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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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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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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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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Issue 11.4: Population Dynamics, Machine Learning, Morphometrics and More

The April issue of Methods is now online!

The latest issue of Methods in Ecology and Evolution is now online! This month’s issue is a little shorter than our last few. But, as they say, good things come in small packages!

Senior Editor Lee Hsiang Liow has selected six Featured Articles this month. You can find out about all of them below. We’ve also got five Applications articles and a Practical Tools article in the April issue that we’re going to cover. Those six papers are freely available to everyone – no subscription required!

On top of all that, the April issue includes articles on camera traps, land cover classification, presence-absence sampling and more.

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Hyperoverlap: Detecting Overlap in n-Dimensional Space

Post provided by Matilda Brown, Barbara Holland, and Greg Jordan

Overlap can help us to learn why Microcachrys
is now only found in the mountains of
Tasmania. ©Greg Jordan

There are many reasons that we might be interested in whether individuals, species or populations overlap in multidimensional space.  In ecology and evolution, we might be interested in climatic overlap, morphological overlap, phenological or biochemical overlap. We can use analyses of overlap to study resource partitioning, evolutionary histories and palaeoenvironmental conditions, or to inform conservation management and taxonomy. Even these represent only a subset of the possible cases in which we might want to investigate overlap between entities. Databases such as GBIF, TRY and WorldClim make vast amounts of data publicly available for these investigations. However, these studies require complex multivariate data and distilling such data into meaningful conclusions is no walk in the park.

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How Do You Measure Birdsong? Introducing Chipper

Post provided by Abigail Searfoss and Nicole Creanza

Today, science extends beyond the research bench or the fieldsite more often than ever before. Scientists are continuously interacting with educators and the general public, and people are reciprocating the interest with a drive to be involved.

A chipping sparrow. ©Kathy Malone, Nashville
chapter of the Tennessee Ornithology Society.

With this integration of science and the public, citizen-science efforts to crowdsource information have become increasingly popular (check out Zooniverse, SciStarter, NASA Citizen Science Projects, Project FeederWatch, and Foldit to get involved!). In the birding community, enthusiasts have been observing and recording birds for decades, but now there are methods for immediate data sharing among the community (eBird).

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Using Shark Scales to Unlock the Secrets of Historical Shark Communities on Coral Reefs

Post provided by Erin Dillon

Close your eyes for a second and imagine a coral reef. What do you think the shark community on that reef looked like historically?

Grey reef sharks on Palmyra Atoll’s forereef. ©Darcy Bradley.

Perhaps you imagined a remote reef with high shark abundance like Fakarava, French Polynesia or Palmyra Atoll, Northern Line Islands. Maybe you thought of a marine protected area such as Jardines de la Reina National Park in Cuba. Or perhaps you relied on your own memories from snorkeling on reefs in the past or photos of reefs taken decades ago.

The answer to this question depends on a reef’s location, given that shark abundances can vary with primary productivity and other oceanographic features. It also depends on which time period you chose as your reference point. Shark abundances can fluctuate over the course of a few hours – as well as over days to years to decades and beyond. Even if you chose the same time and place as the person before you, you might have come up with a slightly different answer. This variation in how we determine baselines – overlaid on a backdrop of natural variation in shark communities over space and time – can contribute to differing perceptions about what’s natural or what a depleted population can possibly be restored to.

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Issue 11.3: Tracking, Slicing, Classifying, Modelling and More

The March issue of Methods is now online!

The latest issue of Methods in Ecology and Evolution is now online! This month’s issue is a little shorter than our last few. But, as they say, good things come in small packages!

Executive Editor Aaron Ellison has selected six Featured Articles this month. You can find out about all of them below. We’ve also got five Applications articles in the March issue that we’re going to cover.

On top of all that, the March issue includes articles on 3D modelling, estimating plant density and more.

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2019 Robert May Early Career Researcher Prize Shortlist

Each year Methods in Ecology and Evolution awards the Robert May Prize to the best paper in the journal by an author at the start of their career. Today we present the shortlisted papers for 2019’s award, based on articles published in volume 10 of the journal.

The winner will be chosen by the journal’s Senior Editors in a few weeks. Keep an eye on the blog for the announcement.

This year’s shortlisted candidates are:

Extracting individual trees from lidar point clouds using treeseg – Andrew Burt

A quantitative framework for investigating the reliability of empirical network construction – Alyssa R. Cirtwill

A novel biomechanical approach for animal behaviour recognition using accelerometers – Pritish Chakravarty

Anacapa Toolkit: An environmental DNA toolkit for processing multilocus metabarcode datasets – Emily E. Curd

MistNet: Measuring historical bird migration in the US using archived weather radar data and convolutional neural networks – Tsung‐Yu Lin

Using quantum dots as pollen labels to track the fates of individual pollen grains – Corneile Minnaar

Untangling direct species associations from indirect mediator species effects with graphical models – Gordana C. Popovic

Matrix methods for stochastic dynamic programming in ecology and evolutionary biology – Jody R. Reimer

Current and emerging statistical techniques for aquatic telemetry data: A guide to analysing spatially discrete animal detections – Kim Whoriskey

Over the next month or so, we’ll be finding out more about these articles. You’ll be able to keep up to date with all of the Robert May Prize news here.