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.

Issue 6.9

Issue 6.9 is now online!

The September issue of Methods is now online!

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

POPART: An integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication-ready figure production. The package also provides a platform for the implementation and distribution of new network-based methods.

Michalis Vardakis et al. provide this month’s first Open Access article. In ‘Discrete choice modelling of natal dispersal: ‘Choosing’ where to breed from a finite set of available areas‘ the authors show how the dispersal discrete choice model can be used for analysing natal dispersal data in patchy environments given that the natal and the breeding area of the disperser are observed. This model can be used for any species or system that uses some form of discrete breeding location or a certain degree of discretization can be applied.

Our September issue also features articles on Animal Movement, Population Dynamics, Statistical Ecology, Biodiversity, Conservation Biology and much more. Continue reading

National Wildlife Day 2015

Happy National Wildlife Day everyone!

Today is 10th National Wildlife Day. As we have done for a few awareness days this year (Bats, Biodiversity and Bees so far) we are marking the day by highlighting some of our favourite Methods in Ecology and Evolution articles on the subject. Obviously ‘wildlife’ is a pretty big topic, so we have narrowed our focus (slightly) to monitoring wildlife (with one or two additional papers that we didn’t want to leave out).

This list is certainly not exhaustive and there are many more wonderful articles on these topics in the journal. You can see more of them on the Wiley Online Library.

If you would like to learn more about National Wildlife Day, you may wish to visit the organisation’s website, follow them on Twitter and Facebook or check out today’s hashtag: #NationalWildlifeDay.

Without further ado though, please enjoy our selection of Methods articles for National Wildlife Day:

Integrating Demographic Data

Our National Wildlife Day celebration begins with an article from our EURING Special Feature. Robert Robinson et al. present an approach which allows important demographic parameters to be identified, even if they are not measured directly, in ‘Integrating demographic data: towards a framework for monitoring wildlife populations at large spatial scales‘. Using their approach they were able to retrieve known demographic signals both within and across species and identify the demographic causes of population decline in Song Thrush and Lawping.


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National Honey Bee Day 2015

Happy National Honey Bee Day everyone!

As you may know, tomorrow (Saturday 22 August) is National Honey Bee Day in the USA. To mark the day we will be highlighting some of the best papers that have been published on bees and pollinators in Methods in Ecology and Evolution.

You can find out more about National Honey Bee Day (and about bees in general) HERE.

Without further ado though, here are a few of the best Methods papers related to Honey Bees:

Wildebeast graze on the cover of MEE 2.5Honey Bee Risk Assessment

Our Honey Bee highlights begin with Hendriksma et al.’s article ‘Honey bee risk assessment: new approaches for in vitro larvae rearing and data analyses‘. Robust laboratory methods for assessing adverse effects on honey bee brood are required for research into the issues contributing to global bee losses. To facilitate this, the authors of this article recommend in vitro rearing of larvae and suggest some appropriate statistical tools for the related data analyses. Together these methods can help to improve the quality of environmental risk assessment studies on honey bees and secure honey bee pollination. As this article was published over two years ago, it can be accessed for free by anyone.

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Advances in Phylogenetic Methods – The Applications Papers

Original Image ©PLOS One Phylogeny

Original Image ©PLOS One Phylogeny

Timed to coincide with Evolution 2015, we have released a new Virtual Issue on Phylogenetic Methods. All of the articles in this Virtual Issue will be freely available for a limited period.

On Friday, we gave some more information about the research articles in this Virtual Issue. In this post, we will be focusing on the Applications papers.

Applications papers introduce new tools for research, which provide practitioners with an important source of information and background on the tools they use. In this Virtual Issue we have highlighted the newest Applications papers that describe how phylogenetic methods are contributing to the fields of ecology and evolution. These include tools with aims as diverse as phylogenetic tree reconstruction and analysing phylogenetic diversity in communities. All Applications papers, not just those in the Virtual Issue, are free to access.

You can see a little more information on each of the Applications Papers below.

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Virtual Issue: Advances in Phylogenetic Methods

Original Image ©PLOS One Phylogeny

Original Image ©PLOS One Phylogeny

Timed to coincide with Evolution 2015, we have released a new Virtual Issue on Phylogenetic Methods. All of the articles in this Virtual Issue will be freely available for a limited period.

An understanding of the tree of life contributes to many facets of biology. This Virtual Issue has assembled studies that showcase the breadth of the utility of phylogenetic trees, including phylogenetic beta diversity, trait evolution, diversification, biodiversity studies, phylogenetic signal, biogeography, ecosystem functioning, and host-pathogen dynamics.

The Research papers included are excellent examples of new ways that phylogenies can be applied to central questions in ecology, evolution and biodiversity, such as measuring niche conservatism, trait evolution and diversification rates. The issue also has articles on barcoding methods, which increasingly are used to understand phylogenetic and functional diversity.

You can see a little more information on each of the articles below.

Continue reading

What is Beta Diversity?

Post provided by Dr Andrés Baselga

Dr Andrés Baselga

A key property of biodiversity is that it is not evenly distributed around the world. In other words, different sites are usually  home to different biological communities. Quantifying the differences among biological communities is a major step towards understanding how and why biodiversity is distributed in the way it is.

The term beta diversity was introduced by R.H. Whittaker in 1960. He defined it as “the extent of change in community composition, or degree of community differentiation, in relation to a complex-gradient of environment, or a pattern of environments”. In his original paper, Whittaker proposed several ways to quantify beta diversity. In its simplest form (which we will call strict sense or multiplicative beta diversity), beta diversity is defined as the ratio between gamma (regional) and alpha (local) diversities (Whittaker, 1960; Jost, 2007). Therefore, it is the effective number of distinct compositional units in the region (Tuomisto, 2010). Essentially, beta diversity quantifies the number of different communities in the region. So it’s clear that beta diversity does not only account for the relationship between local and regional diversity, but also informs about the degree of differentiation among biological communities. This is because alpha and gamma diversities are different if (and only if) the biological communities within the region are different.

It’s easy to demonstrate how beta diversity varies from the minimum to the maximum differentiation of local assemblages in a region. For simplicity, we will quantify biological diversity as species richness (number of species), but it’s important to remember that alpha, beta and gamma diversities can also be defined to account for richness and relative abundances (see Jost, 2007 for a detailed explanation). When local assemblages are all identical (minimum differentiation), alpha diversity equals gamma diversity, and beta diversity equals 1 (figure below).


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International Day for Biological Diversity 2015

Happy International Day for Biological Diversity everyone!

As you may know, today (Friday 22 May) is the United Nations Day for Biodiversity and we are celebrating by highlighting some of the best papers that have been published on biodiversity in Methods in Ecology and Evolution. This is by no means an exhaustive list and you can find many more articles on similar topics on the Wiley Online Library (remember, if you are a member of the BES, you can access all Methods articles free of charge).

If you would like to learn more about the International Day for Biological Diversity, you may wish to visit the Convention on Biological Diversity website, follow them on Twitter or check out today’s hashtag: #IBD2015.

Without further ado though, here are a few of the best Methods papers on Biological Diversity:

Methods Cover - August 2012Biodiversity Soup

We begin with an Open Access article from one of our Associate Editors, Douglas Yu (et al.). This article was published in the August issue of 2012 and focuses on the metabarcoding of arthropods. The authors present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. They also demonstrate that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within-community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information.

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Traits, community ecology and demented accountants

McGill et al. (2006) argued that community ecology had lost its way. Shipley (2010) accused community ecologists of acting like a bunch of demented accountants. Strong words – so what’s the issue exactly?  And what can we do about it?

Dannymanic Image

Doing some end-of-financial-year field work? © Dannymanic

Their beef was that when studying groups of species and their environmental association, ecologists often were not thinking enough about the reasons for variation across species. (In this post we’ll focus on variation in abundance or in environmental response of abundance across species. We’re interpreting “abundance” loosely – counts, biomass, 1-0, whatever.)  While alternative methods are more readily available nowadays, “accountancy” is still common.

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Bat Appreciation Day: The Latest Methodological Advances

Post provided by Kate Jones and the Biodiversity Modelling Research Group

The Funnel-eared bat (Natalus stramineus)

The Funnel-eared bat (Natalus stramineus) – © Veronica Zamora-Gutierrez

Today (17 April) is Bat Appreciation Day! Yes I know, a whole day to appreciate bats. Although my biodiversity modelling research group at University College London would argue that 24 hours is just not enough time to appreciate these cool, yet misunderstood animals, we wanted to mark the day by giving MEE a round-up of the latest methodological advances in bat monitoring and what we hope to see in the next few years.

Bat Detectives and Machine Learning

oisin_pictureOisin Mac Aodha PostDoc – If you have ever tried to spot bats flying around at night you will know that it can be very difficult. However, bats leak information about themselves into the environment in the form of the sounds they make while navigating and feeding. These calls are often too high for us to hear, but we can use devices known as bat detectors to transform them into a form that we can record and listen to. Monitoring bat populations over wide areas or long periods can result in huge amounts of data which is difficult to analyse though. To address this problem, our group, along with Zooniverse, have setup a citizen science project called Bat Detective which asks members of the public help us find bat calls in audio recordings that have been collected from all over Europe (the infographic below gives a bit more information on this). We have had an amazing response to date and our detectives have already located several thousand bat calls. However, to scale up monitoring, we need more automated methods of detecting calls. Using the analysis provided by our Bat Detectives, we are currently working on building algorithms that can automatically tell us if a recording contains a bat call.

In this video we see a visual representation of an audio signal called a spectrogram that features several bat calls. On top you see the result of an automated method we have developed for detecting bat calls. The larger the value, the more certain the algorithm is that there is a bat call at that point in time. Continue reading