Methods papers, Online extras, Statistical methods, Virtual Issues

Statistical Ecology Virtual Issue

StatEcolVI_WebAdAt the last ISEC, in Montpellier in 2014, an informal survey suggested that Methods in Ecology and Evolution was the most cited journal in talks. This reflects the importance of statistical methods in ecology and it is one reason for the success of the journal. For this year’s International Statistcal Ecology Conference in Seattle we have produced a virtual issue that presents some of our best recent papers which cross the divide between statistics and ecology. They range over most of the topics covered at ISEC, from statistical theory to abundance estimation and distance sampling.

We hope that Methods in Ecology and Evolution will be equally well represented in talks in Seattle, and also – just as in Montpellier – some of the work presented will find its way into the pages of the journal in the future.

Without further ado though, here is a brief overview of the articles in our Statistical Ecology Virtual Issue: Continue reading “Statistical Ecology Virtual Issue”

Unknown's avatarIndia Stephenson1 Comment
Journal updates, Methods papers

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.
Continue reading “Issue 7.6: Methods in Ecology and Evolution 5th Anniversary Special Feature”

Unknown's avatarIndia Stephenson1 Comment
Evolution, Meetings, Methods papers, Phylogenetic analysis

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.

Continue reading “RPANDA: A Time Machine for Evolutionary Biologists”

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Methods papers

CO2 Efflux Rates from Dead Organic Matter: Get It Right

Post provided by GBADAMASSI DOSSA

Anthropocene and Climate Change at Glance

As a consequence of human activities the global climate is changing at a rate that is unprecedented in at least the past few centuries, leading to the suggestion that this era should be referred to as the “Anthropocene”. While climate hind-casting and pollen histories in sediments are advancing our understanding of how past ecological ecosystems responded to previous climate changes, forecasting power really depends on how accurately we can predict ecosystem functions that are likely to change in the future.

Despite substantial recent advances in our ability to predict climate change, considerable uncertainty remains – especially in our understanding of how ecosystem functioning could be influenced by climate change and how this may feed back to affect greenhouse-gas fluxes. The decomposition of organic matter in leaf litter and soils accounts for a global flux that is approximately 7 times as large as global anthropogenic emissions. Understanding how climate change will affect carbon held in dead organic matter pools – including leaf litter, woody debris and soil organic carbon – is essential.

Decomposition and Why it Matters

Carbon cycle summary. Note this focuses only in forested or terrestrial ecosystem.
Carbon cycle summary. Note this focuses only in forested or terrestrial ecosystem.

Decomposition is defined as the “physical, chemical and biological mechanisms that transform organic matter into increasingly stable forms” in plant detritus. However, only small part of carbon goes through this process. Most of dead organic matter becomes CO2. Decomposition of organic matter is important because of its link to the global carbon cycle. Simply stated, the carbon cycle consists of carbon inputs via photosynthesis and outputs via respiration. However, while photosynthesis is relatively well studied and understood, respiration – including that of living organisms (autotrophy) and of dead ones (heterotrophy) – is understudied. As a consequence, our understanding of decomposition is much less sophisticated. A substantial amount of greenhouse-gas (CO2, CH4, N2O) production occurs either directly or indirectly from organic matter decomposition, including woody debris. Similar amounts of CO2 efflux exist between fluxes from woody debris decomposition (8.6 Pg yr-1) and fossil fuel burning (9.6 Pg yr-1). So we desperately need a reliable technique to quantify CO2 from decomposition. Continue reading “CO2 Efflux Rates from Dead Organic Matter: Get It Right”

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Conservation and management, Methods papers, Virtual Issues

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

Unknown's avatarIndia Stephenson2 Comments
Conservation and management, Methods papers, Virtual Issues

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

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Conservation and management, Methods papers

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 “What is Dark Diversity?”

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Conservation and management, Methods papers, Statistical methods

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 “Bringing Ecologists and Statisticians Together for the Conservation of Endangered Species”

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Journal updates

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 “Issue 7.5”
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