The mean and variance of phylogenetic diversity under rarefaction

Phylogenetic diversity (PD) depends on sampling intensity, 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 show 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.Comment: Final version to be published in Methods in Ecology and Evolutio

zetadiv:An R package for computing compositional change across multiple sites, assemblages or cases

AbstractSpatial variation in compositional diversity, or species turnover, is necessary for capturing the components of heterogeneity that constitute biodiversity. However, no incidence-based metric of pairwise species turnover can calculate all components of diversity partitioning. Zeta (ζ) diversity, the mean number of species shared by any given number of sites or assemblages, captures all diversity components produced by assemblage partitioning. zetadiv is an R package for analysing and measuring compositional change for occurrence data using zeta diversity. Four types of analyses are performed on bird composition data in Australia: (i) decline in zeta diversity; (ii) distance decay; (iii) multi-site generalised dissimilarity modelling; and (iv) hierarchical scaling. Some analyses, such as the zeta decline, are specific to zeta diversity, whereas others, such as distance decay, are commonly applied to beta diversity, and have been adapted using zeta diversity to differentiate the contribution of common and rare species to compositional change.HighlightsAn R package to analyse compositional change using zeta diversity is presented.Zeta diversity is the mean number of species shared by any number of assemblagesZeta diversity captures all diversity components produced by assemblage partitioningAnalyses relate zeta diversity to space, environment and spatial scaleAnalyses differentiate the contribution of rare and common species to biodiversity</jats:sec

Continental-Scale Assessment of Risk to the Australian Odonata from Climate Change

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

A separate creation : diversity, distinctiveness and conservation of Australian wildlife

Australia is biologically diverse, with around 150 000 described species, representing perhaps 25% of the total number present. However, this biota is more notable for its endemism than its richness (e.g. 94% of Australian frog species are found nowhere else). Australia is distinctive, not only in terms of endemism, but also in terms of evolutionary adaptations (e.g. large hopping mammals) and ecological processes (e.g. nutrient cycling by fire). Distinctiveness is attributed to three principal factors: (1) a long period of geographic isolation; (2) the preponderance of ancient soils low in key nutrients; and (3) an increasingly arid and inherently unpredictable climate. Australia is also unfortunately distinctive in the scale of biodiversity loss since European settlement with 98 species and subspecies listed as extinct, and a further 1700 threatened with extinction. Both for historical extinctions and currently threatened species, habitat loss and introduced species are the key threats, while climate change is the emerging and possibly most significant threat of the twenty-first century. In the face of these perils, Australia’s distinctive wildlife needs special attention because it makes such a large contribution to the biodiversity and cumulative evolutionary history of the planet.23 page(s

Australian family ties : does a lack of relatives help invasive plants escape natural enemies?

Invasive plants may initially be released from natural enemies when introduced to new regions, but once established, natural enemies may accumulate. How closely related invasive species are to species in the native recipient community may drive patterns of herbivore and pathogen damage and therefore, may be important in understanding the success of some invasions. We compared herbivore and pathogen damage across a group of invasive species occurring in natural environments on the east coast of Australia. We examined whether the level of damage experienced by the invasive species was associated with the degree of phylogenetic relatedness between these plants and the native plants within the region. We found that phylogenetic distance to the nearest native relative was a good predictor of herbivore and pathogen damage on the invasive plants, explaining nearly 37 % of the variance in leaf damage. Total leaf damage and the variety of damage types declined with increasing phylogenetic distance to the nearest native relative. In addition, as the phylogenetic distance to the nearest native relative increased, invasive species were colonized by fewer functional guilds and the herbivore assemblage was increasingly dominated by generalist species. These results suggest that invasive species that are only distantly related to those in the native invaded community may be released from specialist natural enemies. Our results indicate that the phylogenetic relatedness of invasive plants to species in native communities is a significant predictor of the rate of colonization by the herbivore and pathogen community, and thus a useful tool to assess invasion potential.12 page(s

Does time since introduction influence enemy release of an invasive weed?

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.14 page(s

Comparison of invertebrate herbivores on native and non-native Senecio species : implications for the enemy release hypothesis

The enemy release hypothesis posits that non-native plant species may gain a competitive advantage over their native counterparts because they are liberated from co-evolved natural enemies from their native area. The phylogenetic relationship between a non-native plant and the native community may be important for understanding the success of some non-native plants, because host switching by insect herbivores is more likely to occur between closely related species. We tested the enemy release hypothesis by comparing leaf damage and herbivorous insect assemblages on the invasive species Senecio madagascariensis Poir. to that on nine congeneric species, of which five are native to the study area, and four are non-native but considered non-invasive. Non-native species had less leaf damage than natives overall, but we found no significant differences in the abundance, richness and Shannon diversity of herbivores between native and non-native Senecio L. species. The herbivore assemblage and percentage abundance of herbivore guilds differed among all Senecio species, but patterns were not related to whether the species was native or not. Species-level differences indicate that S. madagascariensis may have a greater proportion of generalist insect damage (represented by phytophagous leaf chewers) than the other Senecio species. Within a plant genus, escape from natural enemies may not be a sufficient explanation for why some non-native species become more invasive than others.12 page(s

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

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