats such as holes and crevices. The number of organisms declined during the night, although crustacean numbers peaked, while fish and echinoderms were most abundant during day, possibly due to predator-prey interactions. This submarine community is in a state of flux, whereby, community characteristics, including trophic and energetic relationships, varied over small temporal (daily) and spatial (m) scales.

Computer modelling and estimation of recruitment patterns of non-branching coral colonies at three sites in Wakatobi Marine Park, S.E. Sulawesi, Indonesia; implications for coral reef conservation

We have studied growth and estimated recruitment of massive coral colonies at three sites, Kaledupa, Hoga and Sampela, separated by about 1.5 km in the Wakatobi Marine National Park, S.E. Sulawesi, Indonesia. There was significantly higher species richness (P<0.05), coral cover (P<0.05) and rugosity (P<0.01) at Kaledupa than at Sampela. A model for coral reef growth has been developed based on a rational polynomial function, where dx/dt is an index of coral growth with time; W is the variable (for example, coral weight, coral length or coral area), up to the power of n in the numerator and m in the denominator; a1……an and b1…bm are constants. The values for n and m represent the degree of the polynomial, and can relate to the morphology of the coral. The model was used to simulate typical coral growth curves, and tested using published data obtained by weighing coral colonies underwater in reefs on the south-west coast of Curaçao [‘Neth. J. Sea Res. 10 (1976) 285’]. The model proved an accurate fit to the data, and parameters were obtained for a number of coral species. Surface area data was obtained on over 1200 massive corals at three different sites in the Wakatobi Marine National Park, S.E. Sulawesi, Indonesia. The year of an individual's recruitment was calculated from knowledge of the growth rate modified by application of the rational polynomial model. The estimated pattern of recruitment was variable, with little numbers of massive corals settling and growing before 1950 at the heavily used site, Sampela, relative to the reef site with little or no human use, Kaledupa, and the intermediate site, Hoga. There was a significantly greater sedimentation rate at Sampela than at either Kaledupa (P<0.0001) or Hoga (P<0.0005). The relative mean abundance of fish families present at the reef crests at the three sites, determined using digital video photography, did not correlate with sedimentation rates, underwater visibility or lack of large non-branching coral colonies. Radial growth rates of three genera of non-branching corals were significantly lower at Sampela than at Kaledupa or at Hoga, and there was a high correlation (r=0.89) between radial growth rates and underwater visibility. Porites spp. was the most abundant coral over all the sites and at all depths followed by Favites (P<0.04) and Favia spp. (P<0.03). Colony ages of Porites corals were significantly lower at the 5 m reef flat on the Sampela reef than at the same depth on both other reefs (P<0.005). At Sampela, only 2.8% of corals on the 5 m reef crest are of a size to have survived from before 1950. The Scleractinian coral community of Sampela is severely impacted by depositing sediments which can lead to the suffocation of corals, whilst also decreasing light penetration resulting in decreased growth and calcification rates. The net loss of material from Sampela, if not checked, could result in the loss of this protective barrier which would be to the detriment of the sublittoral sand flats and hence the Sampela village.

Bryophyte diversity and community structure on thatched roofs of the Holnicote Estate, Somerset, U.K.

We investigated patterns of bryophyte species richness and community structure, and their relation to roof variables, on thatched roofs of the Holnicote Estate, South Somerset. Thirty-two bryophyte species were recorded from 28 sampled roofs, including the globally rare and endangered thatch moss, Leptodontium gemmascens. Multiple regression analyses revealed that thatch age has a highly significant positive effect on the number of species present, accounting for nearly half the observed variation in species richness after removal of outliers. Aspect has a slight and marginally significant effect on species diversity (accounting for an additional 6% of variation), with north-facing samples having slightly more species. Age also has a significant impact on total bryophyte cover after removal of outlying observations. TWINSPAN analysis of bryophyte cover data suggests the existence of at least five discrete communities. Simple Discriminant Analyses indicate that these communities occupy different ecological subspaces as defined by the measured roof variables, with pitch, aspect and thatch age emerging as especially significant attributes. Contingency Analysis indicates that some communities are disfavoured by water reed as compared to wheat straw. The findings are significant for understanding the structure of bryophyte communities, for evaluating the effect of bryophyte cover on thatch performance, and for conservation of thatch communities, especially those harbouring rare species.

Primary music education: the misrepresentation of the ideals of curricula in research

The author starts from a historical viewpoint to suggest that, at primary level, we have tended to perpetuate a nineteenth-century notion of music education. This is evident in the selection and organisation of musical content in curriculum documents, the scope of the teacher-pupil transaction implicit in these and the assumptions about music education which underpin research on practice conducted at official policy level. In light of the introduction of the 1999 Revised Primary School Curriculum, with its change in emphasis, she notes that it is timely to reconsider the situation. Central to this is the need to challenge the notion of music as a set of delineated skills, to explore the relationship between the primary teacher and music, and to move towards a notion of research which acknowledges the richness of multiple interpretations teachers bring to the curriculum.

Characterization of wheat puroindoline proteins

Puroindoline proteins were purified from selected UK-grown hexaploid wheats. Their identities were confirmed on the basis of capillary electrophoresis mobilities, relative molecular mass and N-terminal amino acid sequencing. Only one form of puroindoline-a protein was found in those varieties, regardless of endosperm texture. Three allelic forms of puroindoline-b protein were identified. Nucleotide sequencing of cDNA produced by RT-PCR of isolated mRNA indicated that these were the 'wild-type', found in soft wheats, puroindoline-b containing a Gly -> Ser amino acid substitution (position 46) and puroindoline-b containing a Trp -> Arg substitution (position 44). The latter two were found in hard wheats. Microheterogeneity, due to short extensions and/or truncations at the N-terminus and C-terminus, was detected for both puroindoline-a and puroindoline-b. The type of microheterogeneity observed was more consistent for puroindoline-a than for puroindoline-b, and may arise through slightly different post-translational processing pathways. A puroindoline-b allele corresponding to a Leu -> Pro substitution (position 60) was identified from the cDNA sequence of the hard variety Chablis, but no mature puroindoline-b protein was found in this or two other European varieties known to possess this puroindoline-b allele. Wheats possessing the puroindoline-b proteins with point mutations appeared to contain lower amounts of puroindoline protein. Such wheats have a hard endosperm texture, as do wheats from which puroindoline-a or puroindoline-b are absent. Our results suggest that point mutations in puroindoline-b genes may confer hard endosperm texture through accumulation of allelic forms of puroindoline-b proteins with altered functional properties and/or through lower amounts of puroindoline proteins.