Tag: evolution

Journal updates

Issue 7.11

Issue 7.11 is now online!

The November issue of Methods is now online!

This month’s issue contains four Applications articles and two Open Access articles, all of which are freely available.

– moveHMM: This R package allows ecologists to process GPS tracking data into series of step lengths and turning angles, and to fit a hidden Markov model to these data, allowing, in particular, for the incorporation of environmental covariates.

– BORIS: An open-source and multiplatform standalone program that allows a user-specific coding environment to be set for a computer-based review of previously recorded videos or live observations. Being open to user-specific settings, the program allows a project-based ethogram to be defined that can then be shared with collaborators, or can be imported or modified.

– inbreedR: An R package that provides functions to measure variance in inbreeding – through the strength of correlation in heterozygosity across marker loci – based on microsatellite and SNP markers with associated P-values and confidence intervals. Within the framework of Heterozygosity–fitness correlation theory, inbreedR also estimates the impact of inbreeding on marker heterozygosity and fitness.

– Terrestrial Precipitation Analysis: This package is comprised of the Precipitation Trends (P-Trend), Precipitation Attributes (P-Att) and Precipitation Manipulation (P-Man) tools. Combined, these web tools allow researchers to easily calculate fundamental precipitation statistics for past, present and projected future precipitation regimes for any terrestrial location in the world.

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Unknown's avatarIndia StephensonLeave a comment
Evolution, Methods papers

Flawed Analysis Casts Doubt on Years of Evolution Research

Below is a press release about the Methods in Ecology and Evolution paper ‘‘Residual diversity estimates’ do not correct for sampling bias in palaeodiversity data‘ taken from the University of Bristol.

Years of research on the evolution of ancient life, including the dinosaurs, have been questioned after a fatal flaw in the way fossil data are analysed was exposed by scientists from the universities of Reading and Bristol.

Studies based on the apparently flawed method have suggested Earth’s biodiversity remained relatively stable – close to maximum carrying capacity – and hinted many signs of species becoming rapidly extinct are merely reflections on the poor quality of the fossil record at that time.

However, new research by scientists at the University of Reading suggests the history of the planet’s biodiversity may have been more dynamic than recently suggested, with bursts of new species appearing, along with crashes and more stable periods.

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Unknown's avatarIndia StephensonLeave a comment
Journal updates

Issue 7.10

Issue 7.10 is now online!

The October issue of Methods is now online!

This month’s issue contains three Applications articles and two Open Access articles, all of which are freely available.

– CODYN: New analytical tools applied to long-term data demonstrate that ecological communities are highly dynamic over time. The R package, library(“codyn”), helps ecologists implement these tools and gain insi–ghts into ecological community dynamics.

– Geometric Morphometrics: A tool for the R statistical environment that optimises the smoothing procedure for 3D surfaces used in Geometric Morphometrics.

– TRAPPER: Open source, multi-user software that facilitates analysis of videos and images, provides spatial filtering and web-mapping, allows flexible implementation of specific data collection protocols, and supports data re-use and (re)discovery.

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Unknown's avatarIndia StephensonLeave a comment
Uncategorized

Peer Review Week: Should we use double blind peer review? The evidence…

Non-blind Peer Review Monster

This week is Peer Review Week, the slightly more popular academic celebration than pier review week. Peer review is an essential part of scientific publication and is – like Churchill’s democracy – the worst system to do it. Except for all of the others. The reason it’s imperfect is mainly that it’s done by people, so there is a natural desire to try to improve it.

One suggestion for improvement is to us double blind reviews. At the moment most journals (including Methods in Ecology and Evolution) use single blind reviewing, where the author isn’t told the identity of the reviewers. The obvious question is whether double blind reviewing does actually improve reviews: does it reduce bias, or improve quality? There have been several studies in several disciplines which have looked at this and related questions. After having looked at them, my summary is that double blind reviewing is fairly popular, but makes little or no difference to the quality of the reviews, and reviewers can often identify the authors of the papers.

Continue reading “Peer Review Week: Should we use double blind peer review? The evidence…”

Unknown's avatarBob O'H12 Comments
Publishing Tips & Tricks

What Makes a Good Peer Review: Peer Review Week

For many academics, especially Early Career Researchers, writing a review can seem like quite a daunting task. Direct training is often hard to come by and not all senior academics have the time to act as mentors. As this week is Peer Review Week, we wanted to provide some advice on what makes a good review and what makes a bad review. This advice has been kindly provided by the Methods in Ecology and Evolution Associate Editors – all of whom are authors and reviewers as well.

The BES Guide to Peer Review in Ecology and Evolution
The BES Guide to Peer Review in Ecology and Evolution

Before we dive into the tips from our Editors though, we want to highlight one of the best resources for anyone looking for peer review guidance – the BES Guide to Peer Review in Ecology and Evolution. This booklet is intended as a guide for Early Career Researchers, who have little or no experience of reviewing journal articles but are interested in learning more about what is involved. It provides a succinct overview of the many aspects of reviewing, from hands-on practical advice about the actual review process to explaining less tangible aspects, such as reviewer ethics. You can get the PDF version of the guide (and the other BES guides) for free on the BES website. Continue reading “What Makes a Good Peer Review: Peer Review Week”

Unknown's avatarIndia Stephenson8 Comments
Uncategorized

Thank You to All of Our Reviewers: Peer Review Week 2016

As many of you will already know, this week is Peer Review Week (19-25 September). Peer Review Week is a global event celebrating the vital work that is done by reviewers in all disciplines. To mark the week, we will be having a series of blog posts about peer review. The theme for this year’s Peer Review Week is recognition for review and we’re starting … Continue reading Thank You to All of Our Reviewers: Peer Review Week 2016

Unknown's avatarIndia StephensonLeave a comment
Journal updates

Issue 7.9

Issue 7.9 is now online!

The September issue of Methods is now online!

This month’s issue contains two Applications articles and three Open Access articles, all of which are freely available.

– Arborist Throw-Line Launcher: A cost-effective and simple alternative for collecting leaves and seeds from tall trees. The authors have also provided some tutorial videos on YouTube.

– ctmm: An R package which implements all of the continuous-time stochastic processes currently in use in the ecological literature and couples them with powerful statistical methods for autocorrelated data adapted from geostatistics and signal processing.

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Unknown's avatarIndia StephensonLeave a comment
Editor Profiles, Journal updates

New Associate Editor: Michael Morrissey

Today, we are pleased to be welcoming a new member of the Methods in Ecology and Evolution Associate Editor Board. Michael Morrissey joins us from the University of St Andrews in Scotland and you can find out a little more about him below.

Michael Morrissey

“I am an evolutionary quantitative geneticist. I am interested in the selection, genetics, and evolutionary trajectories of traits in natural populations. I typically work at the interface of statistics, evolutionary theory, and empirical problems.”

Michael has been an active reviewer for Methods for the past few years and has provided excellent comments and recommendations on a number of papers. He also had an article – ‘In search of the best methods for multivariate selection analysis‘ – published in the journal in 2014 (which will become freely available in October this year).
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Unknown's avatarIndia StephensonLeave a comment
Journal updates

Issue 7.8

Issue 7.8 is now online!

The August issue of Methods is now online!

This month’s issue contains two Applications articles and two Open Access articles, all of which are freely available.

– Plant-O-Matic: A free iOS application that combines the species distribution models with the location services built into a mobile device to provide users with a list of all plant species expected to occur in the 100 × 100 km geographic grid cell corresponding to the user’s location.

– RClone: An R package built upon genclone software which includes functions to handle clonal data sets, allowing:

  • Checking for data set reliability to discriminate multilocus genotypes (MLGs)
  • Ascertainment of MLG and semi-automatic determination of clonal lineages (MLL)
  • Genotypic richness and evenness indices calculation based on MLGs or MLLs
  • Describing several spatial components of clonality

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Unknown's avatarIndia StephensonLeave a comment
Journal updates

Issue 7.7

Issue 7.7 is now online!

The July issue of Methods is now online!

This month’s issue contains two Applications articles and two Open Access articles, all of which are freely available.

– MO-Phylogenetics: A software tool to infer phylogenetic trees optimising two reconstruction criteria simultaneously and integrating a framework for multi-objective optimisation with two phylogenetic software packages.

– PHYLOMETRICS: An efficient algorithm to construct the null distributions (by generating phylogenies under a trait state-dependent speciation and extinction model) and a pipeline for estimating the false-positive rate and the statistical power of tests on phylogenetic metrics..

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Unknown's avatarIndia Stephenson1 Comment