Showing papers by "Andy Purvis published in 2014"

Approaches to defining a planetary boundary for biodiversity

Abstract: The idea that there is an identifiable set of boundaries, beyond which anthropogenic change will put the Earth system outside a safe operating space for humanity, is attracting interest in the scientific community and gaining support in the environmental policy world. Rockstrom et al. (2009) identify nine such boundaries and highlight biodiversity loss as being the single boundary where current rates of extinction put the Earth system furthest outside the safe operating space. Here we review the evidence to support a boundary based on extinction rates and identify weaknesses with this metric and its bearing on humanity's needs. While changes to biodiversity are of undisputed importance, we show that both extinction rate and species richness are weak metrics for this purpose, and they do not scale well from local to regional or global levels. We develop alternative approaches to determine biodiversity loss boundaries and extend our analysis to consider large-scale responses in the Earth system that could affect its suitability for complex human societies which in turn are mediated by the biosphere. We suggest three facets of biodiversity on which a boundary could be based: the genetic library of life; functional type diversity; and biome condition and extent. For each of these we explore the science needed to indicate how it might be measured and how changes would affect human societies. In addition to these three facets, we show how biodiversity's role in supporting a safe operating space for humanity may lie primarily in its interactions with other boundaries, suggesting an immediate area of focus for scientists and policymakers.

A global model of the response of tropical and sub-tropical forest biodiversity to anthropogenic pressures

Abstract: Habitat loss and degradation, driven largely by agricultural expansion and intensification, present the greatest immediate threat to biodiversity. Tropical forests harbour among the highest levels of terrestrial species diversity and are likely to experience rapid land-use change in the coming decades. Synthetic analyses of observed responses of species are useful for quantifying how land use affects biodiversity and for predicting outcomes under land-use scenarios. Previous applications of this approach have typically focused on individual taxonomic groups, analysing the average response of the whole community to changes in land use. Here, we incorporate quantitative remotely sensed data about habitats in, to our knowledge, the first worldwide synthetic analysis of how individual species in four major taxonomic groups—invertebrates, ‘herptiles’ (reptiles and amphibians), mammals and birds—respond to multiple human pressures in tropical and sub-tropical forests. We show significant independent impacts of land use, human vegetation offtake, forest cover and human population density on both occurrence and abundance of species, highlighting the value of analysing multiple explanatory variables simultaneously. Responses differ among the four groups considered, and—within birds and mammals—between habitat specialists and habitat generalists and between narrow-ranged and wide-ranged species.

The PREDICTS database: a global database of how local terrestrial biodiversity responds to human impacts

Abstract: Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species Existing global databases of species’ threat status or population time series are dominated by charismatic species The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project – and avert – future declines We describe and assess a new database of more than 16 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups – including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems – wwwpredictsorguk) We make site-level summary data available alongside this article The full database will be publicly available in 2015

MODISTools – downloading and processing MODIS remotely sensed data in R

Abstract: Remotely sensed data – available at medium to high resolution across global spatial and temporal scales – are a valuable resource for ecologists. In particular, products from NASA's MODerate-resolution Imaging Spectroradiometer (MODIS), providing twice-daily global coverage, have been widely used for ecological applications. We present MODISTools, an R package designed to improve the accessing, downloading, and processing of remotely sensed MODIS data. MODISTools automates the process of data downloading and processing from any number of locations, time periods, and MODIS products. This automation reduces the risk of human error, and the researcher effort required compared to manual per-location downloads. The package will be particularly useful for ecological studies that include multiple sites, such as meta-analyses, observation networks, and globally distributed experiments. We give examples of the simple, reproducible workflow that MODISTools provides and of the checks that are carried out in the process. The end product is in a format that is amenable to statistical modeling. We analyzed the relationship between species richness across multiple higher taxa observed at 526 sites in temperate forests and vegetation indices, measures of aboveground net primary productivity. We downloaded MODIS derived vegetation index time series for each location where the species richness had been sampled, and summarized the data into three measures: maximum time-series value, temporal mean, and temporal variability. On average, species richness covaried positively with our vegetation index measures. Different higher taxa show different positive relationships with vegetation indices. Models had high R2 values, suggesting higher taxon identity and a gradient of vegetation index together explain most of the variation in species richness in our data. MODISTools can be used on Windows, Mac, and Linux platforms, and is available from CRAN and GitHub (https://github.com/seantuck12/MODISTools).

A phylogenetically-informed trait-based analysis of range change in the vascular plant flora of Britain

Abstract: Species distributions are changing, and knowing whether certain character traits predispose species to decline or increase during times of environmental change can shed light on the main drivers of distribution change. Here we conduct a trait-based analysis of range change in the flora of Britain since the 1930s using some of the best plant distribution and trait data available in Europe. We use phylogenetically-informed models based on a recently published, dated, species level plant phylogeny. Traits associated with habitat specialism and competitive ability were related to range change, with more competitive habitat generalists faring better than habitat specialists. We attribute this result to the greater ability of generalists to adapt to environmental perturbation, but also to the negative impacts of agricultural intensification on the flora of Britain, in particular the loss of open, dry habitats. We discovered spatial variation in the main drivers of plant range change and find support for previous evidence that agricultural intensification has been a major driver of distribution change in the flora of Britain over the past 70 years, particularly in southern England.

Metrics and Models of Community Phylogenetics

Abstract: Community phylogenetics combines ideas from community ecology and evolutionary biology, using species phylogeny to explore the processes underlying ecological community assembly. Here, we describe the development of the field’s comparative methods and their roots in conservation biology, biodiversity quantification, and macroevolution. Next, we review the multitude of community phylogenetic structure metrics and place each into one of four classes: shape, evenness, dispersion, and dissimilarity. Shape metrics examine the structure of an assemblage phylogeny, while evenness metrics incorporate species abundances. Dispersion metrics examine assemblages given a phylogeny of species that could occupy those assemblages (the source pool), while dissimilarity metrics compare phylogenetic structure between assemblages. We then examine how metrics perform in simulated communities that vary in their phylogenetic structure. We provide an example of model-based approaches and argue that they are a promising area of future research in community phylogenetics. Code to reproduce all these analyses is available in the Online Practical Material (http://www.mpcm-evolution.com). We conclude by discussing future research directions for the field as a whole.

Temporal validation plots: quantifying how well correlative species distribution models predict species' range changes over time

Abstract: Summary The use of data documenting how species' distributions have changed over time is crucial for testing how well correlative species distribution models (SDMs) predict species' range changes. So far, however, little attention has been given to developing a reliable methodological framework for using such data. We develop a new tool – the temporal validation (TV) plot – specifically aimed at making use of species' distribution records at two times for a comprehensive assessment of the prediction accuracy of SDMs over time. We extend existing presence–absence calibration plots to make use of distribution records from two time periods. TV plots visualize the agreement between change in modelled probabilities of presence and the probability of observing sites gained or lost between time periods. We then present three measures of prediction accuracy that can be easily calculated from TV plots. We present our methodological framework using a virtual species in a simplified landscape and then provide a real-world case study using distribution records for two species of breeding birds from two time periods of intensive recording effort across Great Britain. Together with existing approaches, TV plots and their associated measures offer a simple tool for testing how well SDMs model species' observed range changes – perhaps the best way available to assess their ability to predict likely future changes.

Can trait-based analyses of changes in species distribution be transferred to new geographic areas?

Abstract: Aim Anthropogenic environmental change is having a major impact on biodiversity. By identifying traits that correlate with changes in species range, comparative studies can shed light on the mechanisms driving this change; but such studies will be more useful for conservation if they have true predictive power, i.e. if their trait-based models can be transferred to new regions. We aim to examine the ability of trait-based models to predict changes in plant distribution across seven geographic regions that varied in terms of land cover and species composition. Location Britain and Flanders (Belgium). Methods We estimated distribution change for more than 1000 species for over 70 years of data (1930s to 2004), using data from published plant atlases. We identified regional trait-based models of plant distribution change. Traits included morphological characteristics, Ellenberg values and distribution-based traits. The trait models were then used to predict change in all other regions, with the level of linear correlation between predicted and observed changes in range used as a measure of transferability. We then related transferability to land cover and species similarity between regions. Results We found that trait correlates of range change varied regionally, highlighting the regional variation in the drivers of range change in plants. These trait models also varied in the amount of variation explained, with r 2 values ranging from 0.05 to 0.17. A key cross-regional difference was the variation in the relationship between soil nutrient association (Ellenberg N) and distribution change, which was strongly positive in Flanders and southern England but significantly negative in northern Scotland. We found that transferability between regions was significantly correlated with the level of similarity in land cover. Main conclusions We conclude that trait-based models can predict broad-scale changes in species distributions in regions that share similar land-cover composition; however, predictions between regions with differing land-cover cover tend to be poor.

Modelling ecological communities as if they were DNA

Abstract: Ecologists are interested in understanding and predicting how ecological communities change through time. While it might seem natural to measure this through changes in species' abundances, computational limitations mean transitions between community types are often modelled instead. We present an approach inspired by DNA substitution models that attempts to estimate historic interactions between species, and thus estimate turnover rates in ecological communities. Although our simulations show that the method has some limitations, our application to butterfly community data shows the method can detect signal in real data. Open source C++ code implementing the method is available at this http URL.