The journey from designing to employing an automated radio telemetry system to track monarch butterflies

Post provided by Kelsey E. Fisher

Kelsey Fisher describes the motivations and challenges in the development of a novel automated radio telemetry method to track the movement of butterflies at the landscape scale published in their new Methods article ‘Locating large insects using automated VHF radio telemetry with a multi‐antennae array’.

LB-2X transmitter attached to a monarch butterfly.

Understanding animal movement across varying spatial and temporal scales is an active area of fundamental ecological research, with practical applications in the fields of conservation biology and natural resource management. Advancements in tracking technologies, such as GPS and satellite systems, allow researchers to obtain more location information for a variety of species than ever before. It’s an exciting time for movement ecologists! However, entomologists studying insect movement are still limited because of the large size of tracking devices relative to the small size of insects.

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10th Anniversary Volume 11: Updates on the ClimEx Handbook

Post provided by Aud H. Halbritter

To celebrate the 10th Anniversary of the launch of Methods in Ecology and Evolution, we are highlighting an article from each volume to feature in the Methods.blog. For Volume 11, we have selected ‘The handbook for standardized field and laboratory measurements in terrestrial climate change experiments and observational studies (ClimEx)’ by Halbritter et al. (2019).

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10th Anniversary Volume 10: Evidence synthesis technology and automating systematic reviews

Post provided by Eliza M. grames

To celebrate the 10th Anniversary of the launch of Methods in Ecology and Evolution, we are highlighting an article from each volume to feature on the Methods.blog. For Volume 10, we have selected ‘An automated approach to identifying search terms for systematic reviews using keyword co‐occurrence networks’ by Grames et al. (2019).

In this post, Eliza Grames shares the motivation behind the litsearchr search approach, and developments since the article’s publication.

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10th Anniversary Volume 8: Phylogenetic tree visualization with multivariate data

Post provided by Guangchuang Yu and Tommy Tsan-Yuk Lam

To celebrate the 10th Anniversary of the launch of Methods in Ecology and Evolution, we are highlighting an article from each volume to feature in the Methods.blog. For Volume 8, we have selected ‘ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data‘ by Yu et al. (2016).

In this post, the authors share their inspiration behind the ggtree package for R and present new resources of ggtree and a series of other related packages.

The team publishing the ggtree paper is working in the field of emerging infectious diseases. Particularly the corresponding author Tommy Lam (TL) has been advocating the integration of different biological and epidemiological information in the studies of fast-evolving viral pathogens. The lead author Guangchuang Yu (GY) joined The University of Hong Kong to pursue his doctorate degree under the supervision of TL and Yi Guan (co-author in the paper), as he was very curious about the application of genomics and phylogenetics in the study of emerging infectious diseases.

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Tracking the fate of fish

Post provided by David Villegas Ríos

David Ríos tells us about investigating the movement of aquatic animals using telemetry technology and the new Methods article ‘Inferring individual fate from aquatic acoustic telemetry data’.

Photo by Carla Freitas

Aquatic animal telemetry has revolutionized our understanding of the behaviour of aquatic animals. One of the important advantages of telemetry methods, including acoustic telemetry, is that they provide information at the individual level. This is very relevant because it enables investigating the natural variability in behaviour within populations (like here or here), but also because one can investigate what happens to each individual animal and relate it to its natural behaviour. Knowing “what happens to each individual” is normally referred to as “fate” and it can take many forms: some fish may end-up eaten by predators, other may be fished, some of them may disperse, etc. Knowing the fate of each individual fish is crucial as it links ecological processes at the individual level to evolutionary outcomes at the population level.

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10th Anniversary Volume 6: Nondestructive estimates of above‐ground biomass using terrestrial laser scanning

Post provided by Kim Calders, Glenn Newnham, Andrew Burt, Pasi Raumonen, Martin Herold, Darius Culvenor, Valerio Avitabile, Mathias Disney, and John Armston

To celebrate the 10th Anniversary of the launch of Methods in Ecology and Evolution, we are highlighting an article from each volume to feature in the Methods.blog. For Volume 6, we have selected ‘Nondestructive estimates of above-ground biomass using terrestrial laser scanning by Calders et al. (2014).

In this post, the authors discuss the background and key concepts of the article, and changes in the field that have happened since the paper was published.

Terrestrial laser scanning (TLS) calculates 3D locations by measuring the speed of light between a transmitted laser pulse and its return. Firing hundreds of thousands of pulses per second, these instruments can represent the surroundings in detailed 3D, displaying them as virtual environments made up of high density points. The main applications of commercial instruments in the early 2000s were engineering or mining, but their application in natural forested environments was in its infancy. Forest ecosystems are structurally complex; clear reference points used to register multiple scans are rare and trees move due to wind creating artefacts in the data.

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10th Anniversary Volume 3: paleotree: A Retrospective

Post provided by David bapst

To celebrate the 10th Anniversary of the launch of Methods in Ecology and Evolution, we are highlighting an article from each volume to feature on the Methods.blog. For Volume 3, we have selected ‘paleotree: an R package for paleontological and phylogenetic analyses of evolution‘ by David W. Bapst (2012). In this post, David discusses the background to the Application he wrote as a graduate student, and how the field has changed since.

I was a fourth year graduate student when I first had the idea to make an R package. Quite a few people thought it was a bit silly, or a bit of a time-waste, but I thought it was the right thing to do at the time, and I think it has proven to be the right decision in hindsight.

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Creating a package to infer species coexistence

Post provided by Ignasi Bartomeus, David García-Callejas, and Oscar Godoy

Ignasi Bartomeus and colleagues share the story behind their recent Methods article ‘cxr: A toolbox for modelling species coexistence in R’.

This post recalls the journey on how we ended up developing cxr (acronym for CoeXistence relationships in R), an R package for quantifying interactions among species and their coexistence relationships. In other words, it provides tools for telling apart the situations in which different species can persist together in a community from the cases in which one species completely overcomes another.

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Para, piensa, y ten cuidado con las configuraciones por defecto

Post escrito por Paula Pappalardo (con aportes de Elizabeth Hamman, Jim Bence, Bruce Hungate & Craig Osenberg)

This post is also available in English.

Pasaste meses laboriosamente colectando datos de artículos científicos acerca de tu pregunta favorita, tienes decenas de artículos perfectamente organizados en una base de datos, ya encontraste el programa o código para analizar los datos, y entonces imaginas como tu publicación va a ser la más citada en tu campo de investigación mientras haces unos gráficos lindísimos. Si esto te suena familiar, seguramente has hecho un meta-análisis. Un meta-análisis usa modelos estadísticos para combinar datos de distintas publicaciones para responder a una pregunta específica.

Lo que quizás no te diste cuenta mientras navegabas los pasos del meta-análisis, es que pequeñas decisiones (a veces pareciendo de muy poca importancia) pueden tener grandes efectos en los resultados. Si quieres saber más acerca de una de estas decisiones en particular… ¡sigue leyendo!

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Stop, think, and beware of default options

Post provided by Paula Pappalardo (with contributions from Elizabeth Hamman, Jim Bence, Bruce Hungate & Craig Osenberg)

Esta publicación también está disponible en español.

You spent months carefully collecting data from articles addressing your favorite scientific question, you have dozens of articles neatly arranged on a spreadsheet, you found software or code to analyze the data, and then daydream about how your publication will be the most cited in your field while making cool plots. If that sounds familiar, you have probably done a meta-analysis. Meta-analysis uses statistical models to combine data from different publications to answer a specific question.

What you may not have realized when going down the meta-analysis rabbit hole, is that small, seemingly inconsequential, choices can greatly affect your results. If you want to know about one of them lurking behind the scenes… read on!

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