Issue 11.1: Climate Change, Genomic Divergence, Bayesian Modelling and More

The January issue of Methods is now online!

It’s a new year and the new issue of Methods in Ecology and Evolution is now online!

We’re starting 2020 with a great issue – and ALL of the articles are completely free. And they’ll remain free for the whole year. No subscription required.

You can find out more about our Featured Articles (selected by the Senior Editor) below. We also discuss this month’s Open Access, Practical Tools and Applications articles. There are also articles on species distributions, biotic interactions, taxonomic units and much more.

Featured Articles

10th Anniversary Editorial: This year marks the 10th anniversary of Methods in Ecology and Evolution. To start the celebrations, Executive Editor Rob Freckleton and Senior Editors Aaron Ellison, Lee Hsiang Liow and Bob O’Hara look back over the past ten years and forward to the future of the journal.

Standardising Terrestrial Climate Change Experiments: To overcome the challenges related to data availability and/or compatibility across climate change studies, Halbritter et al. collected best‐practice methods emerging from major ecological research networks and experiments, as synthesised by 115 experts from across a wide range of scientific disciplines. Their Open Access handbook contains guidance on the selection of response variables for different purposes, protocols for standardised measurements of 66 such response variables and advice on data management. You can read more about it in this blog post. 這篇博客文章也有中文版

Islands of Genomic Divergence: We currently lack a quantitative framework to examine the dynamics of genomic landscapes under the complex and nuanced conditions that are found in natural systems. Quilodrán et al. develop an individual‐based simulation to explore the dynamics of diverging genomes under various scenarios of gene flow, selection and genotype–phenotype maps.

GOTIT: GOTIT (Gene Occurrence and Taxa in Integrative Taxonomy) is a database structure and web application for optimising productivity at various steps of a laboratory’s workflow including research project design, sampling gap analysis, sampling planning, species identification, DNA sequencing, information sharing and contributing data to global biodiversity facilities.

Scale-throated Hermit (Phaethornis eurynome). ©Pedro Lorenzo.Estimating the Robustness of Mutualistic Networks: Vizentin‐Bugoni et al. propose a new method to incorporate the potential of species to replace lost partners into a widely used coextinction model to estimate network robustness. In this model, species are allowed to rewire their interactions after initial loss of partners according to probabilities derived from well‐known mechanisms that determine mutualistic interactions, for example, trait matching, phenological overlap and abundances. Find out more in this blog post. Esta publicação no blogue também está disponível em português.

Periodic Mortality Patterns: cyclomort – an R package from Gurarie et al. – estimates the timing, duration and intensity of any number of mortality seasons with reliable confidence intervals. The package includes a model selection approach to determine the number of mortality seasons and to test whether seasons of mortality vary across discrete grouping factors. The lead author explains more about the package (with references to Scandi-noir thrillers and killer pianos) here.

Applications and Practical Tools

The first Practical Tools article of 2020 – ‘Optimizing dissection, sample collection and cell isolation protocols for frugivorous bats‘ – comes from Irving et al. The authors develop optimal procedures for anaesthetizing, necropsy methods, safety, sequence and protocols for cell/tissue extraction and isolation protocols. Their study provides the framework for greater consistency with in vivo bat experiments, application for comparative biology studies and greater engagement of the bat community for suitable protocols to be harmoniously adopted.

Two of this month’s Applications articles have been covered above (GOTIT and cyclomort). But don’t worry, we’ve FIVE more to talk about.

Computing Microclimate: The availability of global weather and terrain datasets, together with increasingly sophisticated microclimate modelling tools, makes the prospect of a global, web‐based microclimate estimation procedure feasible. Kearney et al. have developed such an approach for the r programming environment which integrates existing r packages for obtaining terrain and sub‐daily atmospheric forcing data (elevatr and rncep), and two complementary microclimate modelling packages (NicheMapR and microclima).

AquaFlux: AquaFlux is an R package designed to efficiently process and analyse Thermal Dissipation Probe (TDP) data. This program maximises data collection by continually importing raw TDP values and alerting the user of any malfunctioning sensors. It provides a robust tool to facilitate predictive understanding of plant transpiration.

biodivMapR: Féret and de Boissieu present an R package designed to compute a selection of α‐ and β‐diversity indicators from optical imagery, based on spectral variation hypothesis. biodivMapR builds upon previous work on biodiversity mapping using airborne imaging spectroscopy, and has been adapted in order to process broader range of data sources.

MetaCurator: While metabarcoding and metagenomic approaches are increasingly popular, questions remain about how best to analyse and taxonomically characterize the sequence data produced by such methods. MetaCurator is a software package designed for automated reference sequence curation and highly generalizable across markers and study systems.

Toytree: The goal of toytree is to provide a simple Python equivalent to commonly used tree manipulation and plotting libraries in R, and in doing so, to promote further development of phylogenetic and other tree‐based methods in Python. It provides functions for parsing additional tree formats, generating random trees, inferring consensus trees and drawing grids or clouds from multiple trees to visualize discordance.

Open Access Articles

There’s only one Open Access article that we haven’t already discussed. In ‘Evaluating Bayesian stable isotope mixing models of wild animal diet and the effects of trophic discrimination factors and informative priors‘ Swan et al. evaluate the performance of Bayesian stable isotope mixing models (BSIMMs) in quantifying animal diets and analyse mixing model outcomes with various trophic discrimination factors (TDFs). BSIMMs can provide accurate assessments of diet in wild animals. TDF estimates from the SIDER package performed well. The inclusion of informative priors from conventional methods in Bayesian mixing models can transfer biases into model outcomes, leading to erroneous results.

The Turtle on the Cover

This month’s cover image shows a small turtle (Chelonia mydas) which has just hatched on a sandy beach in The Moluccas, Indonesia. Only a small fraction of these hatchlings reach sexual maturity and reproduce. By participating in the generation of offspring, the individuals that reproduce are also participating in the genetic diversity of the next generation and, potentially, in the accumulation of evolutionary change over time.

In the related article – ‘The multiple population genetic and demographic routes to islands of genomic divergence‘ – Quilodrán et al. propose a novel and flexible framework to simulate the evolution of organisms. The tools integrate the life history of organisms with genetic or genomic information to explore plausible evolutionary scenarios. They use this framework to demonstrate that there are multiple population genetic and demographic ways that can explain the emergence of a heterogeneous genomic landscape, which describes the distribution of differences across genomes. This tool should be useful in elucidating the past and future evolution of any taxa.

Photo credit: © Claudio Quilodrán, University of Oxford

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.

 

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