David A. Nipperess

The Cladistic Basis for the Phylogenetic Diversity (PD) Measure Links Evolutionary Features to Environmental Gradients and Supports Broad Applications of Microbial Ecology’s “Phylogenetic Beta Diversity” Framework

The PD measure of phylogenetic diversity interprets branch lengths cladistically to make inferences about feature diversity. PD calculations extend conventional species-level ecological indices to the features level. The “phylogenetic beta diversity” framework developed by microbial ecologists calculates PD-dissimilarities between community localities. Interpretation of these PD-dissimilarities at the feature level explains the framework’s success in producing ordinations revealing environmental gradients. An example gradients space using PD-dissimilarities illustrates how evolutionary features form unimodal response patterns to gradients. This features model supports new application of existing species-level methods that are robust to unimodal responses, plus novel applications relating to climate change, commercial products discovery, and community assembly.

The use of invertebrates to detect small-scale habitat heterogeneity and its application to restoration practices.

Recent conceptual and technological solutions to biodiversityassessment allow large numbers of invertebrate specimens to beprocessed rapidly and provide researchers and practitioners with a unique tool for characterizing habitats. One applicationof these advances is the ability to detect and monitor small-scale habitat heterogeneity and so provide a measure of ecosystem restoration. This case study presents a test of theefficacy of using invertebrates to assess and monitor ecologicalrestoration following bush regeneration. Eight contiguous habitatpatches within a suburb of northern Sydney, Australia, were selected to represent areas that had undergone different bushregeneration techniques. A nearby and relatively undisturbed area of bushland was also sampled. A total of 57 806 ground-active invertebrate specimens from 35 different orders were collected in pitfall traps. 1 246 ant (Formicidae) specimens were further sorted into 46 ant morphospecies from20 genera. Analyses of the three taxonomic data sets, includingtwo different data transformations, demonstrated that: (i) invertebrate communities successfully characterized different sites, providing a high degree of differentiation among sites;(ii) ordinations of the sites allowed visual assessment of theimpact of each management technique on the habitat relativeto undisturbed habitats; and (iii) characterization of sitescould be achieved using abundance classes or binary countsof ant morphospecies, representing potential cost and timesavings. The project duration was a total of three personweeks and cost less than US

The mean and variance of phylogenetic diversity under rarefaction

3,000 (1999 prices) to complete.Measurement of invertebrate assemblages will provide a toolfor both rapid assessment of management decisions and ameans by which to implement adaptive management and restoration.

Rarefaction and extrapolation of phylogenetic diversity

Phylogenetic diversity (PD) depends on sampling depth, which complicates the comparison of PD between samples of different depth. One approach to dealing with differing sample depth for a given diversity statistic is to rarefy, which means to take a random subset of a given size of the original sample. Exact analytical formulae for the mean and variance of species richness under rarefaction have existed for some time but no such solution exists for PD.We have derived exact formulae for the mean and variance of PD under rarefaction. We confirm that these formulae are correct by comparing exact solution mean and variance to that calculated by repeated random (Monte Carlo) subsampling of a dataset of stem counts of woody shrubs of Toohey Forest, Queensland, Australia. We also demonstrate the application of the method using two examples: identifying hotspots of mammalian diversity in Australasian ecoregions, and characterising the human vaginal microbiome.There is a very high degree of correspondence between the analytical and random subsampling methods for calculating mean and variance of PD under rarefaction, although the Monte Carlo method requires a large number of random draws to converge on the exact solution for the variance.Rarefaction of mammalian PD of ecoregions in Australasia to a common standard of 25 species reveals very different rank orderings of ecoregions, indicating quite different hotspots of diversity than those obtained for unrarefied PD. The application of these methods to the vaginal microbiome shows that a classical score used to quantify bacterial vaginosis is correlated with the shape of the rarefaction curve.The analytical formulae for the mean and variance of PD under rarefaction are both exact and more efficient than repeated subsampling. Rarefaction of PD allows for many applications where comparisons of samples of different depth is required.

Continental-scale assessment of risk to the Australian Odonata from climate change

Summary 1. Traditional species diversity measures do not make distinctions among species. Faith’s phylogenetic diversity (PD), which is defined as the sum of the branch lengths of a phylogenetic tree connecting all species, takes into account phylogenetic differences among species and has found many applications in various research fields. In this paper, we extend Faith’s PD to represent the total length of a phylogenetic tree from any fixed point on its main trunk. 2. Like species richness, Faith’s PD tends to be an increasing function o f sampling effort and thus tends to increase with sample completeness. We develop in this paper the ‘PD accumulation curve’ (an extension of the species accumulation curve) to depict how PD increases with sampling size and sample completeness. 3. To make fair comparisons of Faith’s PD among several assemblages based on sampling data from each assemblage, we derive both theoretical formulae and analytic estimators for seamless rarefaction (interpolation) and extrapolation (prediction). We develop a lower bound of the undetected PD for an incomplete sample to guide the extrapolation; the PD estimator for an extrapolated sample is generally reliable up to twice the size of the empirical sample. 4. We propose an integrated curve that smoothly links rarefaction and extrapolation to standardize samples on the basis of sample size or sample completeness. A bootstrap method is used to obtain the unconditional variances ofPD estimators and to construct the confidence interval of the expected PD for a fixed sample size or fixed degree of sample completeness. This facilitates comparison of multiple assemblages of both rarefied and extrapolated samples. 5. We illustrate our formulae and estimators using empirical data sets from Australian birds in two sites. We discuss the extension of our approach to the case of multiple incidence data and to incorporate species abundances.

MORPHOLOGICAL DISPERSION OF RHYTIDOPONERA ASSEMBLAGES: THE IMPORTANCE OF SPATIAL SCALE AND NULL MODEL

Climate change is expected to have substantial impacts on the composition of freshwater communities, and many species are threatened by the loss of climatically suitable habitat. In this study we identify Australian Odonata (dragonflies and damselflies) vulnerable to the effects of climate change on the basis of exposure, sensitivity and pressure to disperse in the future. We used an ensemble of species distribution models to predict the distribution of 270 (85%) species of Australian Odonata, continent-wide at the subcatchment scale, and for both current and future climates using two emissions scenarios each for 2055 and 2085. Exposure was scored according to the departure of temperature, precipitation and hydrology from current conditions. Sensitivity accounted for change in the area and suitability of projected climatic habitat, and pressure to disperse combined measurements of average habitat shifts and the loss experienced with lower dispersal rates. Streams and rivers important to future conservation efforts were identified based on the sensitivity-weighted sum of habitat suitability for the most vulnerable species. The overall extent of suitable habitat declined for 56–69% of the species modelled by 2085 depending on emissions scenario. The proportion of species at risk across all components (exposure, sensitivity, pressure to disperse) varied between 7 and 17% from 2055 to 2085 and a further 3–17% of species were also projected to be at high risk due to declines that did not require range shifts. If dispersal to Tasmania was limited, many south-eastern species are at significantly increased risk. Conservation efforts will need to focus on creating and preserving freshwater refugia as part of a broader conservation strategy that improves connectivity and promotes adaptive range shifts. The significant predicted shifts in suitable habitat could potentially exceed the dispersal capacity of Odonata and highlights the challenge faced by other freshwater species.

Systematic Conservation Planning for Groundwater Ecosystems Using Phylogenetic Diversity

A series of spatially nested assemblages of Rhytidoponera operational taxonomic units (OTUs) (Formicidae: Hymenoptera) from Sturt National Park, New South Wales, Australia, were examined for patterns of dispersion in multivariate morphological space. Morphological overdispersion within an assemblage, relative to a null model, is hypothesized to be a result of the structuring influence of interspecific competition. We compared up to 45 observed assemblages, from across multiple spatial scales, to two null models. Meta-analysis of the null model analyses indicated a general trend to morphological overdispersion, particularly so at restricted scales. Larger scale assemblages were overdispersed relative to only one of the two null models, which we tentatively interpret as being indicative of different competition-driven mechanisms operating at different spatial scales. We also demonstrate that the observed assemblages represent a larger number of species groups than expected by chance, and that this pattern of phylogenetic overdispersion is closely related to the observed morphological patterns.

Antifungal activity in thrips soldiers suggests a dual role for this caste

Aquifer ecosystems provide a range of important services including clean drinking water. These ecosystems, which are largely inaccessible to humans, comprise a distinct invertebrate fauna (stygofauna), which is characterized by narrow distributions, high levels of endemism and cryptic species. Although being under enormous anthropogenic pressure, aquifers have rarely been included in conservation planning because of the general lack of knowledge of species diversity and distribution. Here we use molecular sequence data and phylogenetic diversity as surrogates for stygofauna diversity in aquifers of New South Wales, Australia. We demonstrate how to incorporate these data as conservation features in the systematic conservation planning software Marxan. We designated each branch of the phylogenetic tree as a conservation feature, with the branch length as a surrogate for the number of distinct characters represented by each branch. Two molecular markers (nuclear 18S ribosomal DNA and mitochondrial cytochrome oxidase subunit I) were used to evaluate how marker variability and the resulting tree topology affected the site-selection process. We found that the sites containing the deepest phylogenetic branches were deemed the most irreplaceable by Marxan. By integrating phylogenetic data, we provide a method for including taxonomically undescribed groundwater fauna in systematic conservation planning.

Does time since introduction influence enemy release of an invasive weed

The social insect soldier is perhaps the most widely known caste, because it often exhibits spectacular weapons, such as highly enlarged jaws or reinforced appendages, which are used to defend the colony against enemies ranging in size from wasps to anteaters. We examined the function of the enlarged forelimbs of soldiers (both male and female) of the eusocial, gall-inhabiting insect Kladothrips intermedius, and discovered that they have little impact on their ability to repel the specialized invading thrips Koptothrips species. While the efficacy of the enlarged forelimb appears equivocal, we show that soldiers secrete strong antifungal compounds capable of controlling the specialized insect fungal pathogen, Cordyceps bassiana. Our data suggest that these thrips soldiers have evolved in response to selection by both macro- and micro-organisms. While it is unknown whether specialized fungal pathogens have been major selective agents in the evolution of the soldier caste in general, they were probably present when sociality first evolved and may have been the primordial enemies of social insects.

Plant phylogeny as a surrogate for turnover in beetle assemblages

Release from natural enemies is considered to potentially play an important role in the initial establishment and success of introduced plants. With time, the species richness of herbivores using non-native plants may increase [species-time relationship (STR)]. We investigated whether enemy release may be limited to the early stages of invasion. Substituting space for time, we sampled invertebrates and measured leaf damage on the invasive species Senecio madagascariensis Poir. at multiple sites, north and south of the introduction site. Invertebrate communities were collected from plants in the field, and reared from collected plant tissue. We also sampled invertebrates and damage on the native congener Senecio pinnatifolius var. pinnatifolius A. Rich. This species served as a control to account for environmental factors that may vary along the latitudinal gradient and as a comparison for evaluating the enemy release hypothesis (ERH). In contrast to predictions of the ERH, greater damage and herbivore abundances and richness were found on the introduced species S. madagascariensis than on the native S. pinnatifolius. Supporting the STR, total invertebrates (including herbivores) decreased in abundance, richness and Shannon diversity from the point of introduction to the invasion fronts of S. madagascariensis. Leaf damage showed the opposite trend, with highest damage levels at the invasion fronts. Reared herbivore loads (as opposed to external collections) were greater on the invader at the point of introduction than on sites further from this region. These results suggest there is a complex relationship between the invader and invertebrate community response over time. S. madagascariensis may be undergoing rapid changes at its invasion fronts in response to environmental and herbivore pressure.