The May issue of Methods in Ecology and Evolution is absolutely packed! We’ve got a new ecoacoustics method from Metcalf et al. and a new inference and forecasting method from Cenci et al. There’s also a forum article on image analysis, and papers on physiology, palaeobiology, capture-recapture and much more. We’ve got SIX papers that are freely available to absolutely everyone this month too.
Find out a little more about the new issue of Methods in Ecology and Evolution (including details about what the diver is doing to the coral in the cover image) below.
Video and Coordinate Animal‐mounted System: Carlos de la Rosa presents VACAMS – an animal‐mounted data collection system that records short, first ‘person’ perspective videos of animal behaviour. It can be used on a range of domestic and semi‐domestic free‐ranging animals, particularly in dense forests where conventional observations are impossible. Carlos also wrote a blog post about VACAMS which you can find in English here and en español aqui.
Quantum Dots as Pollen Labels: In plant reproductive biology, we usually study plant mating without directly tracking pollen movement. This has mostly been because of a lack of suitable pollen‐tracking methods. Until now! Minnaar and Anderson develop and test a new pollen‐tracking technique using quantum dots as pollen‐grain labels. They show that this relatively cheap method could help to address a historically neglected aspect of plant reproductive ecology and evolution.
Leaf and Wood Classification: Leaf and wood separation is a key step to allow a new range of estimates from Terrestrial LiDAR data. A new method from Vicari et al. allows you to separate leaf and wood from single tree point clouds automatically. Their separation method showed results similar to others in literature, but from a completely automated workflow.
State‐switching Continuous‐time Correlated Random Walks: Michelot and Blackwell propose a multistate formulation of the continuous‐time correlated random walk, with an underlying Markov process used as a proxy for the animal’s behavioural state process. Their method makes use of the state‐space model formulation of the continuous‐time correlated random walk, and can accommodate irregular sampling frequency and measurement error.
Detoxifying Enzymes in Terrestrial Invertebrates: Pedersen et al. show why in vitro methods are ineffective to quantify metabolic enzymes in some insects. As an alternative to in vitro measurements, they optimised an ex vivo method for quantification of three major enzyme families.
This issue contains four Applications articles. They’re all freely available to everyone, no subscription required.
plantspec: A major factor limiting the widespread use of near‐infrared spectroscopy by plant ecologists is the availability of free software and calibration data for developing plant chemistry datasets from spectra. Griffith and Anderson present a pair of companion R packages (‘plantspec’ and ‘plantspecDB’) that satisfy this need by providing an entire workflow, from spectra to predicted elemental data.
bmotif: Simmons et al. introduce a package for motif analyses of bipartite networks. They show how it can be used to conduct ecological analyses, using two examples of plant–pollinator networks. This package will help future research to characterise complex networks without discarding important meso‐scale structural detail.
The R Package divDyn: Unbiased time series of diversity dynamics are vital for quantifying the grand history of life. divDyn, a new R package from Kocsis et al. helps you to calculate taxonomic richness, extinction and origination rates from time‐binned fossil data. Our most recent #FossilFriday blog post was about this article. It’s also one of the featured articles this month.
CoordinateCleaner: Species occurrence records are an indispensable resource in ecological, biogeographical and palaeontological research. But issues with data quality, can diminish their usefulness. CoordinateCleaner is an r‐package that scans datasets of species occurrence records for geo‐referencing and dating imprecisions and data entry errors in a standardised and reproducible way. This software package was extensively reviewed and approved by the rOpenSci project.
The Coral on the Cover
This month’s cover image shows a SCUBA-diving PhD student assessing metabolic and biogeochemical functions of a coral reef community in the central Red Sea, Saudi Arabia. These coral communities flourish in some of the most oligotrophic waters of the tropics.
The key to their high productivity is an efficient cycling of energy and nutrients within the reef ecosystem. However, measuring actual rates of productivity, calcification, along with organic matter and nutrient cycling in situ has proven difficult because of logistical constraints and the structural complexity of many benthic habitats.
In their article, Roth et al. present a cost-effective incubation chamber system that can be used over both simple and structurally complex benthic communities. The authors provide detailed construction plans, explain how photogrammetry tools enable accurate normalisation of community-fluxes, and guide through data analysis and interpretation. As a standardised approach, the authors demonstrate the applicability of the chambers on a range of benthic habitats, including rocky-shores with algae, corals, seagrass meadows, and carbonate sands. This tool helps to mitigate the lack of observational and manipulative studies that can be in situ performed in native habitats. It produces widely applicable and realistic assessments on the community level.
Photo credit: © Holger Anlauf