A New Modelling Strategy for Conservation Practice? Ensembles of Small Models (ESMS) for Modelling Rare Species

Post provided by FRANK BREINER, ARIEL BERGAMINI, MICHAEL NOBIS and ANTOINE GUISAN

Rare Species and their Protection

Erythronium dens-canis L. – a rare and threatened species used for modelling in Switzerland. ©Michael Nobis

Erythronium dens-canis L. – a rare and threatened species used for modelling in Switzerland. ©Michael Nobis

Rare species can be important for ecosystem functioning and there is also a high intrinsic interest to protect them as they are often the most original and unique components of local biodiversity. However, rare species are usually those most threatened with extinction.

In order to help prioritizing conservation efforts, the International Union for Conservation of Nature (IUCN) has published criteria to categorize the status of threatened species, which are then published in Red Lists. Changes in a species’ geographical distribution is one of the several criteria used to assign a threat status. For rare species, however, the exact distribution is often inadequately known. In conservation science, Species Distribution Models (SDMs) have recurrently been used to estimate the potential distribution of rare or insufficiently sampled species. Continue reading

Ecological Transcriptomics for Endangered Species: Avoiding the “Successful Operation, but the Patient Died” Problem

Post provided by TILL CZYPIONKA, DANIEL GOEDBLOED, ARNE NOLTE and LEON BLAUSTEIN

Ecological Transcriptomics and Endangered Species

 The small size of the rockpool and the salamander population makes non-invasive sampling a necessity (from left: Tamar Krugman, Alan Templeton, Leon Blaustein). © Arne Nolte

The small size of the rockpool and the salamander population makes non-invasive sampling a necessity (from left: Tamar Krugman, Alan Templeton, Leon Blaustein). © Arne Nolte

Friday was Endangered Species Day – so this is a good time to reflect on what science and scientists can do to support conservation efforts and to reduce the rate of species extinctions. One obvious answer is that we need to study endangered species to understand their habitat requirements as well as their potential for acclimatization and adaptation to changing environmental conditions. This information is crucial to for the design of informed conservation planning. However, for most endangered species the relevant phenotypes are not known a priori, which leaves the well-intentioned scientist asking “which traits should I measure?”. Transcriptome analysis is often a good way to answer to this question.

Transcriptome analysis measures the expression levels of thousands of genes in parallel. This amount of data circumvents the need to decide on a reduced number of traits of unknown relevance and allows for a relatively unbiased phenotypic screen of many traits. In particular, physiological changes, which often influence a species’ distributional range, can be studied using transcriptome analysis. Also, transcriptomics provide a direct connection to the genetic level. This is essential for in-depth analyses of aspects of evolution and might even be helpful for a new kind of conservation planning, which aims to foster endangered species by promoting (supposedly) beneficial hybridization. The integration of transcriptomic analysis with ecological studies is known as ‘Ecological transcriptomics’. Continue reading

What is Dark Diversity?

Post provided by ROB LEWIS & MEELIS PÄRTEL

Our understanding of how biological diversity works has been advanced by a long history of observing species and linking patterns to ecological processes. However, we generally don’t focus as much on those species that aren’t observed, or in other words ‘absent species’. But, can absent species provide valuable information?

Dark diversity – a set of species absent from a particular site but which belong to its species pool – has the potential to be as ecologically meaningful as observed diversity. Part of the species pool concept, understanding dark diversity is relatively straightforward.

The Basic Theory of Dark Diversity

To begin learning about dark diversity, there are two important terms that we need to define: ‘species pool’ and ‘focal community’. A ‘species pool’ is a set of species present in a particular region or landscape that can potentially inhabit a particular observed community because of suitable local ecological conditions.

A ‘focal community’ is the set of species that have been observed in a particular region or landscape (this is the ‘observed community’ and can also be referred to as alpha diversity). For a given focal community to become established, the species within it must have overcome dispersal pressures as well as environmental and biotic filters.

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Continue reading

Bringing Ecologists and Statisticians Together for the Conservation of Endangered Species

Post provided by Cecilia Pinto and Luigi Spezia

The Benefits of High Frequency Data

One of the tagged flapper skates showing the three different kinds of tags. ©Cecilia Pinto

One of the tagged flapper skates showing the three different kinds of tags. ©Cecilia Pinto

High frequency data, like those obtained from individual electronic tags, carries the potential of giving us detailed information on the behaviour of species at the individual level. Such data are particularly useful for marine species, as we can’t observe them directly for long periods of time.

Understanding how individuals use water columns – both at daily and seasonal scales – can help define conservation measures such as restricting fishing activity to reduce by-catch or defining protected areas to help recovering populations or protect spawning and nursery areas. High frequency data have become popular as they give insight to detailed individual foraging behaviour and therefore the specific energetic needs that are linked to reproduction and fitness. Continue reading

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.

From Tree of Life to Web of Life: How Google Images Can Help Ecologists Study Evolution

Below is a press release about the Methods paper ‘Just Google it: assessing the use of Google Images to describe geographical variation in visible traits of organisms‘ taken from the British Ecological Society.

Black sparrowhawks are either completely dark or have a white breast. ©Oggmus

Black sparrowhawks are either completely dark or have a white breast. ©Oggmus

Animals caught on camera by amateur photographers and posted on the web could become an important new tool for studying evolution and other ecological questions, researchers from South Africa have found. Their study – the first of its kind – is published today in Methods in Ecology and Evolution.

Colour polymorphism – when a species has two or more colour types – has fascinated biologists since Darwin. The occurrence of these different colour types often varies geographically, providing a useful way of studying how different colour morphs – or phenotypes – evolve.

But the fieldwork needed to collect these data is time consuming and expensive, so Dr Arjun Amar and his student Gabriella Leighton from the University of Cape Town wondered if ecologists could use the thousands of animal images posted on the internet instead. Continue reading

New Initial Submission Requirements

Submitting to Methods in Ecology and Evolution is now easier than ever!

Formatting manuscripts for submission can take a long time.

Formatting manuscripts for submission can take a long time.

Formatting a manuscript for journal submission can be time-consuming and frustrating work, especially for the first version. To make things a little bit simpler for our authors, we now have just a few small formatting requirements for initial submissions.

To have a paper considered in Methods in Ecology and Evolution it just needs to:

  • Be double line spaced and in a single column
  • Be within the word count (6000-7000 words for Standard Articles, 3000 words for Applications)
  • Include both line and page numbers
  • Have a statement of where you intend to archive your data
  • Follow the standard manuscript structure: Author details, Abstract (must be numbered according to journal style), Keywords, Introduction, Materials and Methods, Results, Discussion

This means that you do not need to worry about the format of your references, the placement of your figures (they can be within the text, at the end of the document or uploaded as separate files), whether or not you have used scientific names or anything else like that. Continue reading

Tips for Publishing Methods Papers in Ecological Journals

At the 2015 Eco-Stats Conference at the University of New South Wales there was a Q&A panel discussion of tips for authors publishing methods papers. The panel was chaired by Methods in Ecology and Evolution Associate Editor David Warton. It included Jane Elith (winner of the Methods Recognition of Achievement award), Associate Editor Matt Schofield and former Associate Editor Shinichi Nakagawa. There was also a late appearance, straight off a long haul flight from China, by Doug Yu (another current Associate Editor).

Continue reading

The Arborist Throw-line Launcher

Collecting leaves or seeds from tall trees is a difficult task that many plant physiologists, ecologists, geneticists and forest managers encounter repeatedly. In a series of videos on the Methods in Ecology and Evolution YouTube channel, Kara N. YoungentobChristina Zdenek and Eva van Gorsel demonstrate how to use the arborist throw-line launcher, which significantly simplifies this task. This new way of collecting seeds and leaves from tall trees is explained in their Applications article ‘A simple and effective method to collect leaves and seeds from tall trees‘. As this is an Applications paper, it is freely available to everyone.

Basic Techniques for the Arborist Throw-line Launcher

The first of the three videos is a basic overview of the method. In this tutorial, the authors teach you how to find the ideal branch, how to use the throw-line launcher and go through some important safety information. Continue reading