We’ve got a bumper issue of Methods in Ecology and Evolution this month. In the 200+ pages, you’ll find articles about measuring species distributions and abundances, integrated population models, and working at the whole-plant scale.
We’ve got six papers that are freely available to absolutely everyone this month too. You can find out about two of the Open Access papers in the Applications and Practical Tools section below. In the third, Chen et al. show that tree assemblages in tropical forest ecosystems can present a strong signal of extensive distributional interspersion.
Find out a little more about the new issue of Methods in Ecology and Evolution below.
What does a zero mean?: Blasco‐Moreno et al. review the different modelling options in relation to the presence of overdispersion and zero inflation, tested through the dispersion and zero inflation indices. They examine the theory of the zero‐inflated models and the use of the score tests to assess overdispersion and zero inflation over a model.
Dealing with Uncertainty Using Boolean Analysis: Should you use uniform priors for species interaction strengths in models to inform conservation decision-making? NO! Kristensen et al. explain why not.
Statistical Techniques for Aquatic Telemetry Data: Keeping with the aquatic theme, Whoriskey et al. have written a review of current statistical methods for analysing detection data derived from fixed telemetry receiver arrays. Their article provides both experienced and novice telemetry researchers with the knowledge and tools to facilitate more comprehensive analysis of detection data.
Accounting for Intraspecific Genomic Relatedness: Are there benefits to accounting for intraspecific genomic relatedness in multi‐species studies? Joly et al. found that doing so yields more accurate and precise fixed effects as well as increased statistical power. Statistical gains can be made by incorporating information on the intraspecific genomic relatedness of individuals in multi‐species studies.
Causal Analysis in Control–Impact Studies: Ecologists often draw causal insights in observational control–impact settings by exploiting research designs that approximate the experimental ideal. Larsen et al. review the challenges of making causal inference in non‐experimental control–impact scenarios as well as a suite of statistical tools specifically designed to overcome such challenges. To harness things like citizen-science data to understand causal impacts of policy changes, we must expand our tool set so that we can improve inference and more confidently advance ecological understanding and science‐informed policy.
Applications and Practical Tools
This issue contains three Applications and two Practical Tools articles (one of which is included in the Featured Articles above). They’re all freely available to everyone, no subscription required.
RNase H‐dependent PCR: Species‐specific, probe‐based quantitative PCR (qPCR) assays are now commonly used to detect aquatic species from environmental DNA. But they can’t always distinguish closely related species. Rodgers et al. have developed species‐specific qPCR assays using RNase H‐dependent PCR (rhPCR) for detecting closely related fish species from environmental DNA.
fishtree: Methodological advances have increased the breadth of taxonomic coverage in phylogenetic data; however, accessing and reusing these data remain challenging. Chang et al. introduce the Fish Tree of Life website and associated r package fishtree to provide convenient access to sequences, phylogenies, fossil calibrations and diversification rate estimates for the most diverse group of vertebrate organisms, the ray‐finned fishes.
pavo 2: Maia et al. introduce the latest iteration of the r package pavo. At its core, the package retains a broad focus on (a) the organization and processing of spectral and spatial data, and tools for the alternating (b) visualization, and (c) analysis of data. Significantly, pavo 2 introduces image‐analysis capabilities, providing a cohesive workflow for the comprehensive analysis of colour patterns. The package has a renewed potential to assist researchers in answering fundamental questions in sensory ecology and evolution. You can find out about the rOpenSci review of this package here.
island R Package: Ontiveros et al. developed an r package, island. It’s a community ecology tool to analyse temporal patterns and explore potential drivers of community dynamics. They present three examples showcasing the uses of our package: detectability estimation and model selection, influence of environmental covariates on community dynamics and estimation of co‐occurrence networks.
The Flower on the Cover
This month’s cover image shows the inflorescences of the exotic plant Senecio pterophorus being consumed by a geometrid Lepidoptera at Montseny Natural Park (Catalonia, Spain). S. pterophorus is a South African species introduced to Europe more than 30 years ago, which co-occurs with another exotic species, S. inaequidens, and two native congeners (S. vulgaris and S. lividus). This system was used to test the Enemy release hypothesis, which predicts that exotic plants will experience a decrease in their natural enemies thus acquiring a competitive advantage over the native vegetation.
When Blasco‐Moreno et al. aimed to compare the number of herbivores on the exotic versus the native species they faced a statistical challenge: due to the nature of the hypothesis, data was expected to be zero inflated (a large number of exotic plants were expected to be undamaged). This case study was the starting point of ‘What does a zero mean? Understanding false, random and structural zeros in ecology‘. In this article the authors explore the modelling options for count data in relation to overdispersion and zero inflation. They also describe a protocol to assist with the statistical analyses of count data.
Photo credit: © Jaume Danés