The latest issue of Methods in Ecology and Evolution is now online!
Senior Editor Aaron Ellison has selected six Featured Articles this month. You can find out about all of them below. We also have eight Applications articles and seven Practical Tools articles in the November issue that are freely available to everyone – no subscription required!
Practical recommendations for determining plant water sources Stable isotope ratios of water have long been used to study where plants take up water from. However, more detailed interrogations of the subsurface and plant domains have revealed under-considered transport and isotopic-fractionation phenomena. In this review, von Freyberg et al. provide several practical recommendations, based on both traditional and recent methods, for characterising plant water sources through using δ18O and δ2H.
Scaling methods in ecological modelling *Open Access* As scaling cannot be avoided in modelling, it should be carefully addressed, and resolved as much as possible. In this paper, Fritsch et al. give an overview of scaling approaches in ecological modelling, proposing to classify them into pre‐model scaling, in‐model scaling and post‐model scaling depending on the timing of the scaling relative to the main modelling process. They show general approaches, examples and potential application problems for each category.
Translating study instruments in cross-cultural research *Free Access* Study instruments used in cross‐cultural research need to maintain equivalency in order to ensure that the results and conclusions are not affected. Translation is a crucial part of research design, so a carefully planned methodological approach needs to be taken to adapt existing tools. Here, Cheung et al. present a concise and easy‐to‐use procedure for researchers in conservation and ecology to translate study instruments. As a demonstration, they adapted the ‘connectedness to nature’ scale into Chinese.
Analysis of intra- and interspecific trait evolution *Free Access* Evolutionary forces affect the distribution of phenotypes both within and among species, but at the macro‐evolutionary scale, the evolution of intraspecific variance is rarely considered. Here, Gaboriau et al. present the bite package, an R and BEAST 2 implementation that extends the JIVE (Joint inter‐ and Intraspecific Variance Evolution) model aimed at the analysis of continuous trait evolution at both inter‐ and intraspecific level. They introduce new frameworks within comparative phylogenetics that explicitly model intraspecific variance.
colorist *Free Access* Maps are essential tools for communicating information about wildlife distributions in space and time. Here, Schuetz et al. present colorist, an R package that facilitates visualisation of animal distributions in space and time using raster inputs. In addition to enabling display of sequential change in distributions through the use of small multiples, colorist provides functions for extracting several features of interest from a sequence of distributions, and for visualising those features within a hue–chroma–luminance colour space.
Integrating airborne remote sensing and field campaigns *Open Access* In recent years, the availability of airborne imaging spectroscopy data has expanded dramatically. To assess their utility for Earth systems research, imaging spectroscopy data acquisitions require integration with large, coincident ground‐based datasets collected by experts. Here, Chadwick et al. provide a framework for integrating airborne and field campaigns to obtain high‐quality data for foliar trait prediction, and document an archive of coincident physical samples collected to support a systems approach to ecological research in the critical zone.
Applications and Practical Tools
We have eight Applications articles and seven Practical Tools article in this month’s issue. Four of them have been covered in our Featured Articles above, so let’s dive into the other 11.
HaplowebMaker and CoMa *Free Access* Haplotype webs and conspecificity matrices have recently been proposed as graphical methods for species delimitation. However, performing such analyses by hand can be error‐prone and time‐consuming, and no program is currently available to generate these graphs automatically. Here, Spöri & Flot present HaplowebMaker and CoMa, two open source online tools that fill this gap.
Unsupervised detection of ancestry tracks *Free Access* The identification of ancestry tracks is a powerful tool to assist the inference of evolutionary events in the genomes of animals and plants. However, algorithms for ancestry track detection typically require labelled reference population data. Here, Utsunomiya et al. combine heuristics with K‐means clustering to deploy a method that can detect ancestry tracks without the provision of lineage labels for reference population data. The resulting algorithm uses phased genotypes to infer individual ancestry proportions and local ancestry.
Phylogenetic species‐distribution modelling *Free Access* Most current applications of model‐based methods in ecological studies do not include phylogenies, despite the well‐known importance of phylogenetic relationships in shaping species distributions and community composition. To fill this gap, Li et al. present the R package phyr, which implements a suite of metrics, comparative methods and mixed models that use phylogenies to understand and predict community composition and other ecological and evolutionary phenomena.
Extrapolation assessment tools for density surface models *Open Access* Ecologists faced with limited sample sizes and shoestring budgets often resort to extrapolating predictive models beyond the range of their data to support management actions. Despite the perils associated with extrapolation, little guidance exists on the best way to identify it when it occurs, leaving users questioning how much credence they should place in model outputs. To address this, Bouchet et al. present dsmextra, a new R package for measuring, summarising and visualising extrapolation in multivariate environmental space.
Simulating forest growth *Free Access* Process‐based forest models (PBMs) are important tools for quantifying forest growth and vulnerability, particularly under climate change. The 3‐PG model (Physiological Processes Predicting Growth) is one of the most widely used forest growth simulators for this purpose worldwide. Here, Trotsiuk et al. present r3PG, a new Fortran implementation of 3‐PG, wrapped into an r package. r3PG can simulate monospecific as well as mixtures of evergreen and deciduous tree species in even‐aged or uneven‐aged stands.
Biogeographical regionalisation *Free Access* Despite the mass production of species distributions and phylogenetic data, statistical and computational infrastructure to successfully incorporate, manipulate and analyse such massive amounts of data have not been fully developed. Here, Daru et al. present phyloregion, an R package for the analysis of biogeographical regionalisation and macroecology, tailored for mega phylogenies and macroecological datasets of ever‐increasing size and complexity.
Semi-portable solar power *Free Access* The use of technology in field ecology is increasing rapidly, requiring equipment that operates autonomously for long time periods. However, commercially available units that provide autonomous solar power are either prohibitively expensive or too small to sustain continuous operation for many devices. Here, Proppe et al. describe a semi‐portable, field deployable solar unit that can provide sustainable power for a wide variety of devices, including passive acoustic recorders, motion‐activated cameras, speakers and microcomputers.
3D‐printed coral models *Free access* Marine ecologists have engineered a range of artificial units to survey benthic communities with varying designs depending on target taxa, life history stage and habitat. In tropical ecosystems, autonomous units have typically lacked microhabitat complexity and short‐term efficacy. In this article, Wolfe & Mumby present RUbble Biodiversity Samplers (RUBS) as a dismantlable lightweight 3D‐printed model to standardize cryptobenthic biodiversity sampling.
Baited remote underwater stereo‐video surveys guide *Open Access* Baited remote underwater stereo‐video systems (stereo‐BRUVs) are a popular tool to sample demersal fish assemblages. Given the rapid uptake of the method, subtle differences have emerged in the way stereo‐BRUVs are deployed and how the resulting imagery is annotated. Here, Langlois et al. provide a standardised protocol for using stereo‐BRUVs to survey demersal fish assemblages and associated benthic habitats, that will reduce methodological variation among researchers. Information on stereo‐BRUVs design, camera settings, field operations and image annotation are all outlined.
Sampling tree flowers *Free Access* Sampling nectar from forest canopies is challenging and current techniques are generally expensive, logistically complex, and often involve additional safety risks and specialised technicians. Here, Scaccabarozzi et al. propose a simple approach based on an easy-to-assemble ground-based tool for sampling tree flowers for subsequent nectar extraction. The tool was used to successfully sample Eucalyptus marginata and Corymbia calophylla at heights of up to 10 m.
Low-cost system for radio tracking animals *Open Access* The use of unmanned aerial vehicles (UAVs) has the potential to considerably improve radio‐frequency (RF)‐based tracking systems. This paper presents details of a fully custom‐built active radio-frequency identification tag and receiver system bespoke to UAVs, compatible with both multi‐rotor and fixed‐wing platforms. Using sheep as a model, Roberts et al. show the suitability of this system for tracking large terrestrial mammals.
The Reef on the Cover
This month’s cover image shows some of the marine life that inhabits the Great Sea Reef of Fiji. Coral reefs provide important habitat for demersal fish such as the damselfish and anemonefish pictured, with the complex 3D structure of the corals offering them refuge from larger predators. The diverse array of organisms that make up a reef’s structure are also highly dynamic; growing, eroding, shifting, settling, or disappearing over time. In recent years, underwater camera‐imaging technology has allowed us to virtually recreate the shape and texture of underwater objects by stitching together many overlapping images. This now allows us to quantitatively analyse physical structures, or construct large‐scale photo‐mosaic maps of the seafloor to view change. In this issue, Bayley & Mogg present a user‐friendly protocol for creating, analysing and visualising large‐scale 3D digital models of reefs using ‘Structure from Motion’ photogrammetry. Their guide is aimed at helping researchers to apply, standardise, and widen the use of this emerging and rapidly developing technology for marine conservation and management. Image credit: ©Daniel Bayley
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.