The September issue of Methods is now online!

We have a larger issue of 14 articles this month, featuring  methods for individual bird recognition, zooplankton sampling, coral health assessment and much more.

Senior Editor Lee Hsiang Liow has selected five featured articles – find out about them below. We also have three Applications, three Practical Tools articles and 11 articles that are freely available to everyone – no subscription required!

Featured Articles

Practical Tools: The In situ Plankton Assemblage eXplorer open access Zooplankton play vital ecological roles that maintain aquatic ecosystems, but imaging them in situ is often costly, requiring sophisticated engineering expertise to operate. Now Pichaya Lertvilai has designed the In situ Plankton Assemblage eXplorer (IPAX), a programmable instrument that has powerful LED illumination and a high‐resolution camera that can image zooplankton in various aquatic habitats. Its low cost facilitates construction and deployment of multiple units that can cover large spatial areas, while its versatility also allows adaptations to many experimental needs for aquatic ecology.

Deep learning for individual recognition in small birds open access

Individual identification is a crucial step to answer many questions in evolutionary biology and is mostly performed by marking animals with tags. Such methods make data collection and analyses time‐consuming and limit the contexts in which data can be collected. Here, Ferreira et al. describe procedures for automating the collection of training data, generating training datasets, and training convolutional neural networks to allow identification of individual birds. The ability to conduct individual recognition of birds without requiring external markers represents a major advance over current methods.

Practical Tools: The elevated mist-net frame free access Standard mist‐netting limits sampling to understorey birds flying < 3 m above ground level. Methodological innovations targeting higher strata birds are important for ecological studies, particularly in tropical forests. Here Lars Haubye Holbech presents a method of applying elevated mist‐net frames (EMF) up to 25–30m using detachable mobile alloy frames, three‐point cable‐wire mounting and state‐of‐the‐art archery and fishing gear for securing anchor lines, excluding the need for tree-climbing or arboreal platforms.

Application: msocc free access Environmental DNA sampling workflows commonly rely on multi‐stage hierarchical sampling designs that induce complicated dependencies within the data. This dependence structure can be intuitively modelled with Bayesian multi‐scale occupancy models, but software for such models are computationally demanding. Here, Stratton et al. present msocc, an R package that implements a data augmentation strategy to fit fully Bayesian, computationally efficient multi‐scale occupancy models.

Robustness of linear mixed-effects models open access Mixed‐effects models involve complex fitting procedures and make several assumptions. Violations of these assumptions are common in real datasets, yet it is not always clear how much they matter to accurate and unbiased estimation. Here, Schielzeth et al. address the consequences of violations in distributional assumptions and the impact of missing random effect components on model estimates. Overall, the results show remarkable robustness of mixed‐effects models that should allow researchers to use mixed‐effects models even if the distributional assumptions are objectively violated.

Applications

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:

adiv free access Current R packages used for biodiversity research focus on limited, particular aspects of biodiversity such as the number and abundance of species. Here Sandrine Pavoine presents adiv, an R package that provides additional methods for analysing biodiversity, including approaches for quantifying species‐based, trait‐based (functional) and phylogenetic diversity within and between communities, and partitioning biodiversity over space and time.

taxadb free access A growing challenge in ecological and evolutionary research is establishing consistent taxonomy when combining data from separate sources. Most researchers lack a fast, consistent, and intuitive way to retrieve taxonomic names. Norman et al. present taxadb, an R package which creates a local database, managed automatically from within R, to provide fast operations on millions of taxonomic names.

Practical Tools

We have three Practical Tools articles in this issue, all free to access. Two of them have been covered in our Featured Articles above, and here is the third:

Complementary coral sampling methods free access
Visual surveys of coral reefs are the primary method managers use to monitor coral health, but are limited to visual signs which occur only after significant stress has accumulated. Here, Greene et al. present an unparalleled, holistic method for characterising coral health, including extraction of coral metabolites for analysis,  preservation of microbiome DNA for sequencing and preservation of coral tissues for histopathology.

Other Open Access Articles

Decay in marine calcifiers We are beginning to see alterations to the structure and properties of animals’ exoskeletons due to ocean acidification, warming and accelerated rates of bioerosion. Here, Fordyce et al. present a significant advancement in the use of micro‐computed tomography (µCT) to studying decalcification in a marine calcifier. They provide a detailed workflow on best practice for µCT image processing and analysis of marine calcifiers, including estimating subresolution microporosity and describing pore space morphological characteristics of macroporosity, in perforate and imperforate exoskeletons.

Modern bone collagen isotope measurements
Guiry & Szpak use a large survey of published collagen amino acid compositions from 193 vertebrate species as well as recent experimental isotopic evidence from 413 modern collagen extracts to demonstrate that the C:N_Atomic range used for ancient samples is not suitable for assessing collagen quality of modern and archived historical samples. For modern tissues, collagen C:N_Atomic falling outside 3.00–3.30 for fish and 3.00–3.28 for mammals and birds can produce systematically skewed isotopic compositions and may lead to significant interpretative errors. These findings are followed by a review of protocols for improving C:N_Atomic criteria for modern collagen extracts.

Chemical traits of single leaves Measures of plant chemical traits are often achieved by merging several leaves, masking potential foliar variation within and among plant individuals. The calibration models developed for converting near-infrared reflectance spectroscopy information to chemical traits are typically based on spectra from merged and milled leaves. Here, Matteo Petit Bon et al. ask whether such calibration models can be applied to spectra derived from whole leaves, providing measures of chemical traits of single leaves.

The Bird on the Cover

This month’s cover portraits an adult male Black‐headed Paradise Flycatcher Terpsiphone rufiventer nigriceps caught with an elevated mist‐net frame (EMF) in a tropical rainforest of south‐west Ghana. The bird was caught during a study to test the efficacy of a new EMF‐system (bottom left corner of the image) developed by Lars H. Holbech to safely and efficiently trap birds in upper‐strata vegetation zones. Capturing this specimen above a narrow forest road was aided by portable speaker playback of its song. This species is often referred to as a species of the ‘understory’ (0‐5m height), but was caught here in ‘upper mid‐story’ (at 15m), emphasising how important elevated mist‐netting is for precise description of avian vertical preferences. This EMF represents a replicable, versatile and manoeuvrable design for catching birds in forest strata>25m above the ground, without need for tree climbing or excessive clearing of vertical net‐lanes in lightly‐cluttered vegetation.
Photo credit: ©Lars H. Holbech.

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.