Assessment of methods to estimate aquatic macrophyte species richness in extrapolated sample sizes

We evaluated six methods to estimate species richness in extrapolated sample size using presence–absence data for aquatic macrophyte assemblages. Methods suitable for assemblages involving terrestrial and non-clonal (unitary) organisms may not be valid for aquatic macrophytes. The extrapolation of a species accumulation curve using a logarithmic function or using a linear model on the log of accumulated sampling units consistently overestimated species richness. The newly proposed Total-Species method gave similar results. The Negative Binomial and Logarithmic Series methods and the recently proposed Binomial Mixture Model were unbiased and accurate. We conclude that current extrapolation techniques are valid for estimation of species richness in macrophyte assemblages, and recommend the Logarithmic Series, Binomial Negative or Binomial Mixture Model methods.     

Molecular phylogenetic diversity of the emerging mucoralean fungus Apophysomyces: Proposal of three new species

BackgroundApophysomyces is a monotypic genus belonging to the order Mucorales. The species Apophysomyces elegans has been reported to cause severe infections in immunocompromised and immunocompetent people. In a previous study of Álvarez et al.³ [J Clin Microbiol 2009;47:1650–6], we demonstrated a high variability among the 5.8S rRNA gene sequences of clinical strains of A. elegans.Material and methodsWe performed a polyphasic study based on the analysis of the sequences of the histone 3 gene, the internal transcribed spacer region of the rDNA gene, and domains D1 and D2 of the 28S rRNA gene, as well as by evaluation of some relevant morphological and physiological characteristics of a set of clinical and environmental strains of A. elegans.Results and conclusionsWe have demonstrated that A. elegans is a complex of species. We propose as new species Apophysomyces ossiformis, characterised by bone-shaped sporangiospores, Apophysomyces trapeziformis, with trapezoid-shaped sporangiospores, and Apophysomyces variabilis, with variable-shaped sporangiospores. These species failed to assimilate esculin, whereas A. elegans was able to assimilate that glycoside. Amphotericin B and posaconazole are the most active in vitro drugs against Apophysomyces.     

Deubiquitinating enzymes: their diversity and emerging roles

A growing number of important regulatory proteins within cells are modified by conjugation of ubiquitin, a well-conserved 76-amino-acid polypeptide. The ubiquitinated proteins are targeted to proteasome for degradation or alternative metabolic fates, such as triggering of plasma membrane endocytosis and trafficking to vacuoles or lysosomes. Deubiquitination, reversal of this modification, is being recognized as an important regulatory step. Deubiquitinating enzymes are cysteine proteases that specifically cleave off ubiquitin from ubiquitin-conjugated protein substrates as well as from its precursor proteins. Genome sequencing projects have identified more than 90 deubiquitinating enzymes, making them the largest family of enzymes in the ubiquitin system. This review will concentrate on recent important findings as well as new insights into the diversity and emerging roles of deubiquitinating enzymes in the ubiquitin-dependent pathway.     

Ecology: linking species diversity and genetic diversity

Although there is a great deal of interest in the biological diversity of species and of genes, it is only recently that researchers have begun to investigate the processes that exert parallel influences on these different levels of diversity.     

The emerging diversity of Rickettsia

The best-known members of the bacterial genus Rickettsia are associates of blood-feeding arthropods that are pathogenic when transmitted to vertebrates. These species include the agents of acute human disease such as typhus and Rocky Mountain spotted fever. However, many other Rickettsia have been uncovered in recent surveys of bacteria associated with arthropods and other invertebrates; the hosts of these bacteria have no relationship with vertebrates. It is therefore perhaps more appropriate to consider Rickettsia as symbionts that are transmitted vertically in invertebrates, and secondarily as pathogens of vertebrates. In this review, we highlight the emerging diversity of Rickettsia species that are not associated with vertebrate pathogenicity. Phylogenetic analysis suggests multiple transitions between symbionts that are transmitted strictly vertically and those that exhibit mixed (horizontal and vertical) transmission. Rickettsia may thus be an excellent model system in which to study the evolution of transmission pathways. We also focus on the emergence of Rickettsia as a diverse reproductive manipulator of arthropods, similar to the closely related Wolbachia, including strains associated with male-killing, parthenogenesis, and effects on fertility. We emphasize some outstanding questions and potential research directions, and suggest ways in which the study of non-pathogenic Rickettsia can advance our understanding of their disease-causing relatives.     

Phylogenetic comparative methods: Harnessing the power of species diversity to investigate welfare issues in captive wild animals

This paper reviews a way of investigating health and welfare problems in captive wild animals (e.g., those in zoos, aviaries, aquaria, or aquaculture systems) that has great potential, but to date has been little used: systematically comparing species with few or no health and welfare issues to those more prone to problems. Doing so empirically pinpoints species‐typical welfare risk and protective factors (such as aspects of their natural behavioral biology): information which can then be used to help prevent or remedy problems by suggesting new ways to improve housing and husbandry, and by identifying species intrinsically best suited to captivity. We provide a detailed, step‐by‐step “how to” guide for researchers interested in using these techniques, including guidance on how to statistically control for the inherent similarities shared by related species: an important concern because simple, cross‐species comparisons that do not do this may well fail to meet statistical assumptions of non‐independence. The few relevant studies that have investigated captive wild animals’ welfare problems using this method are described. Overall, such approaches reap value from the great number and diversity of species held in captivity (e.g., the many thousands of species held in zoos); can yield new insights from existing data and published results; render previously intractable welfare questions (such as “do birds need to fly?” or “do Carnivora need to hunt?”) amenable to study; and generate evidence‐based principles for integrating animal welfare into collection planning.     

Measuring species diversity while counting large mammals: comparison of methods using species-accumulation curves

With a growing need for wildlife conservation and management in the communal lands of Africa, comprehensive ecological monitoring tools need to be developed and evaluated. While wildlife census methods are often compared in terms of precision and accuracy to estimate the population size of various target species, little attention has been paid to the measure of species diversity in mammal communities. A combined measure of abundance and community composition is, however, a crucial source of information in determining conservation priorities and to evaluate the ecosystem responses to management activities. In this study, we present five census methods of large to medium‐sized mammals and compare their efficacy in measuring species diversity. A species accumulation curve analysis is used with a predictive model to estimate the local species richness, the level of completeness of our censuses as well as the effort required to carry out a census. Advantages and limits of each method are discussed through comparison of their respective measure of species richness and their species accumulation rate. Results illustrate a large difference between methods in the ability for species detection, with censuses completed by bicycle offering the best option within the context of a unprotected area.     

From plots to islands: species diversity at different scales

Aim To investigate how plant diversity of whole islands (‘gamma’) is related to alpha and beta diversity patterns among sampling plots within each island, thus exploring aspects of diversity patterns across scales. Location Nineteen islands of the Aegean Sea, Greece. Methods Plant species were recorded at both the whole‐island scale and in small 100 m² plots on each island. Mean plot species richness was considered as a measure of alpha diversity, and six indices of the ‘variation’‐type beta diversity were also applied. In addition, we partitioned beta diversity into a ‘nestedness’ and a ‘replacement’ component, using the total species richness recorded in all plots of each island as a measure of ‘gamma’ diversity. We also applied 10 species–area models to predict the total observed richness of each island from accumulated plot species richness. Results Mean alpha diversity was not significantly correlated with the overall island species richness or island area. The range of plot species richness for each island was significantly correlated with both overall species richness and area. Alpha diversity was not correlated with most indices of beta diversity. The majority of beta diversity indices were correlated with whole‐island species richness, and this was also true for the ‘replacement’ component of beta diversity. The rational function model provided the best prediction of observed island species richness, with Monod’s and the exponential models following closely. Inaccuracy of predictions was positively correlated with the number of plots and with most indices of beta diversity. Main conclusions Diversity at the broader scale (whole islands) is shaped mainly by variation among small local samples (beta diversity), while local alpha diversity is not a good predictor of species diversity at broader scales. In this system, all results support the crucial role of habitat diversity in determining the species–area relationship.     

A comparison of methods to estimate cross-environment genetic correlations

Advanced techniques for quantitative genetic parameter estimation may not always be necessary to answer broad genetic questions. However, simpler methods are often biased, and the extent of this determines their usefulness. In this study we compare family mean correlations to least squares and restricted error maximum likelihood (REML) variance component approaches to estimating cross-environment genetic correlations. We analysed empirical data from studies where both types of estimates were made, and from studies in our own laboratories. We found that the agreement between estimates was better when full-sib rather than half-sib estimates of cross-environment genetic correlations were used and when mean family size increased. We also note biases in REML estimation that may be especially important when testing to see if correlations differ from 0 or 1. We conclude that correlations calculated from family means can be used to test for the presence of genetic correlations across environments, which is sufficient for some research questions. Variance component approaches should be used when parameter estimation is the objective, or if the goal is anything other than determining broad patterns.     

Glycoconjugate vaccines against Salmonella enterica serovars and Shigella species: existing and emerging methods for their analysis

The global spread of enteric disease, the increasingly limited options for antimicrobial treatment and the need for effective eradication programs have resulted in an increased demand for glycoconjugate enteric vaccines, made with carbohydrate-based membrane components of the pathogen, and their precise characterisation. A set of physico-chemical and immunological tests are employed for complete vaccine characterisation and to ensure their consistency, potency, safety and stability, following the relevant World Health Organization and Pharmacopoeia guidelines. Variable requirements for analytical methods are linked to conjugate structure, carrier protein nature and size and O-acetyl content of polysaccharide. We investigated a key stability-indicating method which measures the percent free saccharide of Salmonella enterica subspecies enterica serovar Typhi capsular polysaccharide, by detergent precipitation, depolymerisation and HPAEC-PAD quantitation. Together with modern computational approaches, a more precise design of glycoconjugates is possible, allowing for improvements in solubility, structural conformation and stability, and immunogenicity of antigens, which may be applicable to a broad spectrum of vaccines. More validation experiments are required to establish the most effective and suitable methods for glycoconjugate analysis to bring uniformity to the existing protocols, although the need for product-specific approaches will apply, especially for the more complex vaccines. An overview of current and emerging analytical approaches for the characterisation of vaccines against Salmonella Typhi and Shigella species is described in this paper. This study should aid the development and licensing of new glycoconjugate vaccines aimed at the prevention of enteric diseases.     

Sampling methods for assessing social wasps species diversity in a eucalyptus plantation

Social wasps were collected in a eucalyptus (Eucalyptus urograndis, a genetically enhanced eucalyptus) plantation in Juiz de Fora, state of Minas Gerais, southwestern of Brazil, by using a variety of sampling methods, including active capture and baited traps set at two microhabitats. Six new records of social wasps for this region were obtained during the study: Brachygastra lecheguana Latreille, Polybia ignobilis Haliday, Polybia occidentalis Olivier, Polybia platycephala (Richards), Protonectarina sylveirae Saussure, and Protopolybia exigua Saussure (Hymenoptera: Vespidae). The active capture method sampled the greatest number of species. Baited traps installed in the canopy sampled agreater number of individuals of social wasps than those set on the trunks of eucalyptus trees. Fruit based baits captured a greater number of social wasp species than those baited with a protein derivative. Once no method was able to sample all species, we concluded that the efficiency of a survey can be maximized by using traps with a variety of different baits, in combination with active capture methods.     

From competition to facilitation: how tree species respond to neighbourhood diversity

Studies on tree communities have demonstrated that species diversity can enhance forest productivity, but the driving mechanisms at the local neighbourhood level remain poorly understood. Here, we use data from a large‐scale biodiversity experiment with 24 subtropical tree species to show that neighbourhood tree species richness generally promotes individual tree productivity. We found that the underlying mechanisms depend on a focal tree's functional traits: For species with a conservative resource‐use strategy diversity effects were brought about by facilitation, and for species with acquisitive traits by competitive reduction. Moreover, positive diversity effects were strongest under low competition intensity (quantified as the total basal area of neighbours) for acquisitive species, and under high competition intensity for conservative species. Our findings demonstrate that net biodiversity effects in tree communities can vary over small spatial scales, emphasising the need to consider variation in local neighbourhood interactions to better understand effects at the community level.