Methods Issue 11.10 is now online!

We have a larger issue of 17 articles this month, featuring the ethics of wild animal research, an eco-acoustic monitoring network, a programmable optomotor and much more.

Senior Editor Rob Freckleton has selected six featured articles – find out about them below.

We also have three Applications, one Practical Tools and seven articles that are freely available to everyone – no subscription required!

Featured Articles

The welfare and ethics of research involving wild animals Wild animals are used in both in situ and ex situ research, but guidelines for best practice are not always clearly linked to animal welfare. In this review article, Soulsbury et al. discuss the ethics of using wild animals in scientific research, highlighting issues associated with capture, housing and handling of both vertebrates and invertebrates. They reveal where data is lacking and make recommendations for researchers to implement.

Fig 2 from Sethi et al.

Application: SAFE Acoustics open access Automated monitoring approaches offer large‐scale insights into how ecosystems respond to human pressures. Here, Sethi et al. present the complete implementation of an autonomous acoustic monitoring network deployed in the tropical rainforests of Borneo, providing the open‐source code and design of monitoring devices used to deliver real‐time analyses of the eco‐acoustic data.

ntbox Biodiversity studies rely heavily on estimates of species distributions obtained through ecological niche modelling. Here, Osorio-Olvera et al. describe NicheToolBox (ntbox), an R package that allows users to conduct all processing steps involved in ecological niche modelling. The method is explained in detail and tested by modelling the threatened feline species Leopardus wiedii.

geoorigins open access Biologists often seek to geographically provenance organisms using their traits. Here, Hulme-Beaman et al. present a new spatial provenancing and trait boundary identification methodology, based on correlations between geographic and trait distances that require no a priori group assumptions. This is tested on three datasets (rat and vole dentition and birdsong data), but can be applied to a variety of data types.

Schrödinger’s phenotypes open access The digitisation of museum specimens is allowing us to collectively build large‐scale morphological datasets, but this approach will only be useful if the limits are well‐known. To establish the limits, Borges et al. used two‐dimensional images of plant specimens to test the precision and accuracy of image‐based data and analyses, finding that trait measurements made from images are as precise as those obtained directly from specimens, but as traits diminish in size, the accuracy decreases.

Practical tools: Measuring visual capability: open access Vision is the dominant sense for many animals, and understanding the visual abilities of a species can be key for investigating its behaviour and evolution. However, many techniques for quantifying visual capability are expensive, invasive and/or require specialised equipment. Here, Caves et al. provide instructions for building a low-cost, programmable optomotor apparatus using 3D‐printed materials. They also discuss experimental design considerations for optomotor assays, including a guide that calculates the dimensions of stimuli of varying spatial frequency.


We have three Applications articles in this issue, all free to access. One of them has been covered in our Featured Articles above, so here are the other two:

cxr free access Recent developments in modern coexistence theory (MCT) have advanced our understanding of how species interactions, among themselves and with the environment, influence community dynamics. However, application of MCT to empirical cases is still challenging, which precludes its adoption by ecologists and evolutionary biologists. Here, García‐Callejas et al. present cxr, toolbox for modelling species coexistence in R. To illustrate its functionality and versatility, they provide a complete set of population dynamic models and a dataset from a highly diverse grassland community.

pycoalescence and rcoalescence free access Spatially explicit neutral models represent an important tool in ecology for understanding the processes of biodiversity generation and predicting outcomes at large scales. Here, Thompson et al. present software packages pycoalescence (Python) and rcoalescence (R) that make spatially explicit neutral simulations straightforward and efficient. They also give examples for their application, with a focus on two scenarios of ecological and evolutionary interest—a landscape with habitat fragmentation, and an archipelago of islands.

Other Open Access Articles

Attacker identification from DNA traces Rößler et al. provide a standardised approach for species‐level predator identification by sequencing the mitochondrial DNA left in bite marks on clay models. The method, tested on models of the European fire salamander, opens up new possibilities far beyond the standard use of clay models to date, including food web studies at unprecedented detail, invasive species monitoring as well as biodiversity inventories.

The Cod on the Cover

This month’s cover portraits an Atlantic cod (Gadus morhua) navigating over the seabed in the Tvedestrand fjord, southern Norway. The fish was part of an open access study by Villegas Ríos et al. which developed a new method to determine individual fate in wild fish from the patterns of movements and detections obtained from acoustic telemetry data. The method is able to detect when a fish is harvested by fishers or predated by other animals, but it also identifies fish moving outside the study area (i.e. dispersing), natural mortality patterns and individuals that survive throughout the study period. By providing information at the individual‐level and directly from the wild, the method provides a valuable means of expanding the range of questions that can be answered from aquatic acoustic telemetry data.

Image credit: ©Øystein Paulsen

To keep up to date with Methods newest content, have a look at our Accepted Articles and Early View articles, which will be showing up in issues later this year.