The Field Guide to Sequence-Based Identification of Biodiversity: An Interview with Simon Creer

In a new Methods in Ecology and Evolution podcast, Georgina Brennan (Bangor University) interviews Simon Creer (Bangor University) about his article ‘The ecologist’s field guide to sequence-based identification of biodiversity‘. They talk about about where the idea for the paper came from, what it’s aim are and who will benefit from it. We hear how new sequences can improve and enhance current biomonitoring programmes (and make them quicker and cheaper).

To find out more about Sequence-based Identification of Biodiversity, read the Open Access Methods in Ecology and Evolution article ‘The ecologist’s field guide to sequence-based identification of biodiversity‘.


Achieving Reproducibility in Research

Earlier this month Leila Walker attended a panel discussion imparting ‘Practical Tips for Reproducible Research’, as part of the Annual Meeting of the Macroecology Special Interest Group (for an overview of the meeting as a whole check out this Storify). The session and subsequent drinks reception was sponsored by Methods in Ecology and Evolution. Here, Leila reports back on the advice offered by the panel members.

For anyone interested in viewing further resources from the session, please see here. Also, you may like to consider attending the best practice for code archiving workshop at the 2016 BES Annual Meeting. Do you have any tips for making your research reproducible? Comment on this post or email us and let us know!

This year’s Annual Meeting of the Macroecology SIG was the biggest yet, with around 75 attendees and even representation across the PhD, post-doc and faculty spectrum. The panel discussion aimed to consider what reproducibility means to different people, identify the reproducibility issues people struggle with, and ultimately provide practical tips and tools for how to achieve reproducible research. Each of the participants delivered a short piece offering their perspective on reproducibility, with plenty of opportunity for discussion during the session itself and in the poster and wine reception that followed.

Attendees enjoy a wine reception (sponsored by MEE) whilst viewing posters and reflecting on the Reproducible Research panel discussion. Photo credit: Leila Walker

Attendees enjoy a wine reception (sponsored by MEE) whilst viewing posters and reflecting on the Reproducible Research panel discussion. Photo credit: Leila Walker

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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.

Towards a More Reproducible Ecology

The following post has been provided by Dr Nick Isaac.

Nick is organising the OpenData and Reproducibility Workshop at Charles Darwin House, London on 21 April 2015 (more information below). He is also an Associate Editor for Methods in Ecology and Evolution.

Macro_finalThe open science movement has been a major force for change in how research is conducted and communicated. Reproducibility lies at the heart of the open science agenda. It’s a broad topic, covering how data are shared, interpreted and reported.

Reproducibility has been advanced by a coalition of publishers (who have been embarrassed by a series of high-profile retractions), funding agencies keen that data should be re-useable after the life of a grant, and young researchers taking a more collaborative attitude than previous generations.

There is now a vast range of tools and platforms to help scientists share data and other materials (e.g. Dryad, Github, Figshare) and to create efficient and reproducible workflows (e.g. Sweave, Markdown, Git and, of course, R). There’s even a MOOC (Massive Open Online Course) in Reproducible Research, run out of Johns Hopkins University.

Ecology has lagged behind wet-lab biology and other disciplines in the adoption of reproducibility concepts and there are few examples of ecological studies that are truly reproducible. To address this, we’re running a one-day workshop at Charles Darwin House, London on Tuesday 21 April entitled OpenData & Reproducibility Workshop: the Good Scientist in the Open Science era. Continue reading

New associate editor

Methods is pleased to announce that Nick Isaac has become the newest member of its editorial board, taking up the role of Associate Editor. Nick is a macroecologist at the Centre for Ecology and Hydrology interested in questions about the abundance, distributions, diversity and extinction risk of species:

My research generally involves data that are structured in space, time and/or phylogenetically. I started out using the traditional approach in macroecology of ‘one value per species’, but increasingly I use multilevel models to explore patterns along multiple axes (space, time, species) and at a range of scales. Much of my work has involved developing new methods and/or comparing their statistical properties with existing approaches. Historically I used data on mammals and other vertebrates, but these days I work mostly on insects.

Welcome on board Nick!

Methods in Biogeography

The International Biogeography Society has just held their 5th meeting in Crete and I thought I would pick some highlights that are methods relevant.  This meeting brings together a range of researchers from the intersection of ecology, evolutionary biology, geography, geology and systematics: a truly diverse grouping.

Biogeography is, in essence concerned with the distributions of species and how these change with time. It is no surprise then that phylogenetic analysis was the focus of many talks. Indeed, if there is one thing that sets the talks I saw at this meeting apart from those at more ‘ecological’ meetings, it is the heavy reliance on phylogenetic methods. Relatively recently developed methods for looking at phylogenetic structure in ecological communities were particularly in evidence.

Three talks were particularly methods focussed and described really interesting new approaches and perspectives.

Andy Purvis of Imperial College, UK, looked at how macroevolutionary questions could be tested using different methods and data. His talk emphasised that evolutionary models can be varied and that broad-scale analyses that assume single models could be misleading. For example, using data on all mammal species he showed that the evolution of body mass could be described using an ‘early burst’ model; however when broken up into individual orders, the picture was a highly variable one with different models fitting best to some orders rather than others, and very different rates across groups.

Andy also dealt with niche conservatism, another big theme at this meeting. Niche conservatism is the idea that closely related species share their niches because they inherit them from ancestors. If niches are generally conserved then this is important because, for example, changes to climate or habitat may affect taxonomic groups of species that share similar requirements, or that are historically slow to adapt. Andy made the good point that current definitions are sometimes at odds with each other, and that notions of niche conservatism need to be clearly spelled out.

Also from Imperial, Ally Phillimore took a different perspective. The aim in his research is to link small-scale ecological processes with macroevolution. He described an elegant method for linking within and between population spatial and temporal variation to explore the degree to which adaptation and plasticity drive phenological responses to climate change. Using data on data gathered by the public on egg laying dates in frogs in the UK, Ally showed how his approach could be used to predict how fast populations need to evolve in order to keep up with climate change.

A major issue in the analyis of biogeographical and macroecological data is how to deal with spatialautocorrelation. Pedro Peres Neto from the University of Quebec and Montréal described simulation results that showed how autocorrelation affects the outcomes of statistical tests, and provided some guidelines on the expected outcome of methods. He pointed out that the strength of a relationship between two variables and the source of dependency (whether in the residuals or the predictors) could be factors. One point well made was that spatial and phylogenetic methods for trait data analysis share a lot of similarity and there is a lot of potential for interchange.

These are just three talks I have highlighted as I found them particularly stimulating (and methods relevant), overall the meeting was really enjoyable interesting. And, following the coldest UK December in 100 years, I really do have to congratulate the organisers on their choice of Crete a venue!