The August issue of Methods is now online!
We have a larger issue of 14 articles this month, featuring tools for microbial evolution experiments, automatic biomass estimation of invertebrates, labeling biological samples and much more.
Senior Editor Bob O’Hara has selected five featured articles this month – find out about them below. We also have four Applications, one Practical Tools article and 10 articles that are freely available to everyone – no subscription required!
Automatic identification and biomass estimation of invertebrates open access Monitoring insect populations is important but time-consuming and depends on expert identification. Ärje et al. have developed a system for automatic image-based identification and biomass estimation of invertebrates. It achieved 98% classification accuracy on a dataset of 12 arthropod species.
The omnistat open access Microbial evolution
experiments provide a powerful tool to unravel the molecular basis of adaptive evolution. Continuous cultures allow more accurate control over the environment than sequential batch cultures, but tend to be large and expensive. Here Ekkers et al. present the omnistat, a flexible continuous culture system for prolonged experimental evolution experiments.
PhyloMCL Identification of homology relationships is the first step in many genetic and genomic studies, but the presence of gene duplicates, variation in evolutionary rates of homologs and fusion/fission of genes can lead to misidentification of evolutionary relationships. This study presents PhyloMCL, a Markov clustering algorithm which classifies genes of multiple genomes into hierarchical orthogroups guided by phylogenetic relationships of species and detected polyploidy events.
Practical Tool: The tripod frame free access Acoustic telemetry is increasingly used to observe and monitor animal movements in aquatic environments, but practical deployment mechanisms are needed to sustain consistent data flows in challenging environments. Goossens et al. have developed a tripod frame to facilitate the deployment of acoustic receivers on the seabed, allowing for the recovery of all equipment with an acoustic release system.
Application: nosoi free access Reconstructing transmission chains remains a challenging endeavour, except in rare cases characterised by intense surveillance and epidemiological inquiry. Here Lequime et al. introduce nosoi, an R package that offers a complete, tunable and expandable agent‐based framework to simulate transmission chains under a wide range of epidemiological scenarios for single‐host and dual‐host epidemics.
We have four 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 three:
baRcodeR free access In biology, even small errors in labelling and data management can lead to severe consequences. To reduce potential error, Wu et al. have produced baRcodeR, a software package for quickly generating unique identifier codes and print scannable barcodes on a basic laser printer.
Kernel density n-dimensional hypervolumes free access The use of n‐dimensional hypervolumes in trait‐based ecology is rapidly increasing. Mammola & Cardoso have developed a set of functions to calculate functional diversity indices based on n‐dimensional hypervolumes, including alpha (richness), beta (and respective components), dispersion, evenness, contribution and originality.
assignR free access Methods for inferring geographic origin from the stable isotope composition of animal tissues are widely used in movement ecology, but few computational tools and standards for data interpretation are available. The assignR R package provides a structured, flexible toolkit for isotope‐based migration data analysis and interpretation using a widely-adopted semi‐parametric Bayesian inversion method.
Other open access articles
Commentary: The use of Bayesian priors in Ecology Bayesian data analysis (BDA) is a powerful tool for making inference from ecological data, but its full potential has yet to be realised. In this commentary, Banner et al. provide an overview of how BDA is currently being used in a random sample of articles, discuss implications for inference if current bad practices continue, and highlight sub‐fields where knowledge about the system has improved inference and promoted good statistical practices.
The biodiversity impacts of land conversion
Further progress in reducing biodiversity loss relies on the improved quantification of the connections between drivers of habitat loss and subsequent biodiversity impacts. Here, Durán et al. develop a globally-applicable methodological framework that uses freely and publicly available datasets to quantify the relative impacts of anthropogenic activities on biodiversity.
The Drone on the Cover
This month’s cover image shows an unmanned aerial vehicle (UAV or drone) flying across the badlands of the Oligocene‐aged White River Group of Wyoming, USA (~30 million years old) to verify potential fossils identified autonomously by the UAV the night before. Fossil candidates can now be searched out using fluorescence signatures detected by a laser‐scanning system onboard an autonomous UAV that scans the ground for fossils at night. The new system is detailed by Kaye and Pittman in their open access article and promises to improve how efficiently fossils are discovered in the field. The system also has strong potential for broader application in other areas of ecology and evolution through the identification of other mineral, rock and biological targets.
Photo credit: ©Thomas G Kaye & Michael Pittman.
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.