Using the Smith-Root ANDe System for Wildlife Conservation

POST PROVIDED BY TRACIE SEIMON, PHD

The ANDe system can help researchers tell whether endangered species are present.

The ANDe system can help researchers tell whether endangered species are present.

In recent years, there have been a lot of studies on the use of environmental DNA (eDNA) for species detection and monitoring. This method takes advantage of the fact that organisms shed DNA into the environment in the form of urine, feces, or cells from tissue such as skin. As this DNA stays in the environment, we can use molecular techniques to search for traces of it. By doing this, we can determine if a species lives in a particular place.

At the Wildlife Conservation Society (WCS), we’re integrating and using the ANDe system in combination with ultra-portable qPCR (quantitative polymerase chain reaction) and DNA extraction technologies developed by Biomeme Inc. for eDNA capture and species detection of endangered turtles, and other aquatic organisms. This helps us to better monitor species within our global conservation programs. Continue reading

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Editor Recommendation: The Ecologist’s Field Guide to Sequence-Based Identification of Biodiversity

Post provided by Pierre M Durand

A fossilized species of the diatom Thalassiosira. B. A species of the dinoflagellate Prorocentrum. Image provided by A. Ndhlovu).

A fossilized species of the diatom Thalassiosira. B. A species of the dinoflagellate Prorocentrum. (Image provided by A. Ndhlovu).

As any reader of Methods in Ecology and Evolution will know, advances in technologies and methodologies used by ecologists and evolutionary biologists are never-ending. Coupled with the tendency for researchers to become ever more specialised, this means that keeping up to date with all the advances is challenging at best. Occasionally, new advances revolutionise the kinds of questions we ask and encourage us to develop new approaches to answer them. One of these huge advances emerged from the ‘-omics’ revolution.

The application of -omics methodologies to evolution and ecology has been particularly rapid. These technologies usually aren’t part of the basic science education in these fields – it’s more usual for computational biologists to cross over to ecology and evolution than the other way around. The review by Simon Creer and colleagues ’The ecologist’s field guide to sequence-based identification of biodiversity’ helps bridge this gap. It’s not too technical, but sufficiently detailed, and it provides a very handy overview of how genomics, transcriptomics and their meta-analyses can be applied to evolutionary ecology. The paper is filled with enormously helpful workflows, pointers, examples and, as the title suggests, is a guide for those who are not experts in sequence based technologies. Continue reading

The Global Pollen Project: An Update for Methods Readers

Post Provided by Andrew C. Martin

The Global Pollen Project is an online, freely available tool and data source developed to help people identify and disseminate palynological resources. Palynology – the study of pollen grains and other spores – is used across many fields of study including modern and fossil vegetation dynamics, forensic sciences, pollination, and beekeeping. To help make pollen identification quicker and more transparent, we developed the Global Pollen Project (GPP) – an open, peer-reviewed database of global pollen morphology, where content and expertise is crowdsourced from across the world. Our approach to developing this tool was open: open code, open data, open access. It connects to other data services, including the Global Biodiversity Information Facility and Neotoma Palaeoecology Database, to provide occurrence data for each taxon, alongside pollen images and metadata. Continue reading

HistMapR: 12 Months from Coffee Break Musings to a Debut R Package

Post provided by Alistair Auffret

I was really happy to hear that our paper, ‘HistMapR: Rapid digitization of historical land‐use maps in R’ was shortlisted for the 2017 Robert May Prize, and to be asked to write a blog to mark the occasion. The paper was already recommended in an earlier blog post by Sarah Goslee (the Associate Editor who took care of our submission), and described by me in an instructional video, so I thought that I would write the story of our first foray into making an R package, and submitting a paper to a journal that I never thought I would ever get published in.

Background: Changing Land-Use and Digitizing Maps

Land-use change in Europe is often typified by land-drainage to create arable fields.

Land-use change in Europe is often typified by land-drainage to create arable fields.

Land-use change is largely accepted to be one of the major threats to biodiversity worldwide at the moment. At the same time, a warming climate means that species’ ranges need to move poleward – something that can be hampered by changing land use. Quantifying how land use has changed in the past can help us to understand how species diversity and distributions respond to environmental change.

Unfortunately, quantifying this change by digitizing historical maps is a pretty tedious business. It involves a lot of clicking around various landscape features in a desktop GIS program. So, in many cases, historical land use is only analyzed in a relatively small number of selected landscapes for each particular study. In our group at Stockholm University, we thought that it would be useful to digitize maps over much larger areas, making it possible to assess change in all types of landscape and assess biodiversity responses to land-use change at macroecological scales. The question was, how could we do this? Continue reading

Solo: Developing a Cheap and Flexible Bioacoustic Tool for Ecology and Conservation

Post provided by Robin Whytock

A Solo recorder in the field. ©Tom Bradfer-Lawrence

A Solo recorder in the field. ©Tom Bradfer-Lawrence

Ecologists have long been fascinated by animal sounds and in recent decades there’s been growing interest in the field of ‘bioacoustics’. This has partially been driven by the availability of high-definition digital audio recorders that can withstand harsh field conditions, as well as improvements in software technology that can automate sound analysis.

Sound recordings can be used to study many aspects of animal behaviour in a non-intrusive way, from studying the social dynamics of monkeys or even clownfish to detecting echolocating bats or singing birds. Some species can only reliably be separated in the field by the sounds that they make, such as common and soprano pipistrelle bats. Bat research in general has been revolutionised by commercially available acoustic loggers, with some amazing advances using artificial intelligence to automatically detect bat calls. Continue reading

Code-Based Methods and the Problem of Accessibility

Post provided by Jamie M. Kass, Matthew E. Aiello-Lammens, Bruno Vilela, Robert Muscarella, Cory Merow and Robert P. Anderson

The namesake of our software and founder of the field of biogeography, Alfred Russel Wallace. Photo ©G. W. Beccaloni

The namesake of our software and founder of the field of biogeography, Alfred Russel Wallace. Photo ©G. W. Beccaloni

In ecology, new methods are increasingly being accompanied by code, and sometimes even full command-line software packages (usually in R). This is great, as it makes analyses more reproducible and transparent, which is essential for the development of open science. In an ideal world, code would have informative annotation, generalized functions for multipurpose use, and be written in a legible and consistent manner. After all, the code may be used by ecologists with a wide range of programming experience.

In reality, code is often poorly commented (or not commented at all!), hard to reuse for other projects, and difficult to interpret. To add to that, most code isn’t actively maintained, so users are on their own if they try to commandeer it for new purposes. Further, ecologists with little or no programming knowledge are unlikely to benefit from methods that exist only as poorly documented code. In a positive development, some new methods are accessible through software with graphic user interfaces (GUIs) developed by programmers spending significant time and effort. But too often these end up as tools with flashy controls and insufficient instruction manuals. Continue reading

New Studies Aim to Boost Social Science Methods in Conservation Research

Below is a press release about the Methods Special Feature ‘Qualitative Methods for Eliciting Judgements for Decision Making‘ taken from the University of Exeter.

Scientists have produced a series of papers designed to improve research on conservation and the environment.

A group of researchers have contributed to a Special Feature of the journal Methods in Ecology and Evolution to examine commonly used social science techniques and provide a checklist for scientists to follow.

Traditional conservation biology has been dominated by quantitative data (measured in numbers) but today it frequently relies on qualitative methods such as interviews and focus group discussions. The aim of the special issue is to help researchers decide which techniques are most appropriate for their study, and improve the “methodological rigour” of these techniques. Continue reading

Satellite Data Fusion for Ecologists and Conservation Scientists

What is satellite data fusion, and how can it benefit ecologists and conservation scientists? In a new Methods in Ecology and Evolution video, Henrike Schulte-to-Bühne answers this question using whiteboards and questionable drawing skills.

The availability and accessibility of multispectral and radar satellite remote sensing (SRS) imagery are at an unprecedented high. However, despite the benefits of combining multispectral and radar SRS data, data fusion techniques, including image fusion, are not commonly used in biodiversity monitoring, ecology and conservation. To address this, the authors provide an overview of the most common SRS data fusion techniques, discussing their benefits and drawbacks, and pull together case studies illustrating the added value for biodiversity research and monitoring.

This video is based on the review article ‘Better together: Integrating and fusing multispectral and radar satellite imagery to inform biodiversity monitoring, ecological research and conservation science by Schulte to Bühne and Pettorelli.

The Power of Infinity: Using 3D Fractal Geometry to Study Irregular Organisms

Post provided by Jessica Reichert, André R. Backes, Patrick Schubert and Thomas Wilke

The Problem with the Shape

More than anything else, the phenotype of an organism determines how it interacts with the environment. It’s subject to natural selection, and may help to unravel the underlying evolutionary processes. So shape traits are key elements in many ecological and biological studies.

The growth form of corals is highly variable. ©Jessica Reichert

The growth form of corals is highly variable. ©Jessica Reichert

Commonly, basic parameters like distances, areas, angles, or derived ratios are used to describe and compare the shapes of organisms. These parameters usually work well in organisms with a regular body plan. The shape of irregular organisms – such as many plants, fungi, sponges or corals – is mainly determined by environmental factors and often lacks the distinct landmarks needed for traditional morphometric methods. The application of these methods is problematic and shapes are more often categorised than actually measured.

As scientists though, we favour independent statistical analyses, and there’s an urgent need for reliable shape characterisation based on numerical approaches. So, scientists often determine complexity parameters such as surface/volume ratios, rugosity, or the level of branching. However, these parameters all share the same drawback: they are delineated to a univariate number, taking information from one or few spatial scales and because of this essential information is lost. Continue reading

More New Associate Editors

Today we are welcoming another two Associate Editors to the Methods in Ecology and Evolution. Just like the seven AEs who joined last week, Michael Matschiner (of the University of Basel, Switzerland) and Tiago Bosisio Quental (of the University of São Paulo, Brazil) were both invited to work with the journal following our open call earlier this year. You can find out more about both of them below.

Michael Matschiner

“I am an evolutionary biologist interested in the processes that drive speciation and generate biodiversity. To learn about these processes, I use phylogenetic divergence-time estimation based on genome sequences and the fossil record. Since both of these data sources do not usually conform to expectations in standard phylogenetic workflows (no recombination, no hybridization, no sampling bias), much of my work involves method development to assess the impact of model violations, and to account for them in phylogenetic reconstruction.”

Tiago Bosisio Quental

“I am interested on understanding spatial and temporal patterns of biodiversity and the mechanisms involved in generating species diversity. I have a particular interest in mammals, but my research interests are not limited to a specific taxonomic group but are instead motivated by a range of questions and structured around them. At the moment, I am particularly interested in understanding the role of biotic interactions on biodiversity changes in deep time. The main tools used to approach those questions are molecular phylogenies, fossil record, ecological data and numerical simulation.”

We are thrilled to welcome Michael and Tiago to the Associate Editor Board and we look forward to working with them over the coming years.