Issue 8.2

Issue 8.2 is now online!

The February issue of Methods is now online!

This issue contains four(!) Applications articles and two Open Access articles. These six papers are freely available to everyone – no subscription required.

 Earth Mover’s Distance: The Earth Mover’s Distance (or EMD) is a method commonly used in image retrieval applications. The authors of this paper propose its use to calculate similarity in space use in the framework of movement ecology. This will be helpful for many questions regarding behavioural ecology, wildlife management and conservation.

 warbleR: The R package warbleR is a new package for the analysis of animal acoustic signal structure. It offers functions for downloading avian vocalisations from the open-access online repository Xeno-Canto, displaying the geographic extent of the recordings, manipulating sound files, detecting acoustic signals or importing detected signals from other software, and much more.

– meteR: The open-source R package, meteR directly calculates all of Maximum entropy theory of ecology’s (METE’s) predictions from a variety of data formats; automatically handles approximations and other technical details; and provides high-level plotting and model comparison functions to explore and interrogate models.

– Noise Egg: The Noise Egg is a device that can produce a low-frequency sound, which can be used as an experimental source of noise both in aquaria and in the field. It was developed to study the effects of noise on communication and behaviour in small aquatic animals; however, it could be used for other purposes, such as testing the propagation of certain frequencies in shallow-water habitats.

Continue reading

Lichens and the “health” of ecosystems: we are closer to a global ecological indicator

Below is a press release about the Methods paper ‘Tracking global change using lichen diversity: towards a global-scale ecological indicator‘ taken from the University of Lisbon.

Candelaria pacifica. © Paula Matos

Candelaria pacifica. © Paula Matos

For the first time, it is possible to integrate at the global scale the results obtained with the most widely used methods to evaluate the “health” of ecosystems using lichens. This is the result of a study now published in the journal Methods in Ecology and Evolution, and represents a fundamental step for this indicator to be considered at the global scale and included in the list of indicators of the United Nations.

Lichens have long been successfully used by scientists as ecological indicators – a kind of environment health thermometer. These complex organisms – the yellow or green taints we often see on the surface of tree trunks – are very sensitive to pollution and changes in temperature and humidity. Evaluating how many lichens, of what kind, and their abundance in a certain ecosystem allows scientists to understand the impact that problems like climate change or pollution have on those ecosystems.  Continue reading

Just snap it! Using Digital Cameras to Discover What Birds Eat

Post provided by Davide Gaglio and Richard Sherley

Digital photography has revolutionised the way we view ourselves, each other and our environment. The use of automated cameras (including camera traps) in particular has provided remarkable opportunities for biological research. Although mostly used for recreational purposes, the development of user-friendly, versatile auto-focus digital single lens reflex (DSLR) cameras allows researchers to collect large numbers of high quality images at relatively little cost.

These cameras can help to answer questions such as ‘What does that species feed its young?’ or ‘How big is this population?’, and can provide researchers with glimpses of rare events or previously unknown behaviours. We used these powerful research tools to develop a non-invasive method to assess the diets of birds that bring visible prey (e.g. prey carried in the bill or feet) back to their chicks. Continue reading

Creating Bigger, Better and More Joined-up Habitat Networks

Below is a press release about the Methods paper ‘How to manipulate landscapes to improve the potential for range expansion‘ taken from the University of Liverpool.



Scientists at the University of Liverpool have developed a new ‘route planner’ tool that could help conservationists aid the movement of species as they adapt to a changing climate.

The environmental ranges of many animal and plant species are starting to alter with climate change, as temperatures change and force species to migrate to more suitable climes.

To be able to do this successfully, they will need sufficient habitat in their existing range, their future range, and any intermediate areas to enable populations to survive and thrive. Many conservation initiatives to restore habitats and increase connectivity are trying to address this issue. However, existing modelling tools mainly treat the landscape as static, and it is difficult to use these to plan restoration. Continue reading

Biogeographic Regions: What Are They and What Can They Tell Us?

Post provided by Leonardo Dapporto, Gianni Ciolli, Roger L.H. Dennis, Richard Fox and Tim G. Shreeve

Every species in the world has a unique geographic distribution. But many species have similar ranges. There are many things that can cause two (or more) species to have similar ranges – for example shared evolutionary histories, physical obstacles (mountains, oceans etc.) or ecological barriers limiting their dispersal. As a consequence, different regions of the globe are inhabited by different sets of living organisms.

In the mid-19th century ecologists recognised that the earth could be divided into different biogeographic regions. Alfred Russel Wallace (1823–1913) played a key role in defining and recognising biogeographic regions. He improved the existing maps of  biogeographic regions and provided basic rules to identify them. His observation that some of these regions are home to similar species, despite being far away from each other and separated by significant barriers was the inspiration for Alfred Wegener’s theory of continental drift. In more recent years regionalisation has been used to understand the spatial drivers of biological evolution and to protect those regions characterised by particularly unique flora and fauna.

The biogeographic regions identified by Alfred Russel Wallace from The Geographical Distribution of Animals (1876)

The biogeographic regions identified by Alfred Russel Wallace from The Geographical Distribution of Animals (1876)

Despite the long history of biological regionalisation, the methods to identify biogeographic regions are still being improved. We are currently working in this exciting field of research and recently published ‘A new procedure for extrapolating turnover regionalization at mid-small spatial scales, tested on British butterflies’ in Methods in Ecology and Evolution. Continue reading

Planning Habitat for Very Long-Distance Connectivity under Climate Change

Post provided by JENNY HODGSON

Climate change and habitat fragmentation are interacting threats: it is likely that many species cannot reach newly suitable areas at the cool edge of their range because there is not enough habitat, in the right places, to support range expansion over multiple generations. Conservation efforts are already underway to restore large areas of habitat, and to improve the “connectivity” within networks of habitat. However, there are multiple ways of measuring connectivity and few of them address the scale of shifts that are likely to be needed under climate change. This could be a problem if it leads to inefficient conservation prioritisation.

The Conductance Metric

How conductance generally depends on the amount of habitat in the landscape. Squares show the conductance of landscapes with a random selection of cells chosen to be habitat. The red line is based only on the 100% point and the expectation that conductance is proportional to amount of habitat squared.

How conductance generally depends on the amount of habitat in the landscape. Squares show the conductance of landscapes with a random selection of cells chosen to be habitat. The red line is based only on the 100% point and the expectation that conductance is proportional to amount of habitat squared.

We first developed the conductance metric in 2012 and we found that it is correlated to the speed with which a species can spread through a landscape, from a specified source location to a specified target. A key difference between this and most other connectivity metrics is that it incorporates both reproduction within habitat patches and dispersal between habitat patches, over multiple generations (further explanation here). Sometimes there could be many very well-connected patches in a network, and yet no easy way for a species to cross the landscape from end to end. This could be a problem for the species’ survival, if staying within its current regions of occupancy is unsustainable, for example if it is being pushed northwards by climate change. Continue reading

European Bison, Rewilding and Dung Fungal Spore

Post provided by AMBROISE BAKER

In the US, July is National Bison Month but most people in Europe are totally oblivious to it. I wasn’t even aware of it before being asked to write this blog post in connection with our recent Methods in Ecology and Evolution paper about quantifying population sizes of large herbivores. Some will argue that it is because we don’t ‘do’ day, month, state or national animals on this side of the Atlantic as much as the Americans do.

The European bison survived from extinction thanks to about 50 individuals kept in zoos. The species has been reintroduced in the wild in several European countries but remains ‘Vulnerable’ according to the IUCN criteria.

The European bison survived extinction thanks to ~50 individuals kept in zoos. It has been reintroduced in several countries but remains ‘Vulnerable’. ©4028mdk09

But another reason is that the European bison, Bison bonasus bonasus, is simply not sufficiently well-known or associated with European nature in the public’s mind. This is particularly true in Western Europe where this species has been extinct since medieval times.

Early European accounts from North America reported huge bison populations – with estimates of up to 60 million – moving to and fro in the great bison belt. These past migratory movements across the Great Plains are familiar well beyond the US and feed our view of untamed wilderness prior to the impact of European ’civilisation’. In contrast, there are hardly any records of European bison numbers until just before the last wild one was reported killed in Poland in 1921. Continue reading

Issue 7.7

Issue 7.7 is now online!

The July 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.

– MO-Phylogenetics: A software tool to infer phylogenetic trees optimising two reconstruction criteria simultaneously and integrating a framework for multi-objective optimisation with two phylogenetic software packages.

– PHYLOMETRICS: An efficient algorithm to construct the null distributions (by generating phylogenies under a trait state-dependent speciation and extinction model) and a pipeline for estimating the false-positive rate and the statistical power of tests on phylogenetic metrics..

Continue reading

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


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


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