The sixth issue of the year of Methods in Ecology and Evolution is out now! This issue features four Applications and one Practical Tools article, as well as methods for standardising biologging data, marking mosquitoes, calculating heterogeneity indices and much more. And scroll down to find out the story behind the sleepy seal on this month’s cover!
Distance sampling of high-density species Line-transect distance sampling is widely used to estimate population densities using distances of observed targets from transect lines to model detectability. When target taxa are high density, the frequent measuring of distances may make the method seem impractical. Here, Knights et al. present a method that improves the efficiency of distance sampling when the target species occurs at high density.
Long-term marking of mosquitoes (Practical Tools) Current mark–release–recapture methodologies are limited in their ability to address complex problems in vector biology, such as studying multiple groups overlapping in space and time. Additionally, limited mark retention, reduced post-marking survival and the large effort in marking, collection and recapture all complicate effective insect tracking. Here, Faiman et al. have developed a marking method using a fluorescent dye combined with synthetic DNA tags to informatively and efficiently mark adult mosquitoes. This method can be readily deployed in the field for marking multiple groups of mosquitoes or other insects.
FuzzyQ (Application) Balbuena et al. present the R package ‘Fuzzy Quantification of Common and Rare Species in Ecological Communities’ (FuzzyQ). FuzzyQ shifts the focus from the prevailing species-categorization approach to develop a quantitative framework that seeks to place each species along a rarity-commonness gradient. Given a community surveyed over a number of sites, quadrats, or any other convenient sampling unit, FuzzyQ uses a fuzzy clustering algorithm that estimates a probability for each species to be common or rare based on abundance–occupancy information.
rasterdiv (Application) Ecosystem heterogeneity has been widely recognized as a key ecological indicator of several ecological functions, diversity patterns and change, metapopulation dynamics, population connectivity or gene flow. Here, Rocchini et al. present a rasterdiv, a new R package for calculating heterogeneity indices based on remotely sensed data. They also provide an ecological application at the landscape scale and demonstrate its power in revealing potentially hidden heterogeneity patterns.
Automated detection of wildlife using drones Corcoran et al. review studies from the last 5 years in which wildlife species were detected automatically in drone-acquired imagery to understand how technological constraints, environmental conditions and ecological traits of target species impact detection with automated methods. They find that automated detection could be achieved for a wider range of species and under a greater variety of environmental conditions than reported in previous reviews of automated and manual detection in drone-acquired imagery. A high probability of automated detection could be achieved efficiently using fixed-wing platforms and RGB sensors for species that were large and occurred in open and homogeneous environments with little vegetation or variation in topography while infrared sensors and multirotor platforms were necessary to successfully detect small, elusive species in complex habitats.
Sampling and scaling biological nitrogen fixation Accurately quantifying rates and patterns of biological nitrogen fixation (BNF) in terrestrial ecosystems is essential to characterize ecological and biogeochemical interactions, identify mechanistic controls, improve BNF representation in conceptual and numerical modelling, and forecast nitrogen limitation constraints on future carbon (C) cycling. While many resources address the technical advantages and limitations of different methods for measuring BNF, less systematic consideration has been given to the broader decisions involved in planning studies, interpreting data, and extrapolating results. In this review, Soper et al. present a conceptual and practical road map to study design, study execution, data analysis and scaling, outlining key considerations at each step.
Other Applications articles
SoundShape The field of Bioacoustics has flourished in the past few decades, with numerous initiatives towards its application as a tool for biodiversity conservation. Despite the development of new methods involving computational programming and machine learning algorithms, higher accuracy is still needed for species identification. Here, Rocha & Romano present the SoundShape R package, which focuses on implementing the eigensound method for bioacoustical analysis. Implementation of SoundShape is summarised through a workflow guide, using data from the new package.
rTPC and nls.multstart Quantifying thermal performance curves (TPCs) for biological rates has many applications to important problems such as predicting responses of biological systems—from individuals to communities—to directional climate change or climatic fluctuations. Current software tools for fitting TPC models to data are not adequate for dealing with the immense size of new datasets that are increasingly becoming available. In answer to this, Padfield et al. present a new, reproducible pipeline in R that allows for relatively simple fitting of 24 different TPC models using nonlinear least squares (NLLS) regression. It provides a flexible and reproducible approach that makes the challenging task of fitting multiple TPC models to data accessible to a wide range of users across ecology and evolution.
The Seal on the Cover
This month’s cover image shows a Weddell seal carrying a satellite tag. Satellite tags allow collection of data associated with the movements and behaviour of animals (known as bio-logging data), which is extremely useful for driving conservation. Thousands of bio-logging datasets have been collected for many marine megafauna species, and are now being generated at unprecedented rates. This presents a key opportunity to address current conservation challenges resulting from global environmental change. However, a strong disconnection remains between data collection and their use in conservation and management largely due to a lack of data and metadata standards, resulting in mostly undiscoverable or inaccessible, disparate bio-logging datasets. In this issue, Sequeira et al. provide a standardisation framework to advance the sharing and use of bio-logging data, which will be crucial to advance ecological research and conservation. The proposed framework will promote efficient data collation, usage, and sharing, consistent with the FAIR (Findable, Accessible, Interoperable, and Reusable) and TRUST (Transparency, Responsibility, User focus, Sustainability and Technology) data principles, and ensure: (i) accuracy of data use, (ii) rightful attribution of ownership to those who collect and share the data, and (iii) data preservation security.
Photo credit: ©Robert Harcourt with permit DOC-69331-MAR, IMOS (Integrated Marine Observing System).