Beware the F-test (or, how to compare variances)

This is the author accepted manuscript. The final version is available from Elsevier Masson via the DOI in this record.Biologists commonly compare variances among samples, to test whether underlying populations have equal spread. However, despite warnings from statisticians, incorrect testing is rife. Here we show that one of the most commonly employed of these tests, the F-test, is extremely sensitive to deviations from Normality. The F-test suffers greatly elevated false-positive errors when the underlying distributions are heavy-tailed, a distribution feature which is very hard to detect using standard Normality tests. We highlight and assess a selection of parametric, jackknife and permutation tests, consider their performance in terms of false positives, and power to detect signal when it exists, then show correct methods to compare measures of variation among samples. Based on these assessments, we recommend using Levene’s Test, Box-Anderson Test, Jackknifing or Permutation Tests to compare variances when Normality is in doubt. Levene’s and Box-Anderson tests are the most powerful at small sample sizes, but the Box-Anderson test may not control Type I error for extremely heavy-tailed distributions. As noted previously, do not use F-tests to compare variances.DHod is supported by NERC standard grant NE/L007770/1 and by NERC International Opportunities Fund NE/N006798/1 and DHos by the Leverhulme Trust (RF-2015-001)

Smartphones in ecology and evolution: a guide for the app-rehensive

This is the final version. Available on open access from Wiley via the DOI in this recordSmartphones and their apps (application software) are now used by millions of people worldwide and represent a powerful combination of sensors, information transfer, and computing power that deserves better exploitation by ecological and evolutionary researchers. We outline the development process for research apps, provide contrasting case studies for two new research apps, and scan the research horizon to suggest how apps can contribute to the rapid collection, interpretation, and dissemination of data in ecology and evolutionary biology. We emphasize that the usefulness of an app relies heavily on the development process, recommend that app developers are engaged with the process at the earliest possible stage, and commend efforts to create open-source software scaffolds on which customized apps can be built by nonexperts. We conclude that smartphones and their apps could replace many traditional handheld sensors, calculators, and data storage devices in ecological and evolutionary research. We identify their potential use in the high-throughput collection, analysis, and storage of complex ecological information.Marie Curie Intra‐European FellowshipAcademy of FinlandUniversity of HelsinkiFishmongers' CompanyEuropean Social Fun

Take only photographs, leave only footprints: novel applications of non-invasive survey methods for rapid detection of small, arboreal animals

This is the final version of the article. Available from the publisher via the DOI in this record.The development of appropriate wildlife survey techniques is essential to promote effective and efficient monitoring of species of conservation concern. Here, we demonstrate the utility of two rapid-assessment, non-invasive methods to detect the presence of elusive, small, arboreal animals. We use the hazel dormouse, Muscardinus avellanarius, a rodent of conservation concern, as our focal species. Prevailing hazel dormouse survey methods are prolonged (often taking months to years to detect dormice), dependent on season and habitat, and/or have low detection rates. Alternatives would be of great use to ecologists who undertake dormouse surveys, especially those assessing the need for mitigation measures, as legally required for building development projects. Camera traps and footprint tracking are well-established tools for monitoring elusive large terrestrial mammals, but are rarely used for small species such as rodents, or in arboreal habitats. In trials of these adapted methods, hazel dormice visited bait stations and were successfully detected by both camera traps and tracking equipment at each of two woodland study sites, within days to weeks of installation. Camera trap images and footprints were of adequate quality to allow discrimination between two sympatric small mammal species (hazel dormouse and wood mouse, Apodemus sylvaticus). We discuss the relative merits of these methods with respect to research aims, funds, time available and habitat.The work in this study was undertaken as part of a self-funded PhD and the authors have no support or funding to report for the work outlined in this manuscript

Social evolution of toxic metal bioremediation in Pseudomonas aeruginosa

This is the final version. Available on open access from the Royal Society via the DOI in this recordThere is another ORE record for this publication: http://hdl.handle.net/10871/16448Bacteria are often iron-limited, and hence produce extracellular iron-scavenging siderophores. A crucial feature of siderophore production is that it can be an altruistic behaviour (individually costly but benefitting neighbouring cells), thus siderophore producers can be invaded by non-producing social 'cheats'. Recent studies have shown that siderophores can also bind other heavy metals (such as Cu and Zn), but in this case siderophore chelation actually reduces metal uptake by bacteria. These complexes reduce heavy metal toxicity, hence siderophore production may contribute to toxic metal bioremediation. Here, we show that siderophore production in the context of bioremediation is also an altruistic trait and can be exploited by cheating phenotypes in the opportunistic pathogen Pseudomonas aeruginosa. Specifically, we show that in toxic copper concentrations (i) siderophore non-producers evolve de novo and reach high frequencies, and (ii) producing strains are fitter than isogenic non-producing strains in monoculture, and vice versa in co-culture. Moreover, we show that the evolutionary effect copper has on reducing siderophore production is greater than the reduction observed under iron-limited conditions. We discuss the relevance of these results to the evolution of siderophore production in natural communities and heavy metal bioremediation. © 2014 The Authors Published by the Royal Society. All rights reserved.AXANatural Environment Research Council (NERC)University of Exete

Perils and pitfalls of mixed-effects regression models in biology

This is the final version. Available on open access from PeerJ via the DOI in this recordData Availability: The following information was supplied regarding data availability: The R code used to conduct all simulations in the paper is available in the Supplemental Files.Biological systems, at all scales of organisation from nucleic acids to ecosystems, are inherently complex and variable. Biologists therefore use statistical analyses to detect signal among this systemic noise. Statistical models infer trends, find functional relationships and detect differences that exist among groups or are caused by experimental manipulations. They also use statistical relationships to help predict uncertain futures. All branches of the biological sciences now embrace the possibilities of mixed-effects modelling and its flexible toolkit for partitioning noise and signal. The mixed-effects model is not, however, a panacea for poor experimental design, and should be used with caution when inferring or deducing the importance of both fixed and random effects. Here we describe a selection of the perils and pitfalls that are widespread in the biological literature, but can be avoided by careful reflection, modelling and model-checking. We focus on situations where incautious modelling risks exposure to these pitfalls and the drawing of incorrect conclusions. Our stance is that statements of significance, information content or credibility all have their place in biological research, as long as these statements are cautious and well-informed by checks on the validity of assumptions. Our intention is to reveal potential perils and pitfalls in mixed model estimation so that researchers can use these powerful approaches with greater awareness and confidence. Our examples are ecological, but translate easily to all branches of biology.University of Exete

Reconciling actual and perceived rates of predation by domestic cats

This is the final version. Available on open access from Wiley via the DOI in this recordThe predation of wildlife by domestic cats (Felis catus) is a complex problem: Cats are popular companion animals in modern society but are also acknowledged predators of birds, herpetofauna, invertebrates, and small mammals. A comprehensive understanding of this conservation issue demands an understanding of both the ecological consequence of owning a domestic cat and the attitudes of cat owners. Here, we determine whether cat owners are aware of the predatory behavior of their cats, using data collected from 86 cats in two UK villages. We examine whether the amount of prey their cat returns influences the attitudes of 45 cat owners toward the broader issue of domestic cat predation. We also contribute to the wider understanding of physiological, spatial, and behavioral drivers of prey returns among cats. We find an association between actual prey returns and owner predictions at the coarse scale of predatory/nonpredatory behavior, but no correlation between the observed and predicted prey-return rates among predatory cats. Cat owners generally disagreed with the statement that cats are harmful to wildlife, and disfavored all mitigation options apart from neutering. These attitudes were uncorrelated with the predatory behavior of their cats. Cat owners failed to perceive the magnitude of their cats' impacts on wildlife and were not influenced by ecological information. Management options for the mitigation of cat predation appear unlikely to work if they focus on "predation awareness" campaigns or restrictions of cat freedom. We consider both the ecological consequence of owning a domestic cat and the attitudes of cat owners. Our findings suggest cat owners fail to perceive the magnitude of their cats' impacts on wildlife, with no correlation between the observed and predicted prey return rates among predatory cats. On the basis of opinions of cat owners in this study, management options for the mitigation of cat predation appear unlikely to work if they focus on "predation awareness" campaigns, or restrictions of cat freedom.International Fund for Animal WelfareUniversity of ExeterEuropean Social FundNatural Environment Research Council (NERC

Anthropogenic and ecological drivers of amphibian disease (ranavirosis)

This is the final version. Available on open access from Public Library of Science via the DOI in this recordData Availability: The data analysed in this manuscript has been deposited in Dryad (doi:http://dx.doi.org/10.5061/dryad.66k59). Third party data was obtained from Froglife and are therefore available through the charity Froglife (Registered Charity No. 1093372 in England and Wales). Please submit queries for data to [email protected] and asking for access to the data for research purposes. Further contact details can also be found on their website http://www.froglife.org/contact-us/.Ranaviruses are causing mass amphibian die-offs in North America, Europe and Asia, and have been implicated in the decline of common frog (Rana temporaria) populations in the UK. Despite this, we have very little understanding of the environmental drivers of disease occurrence and prevalence. Using a long term (1992-2000) dataset of public reports of amphibian mortalities, we assess a set of potential predictors of the occurrence and prevalence of Ranavirus-consistent common frog mortality events in Britain. We reveal the influence of biotic and abiotic drivers of this disease, with many of these abiotic characteristics being anthropogenic. Whilst controlling for the geographic distribution of mortality events, disease prevalence increases with increasing frog population density, presence of fish and wild newts, increasing pond depth and the use of garden chemicals. The presence of an alternative host reduces prevalence, potentially indicating a dilution effect. Ranavirosis occurrence is associated with the presence of toads, an urban setting and the use of fish care products, providing insight into the causes of emergence of disease. Links between occurrence, prevalence, pond characteristics and garden management practices provides useful management implications for reducing the impacts of Ranavirus in the wild

Habitat preferences of hazel dormice Muscardinus avellanarius and the effects of tree-felling on their movement

This is the final version of the article. Available from the publisher via the DOI in this record.Modern management of multifunctional woodlands must address many and various demands, including for recreation, timber production and the conservation of biodiversity. The responses of individuals and populations of protected species to woodland management and habitat change are often not well understood. Using radio-tracking and LiDAR, we investigated the short-term habitat preferences of hazel dormice Muscardinus avellanarius, and their ranging and resting behaviours before and after small-scale tree felling, following a before-after control-impact design. Mean dormouse home range size was 0.51 Ha (±0.07 SE, n = 16) and did not vary between sexes or among sites, though heavier animals had smaller ranges. Dormice preferred mid-height woodland habitat (5–10 m tall), with low proportions of high forest (over 10 m tall), for both ranging and resting sites. Ranging habitats were often located on woodland edges and relatively dense vegetation. Dormice preferentially used yew, rowan and hazel during ranging. There was no difference in the distances travelled by dormice before and after felling, but dormice in areas where trees had been felled showed less evidence of a shift in ranging area than those in unfelled areas. Although the limited response of dormice to tree felling activities has the potential to be associated with increased mortality and/or limited dispersal of individual dormice, the requirements of dormice for mid-successional and edge habitats that arise after tree removal means that a dynamic optimum of felling and regeneration is essential for conservation of dormouse populations.CEDG’s work was supported by a PhD studentship funded by The Forestry Commission and the Natural Environment Research Council

Distribution and habitat use of a cryptic small cetacean, the Burmeister's porpoise, monitored from a small-scale fishery platform

This is the final version. Available from Frontiers Media via the DOI in this record. There is widespread evidence that small-scale fisheries (SSF) bycatch threatens many populations of small cetaceans, yet conservation efforts are often limited by a lack of basic knowledge regarding their abundance, distribution, and habitat use. Here, we used passive acoustic monitoring from an SSF platform-of-opportunity to better characterize the distribution and habitat use of small cetaceans in northern Peru, focussing on the little-known Burmeister's porpoise Phocoena spinipinnis. From 2009 to 2012, acoustic click detectors (C-PODs) were attached to fishing nets for the duration of 116 fishing sets (30 fishing trips). Dolphins (unspecified delphinids) and porpoises were recorded around 71 and 22% of fishing sets, respectively. The probability of occurrence and buzzing behavior (a proxy for foraging), and time spent, were linked to both static and dynamic environmental variables to examine the drivers of habitat use. Dolphin activity was spread evenly throughout the fishing area and was not linked to any habitat variables. In contrast, porpoises were detected in neritic waters, and habitat models performed well, identifying preferences for shallow (< 200 m depth) and cooler (17-18°C) waters, close (< 50 km) to shore. The high bycatch rate of small cetaceans in Peruvian SSF gave us the unique opportunity to investigate the link between bycatch and cetacean activity around vessels. We found a positive relationship between the likelihood of a bycatch event and acoustic presence for both dolphins and porpoises, however as we did not know the timing of entanglement, we could not link vocalization rates to mortality events. Nonetheless, as small cetaceans (particularly dolphins) frequently encounter fishing boats, the likelihood of entanglements may be reduced through effective efforts to alert animals to the presence of the net, either acoustically (using acoustic alarms) or visually. This study demonstrates that passive acoustic monitoring from a fisheries platform can provide insights into the distribution and habitat use of small cetaceans at relatively low cost, and is likely to be suitable in regions with low monitoring effort and high fishing pressure.Natural Environment Research CouncilEuropean UnionDarwin Initiativ