Tom A. August

Statistics for citizen science: extracting signals of change from noisy ecological data

Summary 1. Policy-makers increasingly demand robust measures of biodiversity change over short time periods. Longterm monitoring schemes provide high-quality data, often on an annual basis, but are taxonomically and geographically restricted. By contrast, opportunistic biological records are relatively unstructured but vast in quantity. Recently, these data have been applied to increasingly elaborate science and policy questions, using a range of methods. At present, we lack a firm understanding of which methods, if any, are capable of delivering unbiased trend estimates on policy-relevant time-scales. 2. We identified a set of candidate methods that employ data filtering criteria and/or correction factors to deal with variation in recorder activity. We designed a computer simulation to compare the statistical properties of these methods under a suite of realistic data collection scenarios. We measured the Type I error rates of each method–scenario combination, as well as the power to detect genuine trends. 3. We found that simple methods produce biased trend estimates, and/or had low power. Most methods are robust to variation in sampling effort, but biases in spatial coverage, sampling effort per visit, and detectability, as well as turnover in community composition, all induced some methods to fail. No method was wholly unaffected by all forms of variation in recorder activity, although some performed well enough to be useful. 4. We warn against the use of simple methods. Sophisticated methods that model the data collection process offer the greatest potential to estimate timely trends, notably Frescalo and occupancy–detection models. 5. The potential of these methods and the value of opportunistic data would be further enhanced by assessing the validity of model assumptions and by capturing small amounts of information about sampling intensity at the point of data collection.

Declining resilience of ecosystem functions under biodiversity loss

The composition of species communities is changing rapidly through drivers such as habitat loss and climate change, with potentially serious consequences for the resilience of ecosystem functions on which humans depend. To assess such changes in resilience, we analyse trends in the frequency of species in Great Britain that provide key ecosystem functions—specifically decomposition, carbon sequestration, pollination, pest control and cultural values. For 4,424 species over four decades, there have been significant net declines among animal species that provide pollination, pest control and cultural values. Groups providing decomposition and carbon sequestration remain relatively stable, as fewer species are in decline and these are offset by large numbers of new arrivals into Great Britain. While there is general concern about degradation of a wide range of ecosystem functions, our results suggest actions should focus on particular functions for which there is evidence of substantial erosion of their resilience.

Alphacoronavirus detected in bats in the United Kingdom

This study presents the first record of coronavirus in British bats. Alphacoronavirus strains were detected in two of seven bat species, namely Myotis nattereri and M. daubentonii. Virus prevalence was particularly high in the previously unrecognized host M. nattereri, which can live in close proximity to humans.

Sympatric Woodland Myotis Bats Form Tight-Knit Social Groups with Exclusive Roost Home Ranges

Background The structuring of wild animal populations can influence population dynamics, disease spread, and information transfer. Social network analysis potentially offers insights into these processes but is rarely, if ever, used to investigate more than one species in a community. We therefore compared the social, temporal and spatial networks of sympatric Myotis bats (M. nattereri (Natterers bats) and M. daubentonii (Daubentons bats)), and asked: (1) are there long-lasting social associations within species? (2) do the ranges occupied by roosting social groups overlap within or between species? (3) are M. daubentonii bachelor colonies excluded from roosting in areas used by maternity groups? Results Using data on 490 ringed M. nattereri and 978 M. daubentonii from 379 colonies, we found that both species formed stable social groups encompassing multiple colonies. M. nattereri formed 11 mixed-sex social groups with few (4.3%) inter-group associations. Approximately half of all M. nattereri were associated with the same individuals when recaptured, with many associations being long-term (>100 days). In contrast, M. daubentonii were sexually segregated; only a quarter of pairs were associated at recapture after a few days, and inter-sex associations were not long-lasting. Social groups of M. nattereri and female M. daubentonii had small roost home ranges (mean 0.2 km2 in each case). Intra-specific overlap was low, but inter-specific overlap was high, suggesting territoriality within but not between species. M. daubentonii bachelor colonies did not appear to be excluded from roosting areas used by females. Conclusions Our data suggest marked species- and sex-specific patterns of disease and information transmission are likely between bats of the same genus despite sharing a common habitat. The clear partitioning of the woodland amongst social groups, and their apparent reliance on small patches of habitat for roosting, means that localised woodland management may be more important to bat conservation than previously recognised.

The priority species indicator: measuring the trends in threatened species in the UK

We describe the development of two complementary priority species indicators (PSIs) to help the UK to report progress towards Aichi target 12 on the status of known threatened species. Based on species identified as national conservation priorities, the indicators present average changes in (i) 213 species for which trends in relative abundance are available from structured monitoring schemes, and (ii) 179 species for which trends in frequency of occurrence were modelled from data sets of unstructured biological records. Both indicators show substantial declines in priority species since 1970, of 67% and 40%, respectively, although the rate of decline in the relative abundance-based PSI may have lessened over the last five years (2007–2012). We discuss the biases and weaknesses of the indicators at present, and put forward suggestions as how these may be addressed, including through the development of a third PSI.

The zoon r package for reproducible and shareable species distribution modelling

1. The rapid growth of species distribution modelling (SDM) as an ecological discipline has resulted in a large and diverse set of methods and software for constructing and evaluating SDMs. The disjointed nature of the current SDM research environment hinders evaluation of new methods, synthesis of current knowledge and the dissemination of new methods to SDM users. 2. The zoon r package aims to overcome these problems by providing a modular framework for constructing reproducible SDM workflows. zoon modules are interoperable snippets of r code, each carrying a SDM method that zoon combines into a single analysis object. 3. Rather than defining these modules, zoon draws modules from an open, version-controlled online repository. zoon makes it easy for SDM researchers to contribute modules to this repository, enabling others to rapidly deploy new methods in their own workflows or to compare alternative methods. 4. Each workflow object created by zoon is a rerunnable record of the data, code and results of an entire SDM analysis. This can then be easily shared, scrutinised, reproduced and extended by the whole SDM research community. 5. We explain how zoon works and demonstrate how it can be used to construct a completely reproducible SDM analyses, create and share a new module, and perform a methodological comparison study.

Extinction risk from climate change is reduced by microclimatic buffering

Protecting biodiversity against the impacts of climate change requires effective conservation strategies that safeguard species at risk of extinction1. Microrefugia allowed populations to survive adverse climatic conditions in the past2,3, but their potential to reduce extinction risk from anthropogenic warming is poorly understood3–5, hindering our capacity to develop robust in situ measures to adapt conservation to climate change6. Here, we show that microclimatic heterogeneity has strongly buffered species against regional extirpations linked to recent climate change. Using more than five million distribution records for 430 climate-threatened and range-declining species, population losses across England are found to be reduced in areas where topography generated greater variation in the microclimate. The buffering effect of topographic microclimates was strongest for those species adversely affected by warming and in areas that experienced the highest levels of warming: in such conditions, extirpation risk was reduced by 22% for plants and by 9% for insects. Our results indicate the critical role of topographic variation in creating microrefugia, and provide empirical evidence that microclimatic heterogeneity can substantially reduce extinction risk from climate change.Topographic variations result in microclimatic heterogeneity that can substantially reduce extinction risk from climate change, according to a study of 430 climate-threatened and range-declining species in England.