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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Issue 7.6: Methods in Ecology and Evolution 5th Anniversary Special Feature

Issue 7.6 is now online!

The June issue of Methods, which includes our latest Special Feature – “5th Anniversary of Methods in Ecology and Evolution” – is now online!

Our 5th Anniversary Special Feature is a collection of six articles (plus an Editorial from Executive Editor Rob Freckleton) that highlights the breadth and depth of topics covered by the journal so far. It grew out of our 5th Anniversary Symposium – a joint event held in London, UK and Calgary, Canada and live-streamed around the world in April 2015 – and contains papers by Associate Editors, a former Robert May prize winner and regular contributors to the journal.

The six articles are based on talks given at last May’s Symposium. They focus on:

In his Editorial for the Special Feature, Rob Freckleton looks to the future. In his words: “we hope to continue to publish a wide range of papers on as diverse a range of topics as possible, exemplified by the diversity of the papers in this feature”.

All of the articles in the Special Feature will be freely available for a limited time. In addition to this, two of the articles (Shedding light on the ‘dark side’ of phylogenetic comparative methods and Perturbation analysis of transient population dynamics using matrix projection models) are Open Access.
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RPANDA: A Time Machine for Evolutionary Biologists

Post provided by HÉLÈNE MORLON

Yesterday saw the start of this year’s annual Evolution meeting and to celebrate Hélène Morlon has written a blog post discussing the amazingly versatile RPANDA package that she is developing with her research group. A description of RPANDA was published in the journal earlier this year and, like all our Applications papers, is freely available to read in full.

If you are attending Evolution, as well as attending the fabulous talks mentioned by Hélène below, do stop by booth 125 to see our BES colleague Simon Hoggart. Simon is the Assistant Editor of Journal of Animal Ecology and would be happy to answer your questions about any of our journals or any of the other work we do here at the BES.

RPANDA: a time machine for evolutionary biologists

Imagine “Doc”, Marty’s friend in Back to the Future, trying to travel back millions of years in an attempt to understand the history of life. Instead of building a time machine from a DeLorean sports car powered by plutonium, he could dig fossils, or more likely, he would use molecular phylogenies.

Molecular phylogenies are family trees of species that can be built from data collected today: the genes (molecules) of present-day species (Fig 1). They are often thought of as trees, in reference to Darwin’s tree of life. The leaves represent the present: species that can be found on Earth today. The branches represent the past: ancestral species, which from time to time split, giving rise to two independent species. The structure of the tree tells us which species descend from which ancestors, and when their divergence happened.

birds_phylog

Fig 1: The phylogenetic tree of all birds (adapted from Jetz et al. 2012). Each bird order is represented by a single bird silloutter and a specific colour (the most abundant order of Passeriformes, for example is represented in dark orange). Each terminal leaf represents a present-day bird species, while internal branches represent the evolutionary relationships among these species.

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Issue 7.5

Issue 7.5 is now online!

The May 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.

piecewiseSEM: A practical implementation of confirmatory path analysis for the R programming language. This package extends the method to all current (generalized) linear, (phylogenetic) least-square, and mixed effects models, relying on familiar R syntax. The article also includes two worked examples.

 RPANDA: An R package that implements model-free and model-based phylogenetic comparative methods for macroevolutionary analyses. It can be used to:

  1. Characterize phylogenetic trees by plotting their spectral density profiles
  2. Compare trees and cluster them according to their similarities
  3. Identify and plot distinct branching patterns within trees
  4. Compare the fit of alternative diversification models to phylogenetic trees
  5. Estimate rates of speciation and extinction
  6. Estimate and plot how these rates have varied with time and environmental variables
  7. Deduce and plot estimates of species richness through geological time. Continue reading

New Associate Editor: Will Pearse

Today, we are pleased to be welcoming a new member of the Methods in Ecology and Evolution Associate Editor Board. Will Pearse joins us from McGill University in Canada and you can find out a little more about him below.

Will Pearse

“I am an evolutionary ecologist and use phylogeny to link the evolution of species’ traits with their ecological community assembly. I’m interested in phylogenetic methods, macro-evolution of species’ traits, community assembly and developing new statistical tools for all of the above.”

Will is a former winner of the Robert May Early Career Researcher Award. He won the prize in 2013 for his Applications article ‘phyloGenerator: an automated phylogeny generation tool for ecologists‘ (co-authored with Andy Purvis). phyloGenerator is an open-source, stand-alone Python program, that makes use of pre-existing sequence data and taxonomic information to largely automate the estimation of phylogenies. He has also recently had a paper on a R package that allows for measurement, modelling and simulation of phylogenetic structure in ecological data published in Bioinformatics. The article, ‘pez: phylogenetics for the environmental sciences‘, was co-authored with Marc CadotteJeannine Cavender-BaresAnthony IvesCaroline TuckerSteve Walker and Matthew Helmus.

We are thrilled to welcome Will as a new Associate Editor and we look forward to working with him on the journal.

Demography and Big Data

Post provided by BRITTANY TELLER, KRISTIN HULVEY and ELISE GORNISH

Follow Brittany (@BRITTZINATOR) and Elise (@RESTORECAL) on Twitter

To understand how species survive in nature, demographers pair field-collected life history data on survival, growth and reproduction with statistical inference. Demographic approaches have significantly contributed to our understanding of population biology, invasive species dynamics, community ecology, evolutionary biology and much more.

As ecologists begin to ask questions about demography at broader spatial and temporal scales and collect data at higher resolutions, demographic analyses and new statistical methods are likely to shed even more light on important ecological mechanisms.

Population Processes

Midsummer Opuntia cactus in eastern Idaho, USA. © B. Teller.

Midsummer Opuntia cactus in eastern Idaho, USA. © B. Teller.

Traditionally, demographers collect life history data on species in the field under one or more environmental conditions. This approach has significantly improved our understanding of basic biological processes. For example, rosette size is a significant predictor of survival for plants like wild teasel (Werner 1975 – links to all articles are at the end of the post), and desert annual plants hedge their bets against poor years by optimizing germination strategies (Gremer & Venable 2014).

Demographers also include temporal and spatial variability in their models to help make realistic predictions of population dynamics. We now know that temporal variability in carrying capacity dramatically improves population growth rates for perennial grasses and provides a better fit to data than models with varying growth rates because of this (Fowler & Pease 2010). Moreover, spatial heterogeneity and environmental stochasticity have similar consequences for plant populations (Crone 2016). Continue reading

Issue 7.2: Demography Beyond the Population

Issue 7.2 is now online!

Sagebrush steppe in eastern Idaho, USA

© Brittany J. Teller

The February issue of Methods is now online! As you may have seen already, it includes the BES cross-journal Special Feature: “Demography Beyond the Population“. There are also eight other wonderful articles to read.

We have four articles in the Demography Beyond the Symposium Special Feature. You can read an overview of them by two of the Feature’s Guest Editor Sean McMahon and Jessica Metcalf here (Sean and Jessica are also Associate Editors of Methods).

If you’d like to find out more about each of the individual papers before downloading them, we have blog posts about each one. Daniel Falster and Rich Fitzjohn discuss the development of plant and provide some advice on creating simulation models in Key Technologies Used to Build the plant Package (and Maybe Soon Some Other Big Simulation Models in R). There is a look back at the evolution of Integral Projection Models from Mark Rees and Steve Ellner in How Did We Get Here From There? A Brief History of Evolving Integral Projection Models. In Inverse Modelling and IPMs: Estimating Processes from Incomplete Information Edgar González explains how you can estimate process that you can’t observe. And keep an eye out for Brittany Teller’s blog post coming next week!

Don’t wait too long to get the Demography Beyond the Population Special Feature papers though, they’re freely available for a limited time only

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Methods in Ecology and Evolution 2015: The Year in Review

Happy New Year! We hope that you all had a wonderful Winter Break and that you’re ready to start 2016. We’re beginning the year with a look back at some of our highlights of 2015. Here’s how last year looked at Methods in Ecology and Evolution.

The Articles

We published some amazing articles in 2015, too many to mention them all here. However, we would like to say a massive thank you to all of the authors, reviewers and editors who contributed to the journal last year. Without your hard work, knowledge and generosity, the journal would not be where it is today. We really appreciate all of your time and effort. THANK YOU!

mee312268_CoverOpportunities at the Interface between Ecology and Statistics

There was only one Special Feature in the journal this year, but it was a great one. Arising from the 2013 Eco-Stats Symposium at the University of New South Wales and guest edited by Associate Editor David Warton, Opportunities at the Interface between Ecology and Statistics was one of the highlights of 2015 for us. It consists of seven articles written collaboratively by statisticians and ecologists and highlights the benefits of cross-disciplinary partnerships. Continue reading

New Associate Editor: Anne Chao

Today, we are pleased to be welcoming a new member of the Methods in Ecology and Evolution Associate Editor Board. Anne Chao joins us from the National Tsing Hua University in Taiwan and you can find out a little more about her below.

Anne Chao

Anne Chao

“I am 60% statistician, 30% mathematician and 10% ecologist. Mathematical and statistical problems in ecology and evolution fascinate me. My current research interests include statistical inferences of biodiversity measures (for example taxonomic, phylogenetic, and functional diversities along with related similarity/differentiation indices), and statistical analysis of ecological and environmental survey data (such as standardising biological samples and rarefaction/extrapolation techniques).”

Anne has been very engaged with the journal over the past few years as a regular reviewer and as an author. Her first article in Methods, Entropy and the species accumulation curve‘ (written with YT Wang and Lou Jost) was published in 2013 and is now freely available. Continue reading

Issue 6.11

Issue 6.11 is now online!

The November issue of Methods is now online!

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

mvMORPH: A package of multivariate phylogenetic comparative methods for the R statistical environment which allows fitting a range of multivariate evolutionary models under a maximum-likelihood criterion. Its use can be extended to any biological data set with one or multiple covarying continuous traits.

Low-cost soil CO2 efflux and point concentration sensing systems: The authors use commercially available, low-cost and low-power non-dispersive infrared (NDIR) CO2 sensors to develop a soil CO2 efflux system and a point CO2 concentration system. Their methods enable terrestrial ecologists to substantially improve the characterization of CO2 fluxes and concentrations in heterogeneous environments.

This month’s Open Access article comes from Jolyon Troscianko and Martin Stevens. In ‘Image calibration and analysis toolbox – a free software suite for objectively measuring reflectance, colour and pattern‘ they introduce a toolbox that can convert images to correspond to the visual system (cone-catch values) of a wide range of animals, enabling human and non-human visual systems to be modelled. The toolbox is freely available as an addition to the open source ImageJ software and will considerably enhance the appropriate use of digital cameras across multiple areas of biology. In particular, researchers aiming to quantify animal and plant visual signals will find this useful. This article received some media attention upon Early View publication over the summer. You can read the Press Release about it here.

Our November issue also features articles on Population Genetics, Macroevolution, Modelling species turnover, Abundance modelling, Measuring stress and much more. Continue reading