Uma breve história sobre o pacote R ‘metan’

Post ESCRITO POR Tiago Olivoto

This post is also available in English

Em nosso recente artigo na Methods in Ecology and Evolution, Alessandro D. Lúcio e eu descrevemos um novo pacote R para análise de ensaios multi-ambientes chamado metan. Ensaios multi-ambientes são um tipo de ensaio em programas de melhoramento de plantas, onde vários genótipos são avaliados em um conjunto de ambientes. A análise desses dados requer a combinação de várias abordagens, incluindo manipulação, visualização e modelagem de dados. A versão estável mais recente do metan (v1.5.1) está disponível agora no repositório CRAN. Então, pensei em compartilhar a história da minha primeira incursão no uso do R criando um pacote e submetendo um artigo para uma revista que nunca havia submetido antes.

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A brief history about the R package ‘metan’

Post provided by Tiago Olivoto

Este post também pode ser lido em Português

In our recent paper in Methods in Ecology and Evolution, Alessandro Lúcio and I describe a new R package, metan, for multi-environment trial analysis. Multi-environment trials are a kind of trial in plant breeding programs where several genotypes are evaluated in a set of environments. Analyzing such data requires the combination of several approaches including data manipulation, visualization and modelling. The latest stable version of metan (v1.5.1) is now on CRAN. So, I want to share the history about my first foray into using R, creating an R package, and submitting a paper to a journal that I’ve never had submitted before.

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An interview with the editors of “Population Ecology in Practice”: Part I

Post provided by Daniel Caetano

Today we bring the first part of an interview with Dennis Murray and Brett Sandercock about their brand new book in population ecology methods: “Population Ecology in Practice.” The editors were kind enough to share some interesting backstage information with us.

Snowshoe hare in winter

Population Ecology in Practice introduces a synthesis of analytical and modelling approaches currently used in demographic, genetic, and spatial analyses. Chapters provide examples based on real datasets together with a companion website with study cases and exercises implemented in the R statistical programming language.

Stay tuned for the second part of this interview, where we talk about some of the challenges of editing a large book and the editors share essential advice for anyone looking into leading such a project!

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10th Anniversary Volume 1: The Art of Modelling Range-Shifting Species

Post provided by Jane Elith, Mike Kearney and Steven Phillips  

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 1, we have selected ‘The art of modelling range-shifting species’ by Elith et al. (2010).  In this post, first author, Professor Jane Elith, discusses the background and key concepts of the article, and how things have changed since the paper was published.

Illustration of the idea that model settings affect prediction.

We started work on this manuscript around 2008, prompted by increasing use of species distribution models for climate change and invasive species problems. At that stage there was growing recognition of the problems in these applications (e.g. see a recent MEE review on transferability) but relatively few tools for dealing with them. In our view, if correlative models are to be used for such purposes, the data and models require special attention.

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Gaining Genetic and Epigenetic Data from a Single Established Next-Generation Sequencing Approach

Post provided by Marco Crotti

How organisms adapt to the environment they live in is a key question in evolutionary biology. Genetic variation, i.e. how individuals within populations differ from each other in terms of their DNA, is an essential element in the process of adaptation. It can arise through different mechanisms, including DNA mutations, genetic drift, and recombination.

Example of how genetic drift can occur over generations via random sampling (i.e. random mating) in a population. (Picture credit: Gringer).

Differences in DNA sequences between individuals can results in differences in the expression of genes. This can therefore determine the organism’s capacity to grow, develop, and react to environmental stimuli. However, a growing body of literature reveals that there are other ways organisms can change the way they interact with the world without mutations in the DNA sequence.

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Issue 11.5: Our May issue is now online!

The May issue of Methods is now online!11.5 Cover jpeg

As well as four Application and two Practical Tools articles, the latest issue of Methods in Ecology and Evolution includes six Featured Articles handpicked by our editors – you can find out more about them below.

 

 

Featured Articles

Tree-based inference of species interaction networks from abundance data
To be relevant, any network inference methodology needs to handle count data and to account for possible environmental effects. It also needs to distinguish between direct interactions and indirect associations, and graphical models provide a convenient framework for this purpose. A new method from Momal et al. meets these requirements and compares well with state-of-the-art approaches, even when the underlying graph strongly differs from a tree.

Modifying twisted nematic LCD screens to create dichromatic visual stimuli with LEDsPractical Tools
Didion et al. present a cost-effective way of modifying a twisted nematic LCD screen that utilises coloured LEDs, that allows measuring animals’ sensitivity to, and discrimination between, wavelengths of light. It has the benefit of not requiring a-priori knowledge of animals’ photoreceptor classes. This technique overcomes many of the limitations of RGB-based LCD screens in a cost-effective way, and allows more accurate testing of the role of colour in visually guided behaviours.x

moveVis: Animating movement trajectories in synchronicity with static or temporally dynamic environmental data in rApplication – Available Open Access
moveVis automates the processing of movement and environmental data to turn them into an animation. This includes (a) the regularisation of movement trajectories enforcing uniform time instances and intervals across all trajectories, (b) the frame-wise mapping of movement trajectories onto temporally static or dynamic environmental layers, (c) the addition of customisations, for example, map elements or colour scales and (d) the rendering of frames into an animation encoded as GIF or video file.

streamA simple, reliable method for long-term, in-stream data logger installation using rock-climbing softwarePractical Tools
Long-term deployment of in-stream data loggers provides valuable information about stream conditions, particularly in times when streams are difficult to sample manually. Fogg et al. present a method for data logger installation in streams using rock-climbing hardware that is simple to assemble, economical and minimally invasive.

Exploring density- and frequency-dependent interactions experimentally: An r program for generating hexagonal fan designsApplication
Species interactions and diversity are strongly impacted by local processes, with both the density of a focal species and its frequency in the community being important. Hexagonal fan designs can include a range of both densities and frequencies in a single plot, providing large economies in space and material. Rozins et al. present an R program whereby the user can rapidly view a variety of designs and determine the configurations that work best with their space and material constraints.

Multi-species occupancy models as robust estimators of community richness Understanding patterns of diversity is central to ecology and conservation, yet estimates of diversity are often biased by imperfect detection. Tingley et al. use both simulations and an empirical dataset to evaluate bias, precision, accuracy and coverage of estimates of N from multi-species occupancy models compared to the widely applied iChao2 non-parametric estimator.

Application and Practical Tools articles

We’ve got four Application and two Practical Tools articles in this month’s issue of Methods in Ecology and Evolution. Four of them have been covered in our Featured Articles above, so here are the other two:

GCM compareR: A web application to assess differences and assist in the selection of General Circulation Models for climate change researchice

Climate change research often relies on downscaled general circulation models (GCMs) to project future climate scenarios. As more than 35 GCMs are available at a resolution of 10km and finer, methods are needed to choose which GCM projection is appropriate to use for a region of interest. GCM compareR is a new open-source web app for comparing GCMs, allowing the informed selection from the range of available projections by researchers and policy makers.

AragoJ – A free, open-source software to aid single camera photogrammetry studies Close-range photogrammetry retrieves quantitative information about objects using photography. While software options for extracting information from 3D reconstructions exists, tools for 2D images are scarce, often tailored to specific applications. AragoJ is an open-source software, designed to integrate all steps in 2D close-range photogrammetry in a single program.

 

The flower on the cover

11.5 Cover jpeg

This issue’s cover shows an experimental array of Silene latifolia flowers, used to study the spread of the anther‐smut pathogen, Microbotryum lychnidis‐dioicae. The array contains a mixture of healthy and diseased flowers, where the influence of the pathogen is to replace the pollen with dark‐colored fungal spores that are conspicuous against the white flower background. Pollinators then pick up and distribute the spores during normal foraging visits.

In their article, Rozins et al. address the difficulty in designing experimental arrays that examine species interactions with a combination of density and frequency‐dependent effects. In addition to such vector‐borne disease transmission, local competition within plant communities are strongly influenced by density and frequency‐dependent responses to species composition and abundance. The authors demonstrate the merit of radial hexagonal fan designs over more traditional systematic grid arrays. To facilitate experimental studies and to ease implementation, they present an R program whereby the user can rapidly view a variety of designs and determine the configurations that work best with their space and material constraints. Photo credit: ©Michael E. Hood, Amherst College

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.

The Ecology of Dance

Post provided by Chloe Robinson

Dance has been part of human culture for millennia. Some scholars refer to dance as a specific language, dependent on the space and time in which it exists and dependent on the power structures that rule in that time. April 29th marks International Dance Day; a day initiated in 1982 by the International Dance Committee of the UNESCO International Theatre Institute to commemorate the birthday of Jean-Georges Noverre, a distinguished French choreographer.

Male Maratus volans peacock spider. Picture credit: Jürgen Otto.

For humans, dance is considered a sacred ritual, sometimes a form of communication and sometimes an important social and courtship activity. A recent study has even linked the innate ability to dance with greater survival rates in prehistoric times. However, for certain species of wild animal, dance-like behaviours are crucial for communication and mating. In this blog, I am going to highlight the evolutionary foundations of dance in wild animals and explore some of the ways that dance is used in ecology.

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2019 Robert May Prize Winner: Corneile Minnaar

The Robert May Prize is awarded annually for the best paper published in Methods in Ecology and Evolution by an Early Career Researcher. We’re delighted to announce that the 2019 winner is Corneile Minnaar, for his article ‘Using quantum dots as pollen labels to track the fates of individual pollen grains‘.

A central component of an organism’s fitness is its ability to successfully reproduce. This includes finding a potential mate and successful mating. For plants, movement of pollen from an anther to a conspecific stigma is essential for successful reproduction, but directly tracking movement of individual pollen grains heretofore has been impossible (with the exception of those species of orchids and milkweeds whose pollen comes in large packages (pollinia)). Knowing how pollen move around, whether or not they successfully fertilize ovules, is also central to understanding the evolution and ecology of flowering plants (angiosperms) and floral traits.

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Earth Day 2020: Monitoring Biodiversity for Climate Action

Post provided by Chloe Robinson

The demands of a growing human population are putting increasing pressure on the Earth’s natural systems and services. Dubbed the ‘Anthropocene’, we are currently living in a period where human actions are directly altering many earth processes, including atmospheric, geologic, hydrologic and biospheric processes. Climatic change and the resulting consequences, including rising temperatures, changing precipitation (i.e. rainfall, snow etc) and increase in frequency of storm events, represent the biggest challenge to our future and the life-support ecosystems that make our world habitable.

Artist’s interpretation of global climate change. Photo credit: Pete Linforth/Pixabay.

In 1970, Earth Day was launched as a modern environmental movement and a unified response to an environment in crisis. Earth Day has provided a platform for action, resulting in the creation of the Environmental Protection Agency (EPA), The Clean Air, Clean Water and Endangered Species Acts in the US and more globally. This year, 22 April marks the 50th anniversary of Earth Day, and the number one environmental crisis theme which needs immediate attention is ‘Climate Action’. Many of our ecosystems on earth are degrading at an alarming pace and we are currently experiencing a species loss at a rate of tens or hundreds of times faster than in the past. 

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Anacapa Toolkit: Automating the Cataloguing of Biodiversity

Post provided by Emily Curd

Imagine that you want to catalogue all of the biodiversity (all of the living organisms) from a particular location; how many trained experts would that require? How many person hours would it take to collect and identify all of the rare, well-disguised, and microscopic organisms? How many of these organisms would have to be removed from the environment and taken back to a lab for taxonomic analysis.

With eDNA, you can survey the presence of this gorgeous opalescent nudibranch without capturing or even touching it.
©Natural History Museum of Los Angeles County — Amanda Bemis & Brittany Cumming

Although there is no substitute for human expertise, we have begun using the traces of DNA that organisms leave behind (e.g. excretions, skin and hair cells) in the environment to catalogue biodiversity. These traces of DNA, referred to as environmental DNA, can persist in the environment for minutes or can persist for centuries depending on where they end up. This field of environmental DNA (eDNA) is rapidly becoming an effective tool to complement surveys of biodiversity, both past and present.

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