At Last, a Paleobiologist is a Senior Editor for Methods in Ecology and Evolution!

Post provided by Lee Hsiang Liow

An Asian, female Senior Editor under 45? Progressive! I have loved Methods in Ecology and Evolution since it appeared in 2010 and am thrilled to have been selected to join Rob, Bob and Jana to help with the journal’s continued development.

OK, so you want to know who the new Senior Editor on the MEE block is.  I’m just another scientist, I guess. On the outside, we look different but on the inside, we’re all the same. (OK, perhaps we are a little different, even on the inside, but that makes life and research interesting, right?)

Here’s my academic life history: I did my Bachelors thesis on the systematics/phylogenetics of an obscure group of marine pulmonate slugs with one of the greatest Icelandic biologists I know, Jon Sigurdsson, at the National University of Singapore. I followed this up with an almost-half-year stint at the Museum of Natural Science in Berlin as a “nobody”, digitizing data. Then I won the academic lottery and headed up to Uppsala to do my masters in conservation biology on tropical pollinator diversity, (un)supervised by two amazing supervisors that never met each other, the late Navjot Sodhi (National University of Singapore) and Thomas Elmqvist, now at Stockholm University. Continue reading

Decoupling Functional and Phylogenetic Dissimilarity between Organisms

Francesco de Bello describes the main elements of the method he has recently published in Methods in Ecology and Evolution. The method aims at decoupling and combining functional trait and phylogenetic dissimilarities between organisms. This allows for a more effective combination of non-overlapping information between phylogeny and functional traits. Decoupling trait and phylogenetic information can also uncover otherwise hidden signals underlying species coexistence and turnover, by revealing the importance of functional differentiation between phylogenetically related species.

In the video Francesco visually represents what the authors think their tool is doing with the data so you can see its potential. This method can provide an avenue for connecting macro-evolutionary and local factors affecting coexistence and for understanding how complex species differences affect multiple ecosystem functions.

This video is based on the article ‘Decoupling phylogenetic and functional diversity to reveal hidden signals in community assembly‘ by de Bello et al.


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.

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

New Associate Editors

Over the next few weeks we will be welcoming three new Associate Editors to Methods in Ecology and Evolution. Susan Johnston (University of Edinburgh, UK) became a member of the Associate Editor Board on Monday 5 October. She will be joined on 19 October by Natalie Cooper (Natural History Museum, London, UK) and finally by Luísa Carvalheiro (University of Brasília, Brazil) on 2 November. You can find out more about all three of our new Associate Editors below.

Susan Johnston

Susan Johnston“My research focuses on using genomic information to understand evolution in natural populations. I adapt mixed model approaches to determine the genetic architecture of interesting traits (e.g. estimating heritability, genome-wide association studies, outlier analyses) to examine its relationship with fitness or importance in local adaptation. I am interested in the potential of affordable genomics to answer evolutionary and ecological questions in wild systems, and how to deal with various statistical issues arising from such studies in small and/or structured populations.”

Susan’s most recently published article is ‘Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population‘, co-authored with T. Aykanat, P. Orell, E. Niemelä, J. Erkinaro and C.R. Primmer. The findings suggest that different evolutionary processes affect sub-populations of Atlantic salmon and that hybridization and subsequent selection may maintain low genetic differentiation without hindering adaptive divergence. This article was published in Molecular Ecology.

Natalie Cooper

Natalie Cooper“I am an evolutionary biologist, focusing mainly on macroevolution and macroecology. My interests include phylogenetic comparative methods, morphological evolution, using museum specimens in research, and integrating neontological and palaeontological data and approaches for understanding broad-scale patterns of biodiversity.”

Natalie has recently been published in Molecular Phylogenetics and Evolution (‘Effects of missing data on topological inference using a Total Evidence approach‘ with T. Guillerme) and in Evolution (‘Investigating evolutionary lag using the species-pairs evolutionary lag test (SPELT)‘ with C.L. Nunn). She was also a speaker at the Methods in Ecology and Evolution 5th Anniversary Symposium. Her presentation, ‘Limitations of Phylogenetic Comparative Methods‘, is freely available on YouTube.

Luísa Carvalheiro

Luisa Carvalheiro“My research focuses on community ecology & conservation. I have particular interest in the study of dynamics of biodiversity through time and space; and on the evaluation of how such biotic changes affect ecosystem functioning and ecosystem services, considering how the complex network of ecological interactions in which species are integrated mediates such changes.”

Earlier this year Luísa’s article ‘Susceptibility of pollinators to ongoing landscape changes depends on landscape history‘ (with J. Aguirre-Gutiérrez, J.C. Biesmeijer, E.E. van Loon, M. Reemer, and M.F. Wallis De Vries) was published in Diversity and Distributions. The article emphasizes the limited value of a one-size-fits-all biodiversity conservation measures and highlights the importance of considering landscape history when planning biodiversity conservation actions. This article is Open Access. Luísa was also the lead author of ‘The potential for indirect effects between co-flowering plants via shared pollinators depends on resource abundance, accessibility and relatedness‘ an Open Access article published in Ecology Letters last year.

We are thrilled to welcome Susan, Natalie and Luísa to the Associate Editor Board and we look forward to working with them over the coming years.

Top 10 speciation and evolution papers

Methods will be attending the next ITN Speciation conference 2012 in Jyväskylä, Finland and to mark the occasion, the editorial team has put together a list of some our most relevant work in speciation and evolution.

Applications – concise papers describing new software, equipment, or other practical tools:

Molecular ecology, phylogeny and evolution

If you are going there, stop by to talk to me, Graziella Iossa, journal coordinator. See you on 26-28 February, 2012, at the University of Jyväskylä, Finland!