Capturing the Contribution of Rare and Common Species to Turnover: A Multi-Site Version of Generalised Dissimilarity Modelling

Post provided by Guillaume Latombe and Melodie A. McGeoch

Understanding how biodiversity is distributed and its relationship with the environment is crucial for conservation assessment. It also helps us to predict impacts of environmental changes and design appropriate management plans. Biodiversity across a network of local sites is typically described using three components:

  1. alpha (α) diversity, the average number of species in each specific site of the study area
  2. beta (β) diversity, the difference in species composition between sites
  3. gamma (γ) diversity, the total number of species in the study area.
Two tawny frogmouths, a species native to Australia. ©Marie Henriksen.

Two tawny frogmouths, a species native to Australia. ©Marie Henriksen.

Despite the many insights provided by the combination of alpha, beta and gamma diversity, the ability to describe species turnover has been limited by the fact that they do not consider more than two sites at a time. For more than two sites, the average beta diversity is typically used (multi-site measures have also been developed, but suffer shortcomings, including difficulties of interpretation). This makes it difficult for researchers to determine the likely environmental drivers of species turnover.

We have developed a new method that combines two pre-existing advances, zeta diversity and generalised dissimilarity modelling (both explained below). Our method allows the differences in the contributions of rare versus common species to be modelled to better understand what drives biodiversity responses to environmental gradients. Continue reading

Issue 8.3

Issue 8.3 is now online!

The March issue of Methods is now online!

This issue contains two Applications articles and one Open Access article. These three papers are freely available to everyone, no subscription required.

 Solo: Solo audio recorders are inexpensive, easy to construct and record audible sound continuously for around 40 days. The paper also has a video tutorial explaining how to assemble the required hardware and comes with a companion website with more information.

 The third dimension: A novel design to obtain three-dimensional data on the movements of aquatic organisms at depths of up to 140m. The set-up consists of two synchronised high-speed cameras fixed to two articulated arms and can be used for any underwater applications that require synchronized video recordings of medium- to large-sized animals.

Continue reading

Carson’s Call: An Inspiration for Ecologists Working in a Post-Truth World

Post provided by Will Pearse

Rachel Carson (1940) Fish & Wildlife Service employee photo.

Rachel Carson (1940) Fish & Wildlife Service employee photo.

I can’t think of a more inspirational and influential ecologist than Rachel Carson. Nearly fifty years ago she released a book called Silent Spring, which argued that pesticides such as DDT were cascading up through food chains causing the death or sterilisation of birds and other animals. The publication of her book provoked public debate, likely in part because it was serialised in The New Yorker, and led to a paradigm shift in US and (arguably) global pest control policy.

With the full support of the scientific community to verify her facts and arguments, she was able to defeat the chemical industry’s backlash and galvanise public opinion in her favour. The 2005 Stockholm Convention, in which DDT was banned from agricultural use, would likely have never happened if it were not for her work.

“In a post-truth world where trust in the scientific process is being eroded almost daily, Rachel Carson is a perfect example of how we can speak out and be heard while still being scientists.”

Continue reading

Influential Women in Ecological Network Research

Post provided by Katherine Baldock and Luísa G. Carvalheiro


©Luísa G. Carvalheiro

Ecological networks represent interactions between different biotic units in an ecosystem and are becoming an increasingly popular tool for describing and illustrating a range of different types of ecological interactions. Food webs – which provide a way to track and quantify the flow of energy and resources in ecosystems – are among the most studied type of ecological networks. These networks usually represent species (nodes) which are connected by pairwise interactions (links) and they play a central role in improving our understanding of ecological and evolutionary dynamics.

Historically, food webs described antagonistic relationships (e.g. plant-herbivore or host-parasitoid networks) but the approach has been developed in recent years to include mutualistic networks (e.g. plant-pollinator networks, phorophyte-epiphyte networks). The development of network ecology, including ever more sophisticated methods to analyse ecological communities, has been driven forward by an enthusiastic community of ecologists, theoreticians and modellers working together to enhance our understanding of how communities interact.

In this blog post, we’ll describe the important role played by female scientists in the development of network ecology, focusing on the contributions by two ground-breaking ecologists and also highlighting contributions from a range of other scientists working in this field. Continue reading

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