Biodiversity Monitoring by Plant Proxy is Cheap and Easy: Here’s How and Why

Post provided by Rasmus Ejrnæs, Ane Kirstine Brunbjerg & Hans Henrik Bruun

Could we use the plants in this swamp forest to predict the diversity of other species?

Local communities and regional biotas are built of hundreds, if not thousands, of species. Most of these species are small-bodied and discreet lifeforms. So it’s no wonder that naturalists have almost always focused their attention on conspicuous species of their particular liking. Why plants then? Well, plants are practical and efficient. They “stand still and wait to be counted”, as the eminent population biologist John Harper put it. No matter the weather, from spring to autumn. There are enough plant species to show contrasts between sites, and yet they can usually be identified to species level in the field.

You Can’t Predict the Diversity of Beetles from Lichens… Can You?

Unfortunately, the overwhelming scientific consensus seems to be that any particular taxonomic group won’t adequately represent the biodiversity of other taxonomic groups. The idea of surrogacy seems to hit the same hard wall as most attempts to provide generally working models for variation in biodiversity at local and regional scales. Biodiversity remains one of the largest scientific research questions without good general answers. Continue reading

How Many Animals are Infected with Chronic Wasting Disease?

Post provided by Hildegunn Viljugrein

©Alexandre Buisse

©Alexandre Buisse

The discovery of Chronic Wasting Disease (CWD) in Norway in 2016 has led to extensive measures and testing of deer in Norway. Since 2018 there have been similar measures within the EU. But how many deer need to be tested before we can be (almost) certain that a population is not infected by CWD?

In our article – ‘A method that accounts for differential detectability in mixed samples of long‐term infections with applications to the case of Chronic Wasting Disease in cervids’ – we provide important tools for estimation of prevalence and likelihood of finding infected animals in a given population. The paper is a result of a collaborative work between a multidisciplinary group of scientists from the Norwegian Veterinary Institute, Norwegian Institute for Nature Research and Prof. Atle Mysterud from Centre for Ecological and Evolutionary Synthesis at the University of Oslo. Continue reading

Spatial Capture-Recapture: The Pros and Cons of Aggregating Detections

Post provided by Cyril Milleret

Spatial Capture-Recapture and Computation Time

SCR models simultaneously estimate the detection function and density of individual activity centres. A half-normal detection model is generally used.

SCR models simultaneously estimate the detection function and density of individual activity centres. A half-normal detection model is generally used.

The estimation of population size is one of the primary goals and challenges in wildlife ecology. Within the last decade and a half, a new class of tools has emerged, allowing us to estimate abundance and other key population parameters in specific areas. So-called spatial capture-recapture (SCR) models are growing in popularity not only because they can map abundance, but also because they can be fitted to data collected from a variety of monitoring methods. For example, the ever increasing use of non-invasive monitoring methods, such as camera trapping and non-invasive genetic-sampling, is one of the reason that makes SCR models so popular.

One other strengths of SCR models is the ability to make population level inferences. But the wider the region you’re monitoring, the greater the computational burden, challenging the use of such methods at really large scale. Continue reading

R2ucare: An Interview with Olivier Gimenez

At the International Statistical Ecology Conference in St Andrews this July (ISEC 2018) David Warton interviewed Olivier Gimenez about R2ucare. R2ucare is an R package for goodness-of-fit tests for capture-recapture models. The full Methods in Ecology and Evolution article on this package – R2ucare: An r package to perform goodness‐of‐fit tests for capture–recapture models – was published in the July 2018 issue of the journal.

David and Olivier also discuss some tips for creating R packages. They mention that if you’re new to writing R packages, there are some excellent resources online. Here’s one of them: A Quickstart Guide for Building Your First R Package

We’ll have more of David’s interviews from the ISEC coming out over the next few weeks. Keep an eye out for them here and on the Methods in Ecology and Evolution YouTube channel.

You can find David’s first ISEC interview (with Kate Jones) here.

What the Past Can Tell Us About the Future: Notes from Crossing the Palaeontological – Ecological Gap

Post provided by Karen Bacon

I had the pleasure of delivering one of the plenary talks at the first (hopefully of many) Crossing the Palaeontological – Ecological Gap meeting held in the University of Leeds on August 30th and 31st. I’m a geologist and a botanist, so this is a topic that’s close to my heart and my professional interests.

How Palaeoecology Can Help Us Today

©Gail Hampshire

©Gail Hampshire

As we move into an ecologically uncertain future with pressures of climate change, land-use change and resource limitations, the fossil record offers the only truly long-term record of how Earth’s ecosystems respond to major environmental upheaval driven by climate change events. The fossil record is, of course, not without its problems – there are gaps, not everything fossilises in the same way or numbers, and comparisons to today’s ecology are extremely difficult.  It’s these difficulties (and other challenges) that make the uniting of palaeontology and ecology essential to fully address how plants, animals and other organisms have responded to major changes in the past. Perhaps uniting them could give us an idea of what to expect in our near-term future, as carbon dioxide levels return to those not previously experienced on Earth since the Pliocene, over 2 million years ago. Continue reading

Ten Top Tips for Reviewing in a Language You Aren’t Fluent In

Science is global, which means that peer review is a global activity. When Editors look for people to review manuscripts, they want to find the best people to comment on the topic – regardless of their background or primary language. While science and peer review are conducted in different languages all around the world, English has become the international language of science (for reasons we won’t go into in this post). English doesn’t just belong to people from English-speaking countries, it belongs to all scientists. For some people though, language can feel like a barrier to reviewing scientific papers.

That’s not to say that all non-native English speakers struggle with the language. Many reviewers for whom English is a second language have only ever reviewed in English and will only ever review in English and are comfortable, confident and experienced in the task. For some, reviewing in a second language is not all that different to reviewing in their native tongue. Many people who did not grow up speaking English are great English speakers, but for those who didn’t get much of their scientific training in English, language can impose an unwanted and unnecessary disadvantage.

The theme of this year’s Peer Review Week is Diversity in Peer Review, so we’ve asked the Methods in Ecology and Evolution Associate Editors for some advice on reviewing in a second language. We hope that these tips will help people who aren’t fluent in their second (or third, fourth, etc.) language to feel more confident reviewing in it. Our journal is published in English, so we’ve focused on English as a second language in this post. However, the advice should be helpful regardless of what language your reviewing in or whether you’re a native speaker. Continue reading

Crossing the Palaeontological-Ecological Gap

Today is the first day of the Crossing the Palaeontological-Ecological Gap (CPEG) conference. The aim of the conference is to open a dialogue between palaeontologists and ecologists who work on similar questions but across vastly different timescales. This splitting of temporal scales tends to make communication, data integration and synthesis in ecology harder. A lot of this comes from the fact that palaeontologists and ecologists tend to publish in different journals and attend different meetings.

Methods in Ecology and Evolution is one of few ecological journals that attracts submissions from both ecologists and palaeontologists. To highlight this, we’ve released a Virtual Issue, also called Crossing the Palaeontological-Ecological Gap. Continue reading

Bats, Acoustic Methods and Conservation 4.0: An Interview with Kate Jones

At this year’s International Statistical Ecology Conference (ISEC 2018) David Warton interviewed Kate Jones, Chair in Ecology and Biodiversity at University College, London. Their conversation mainly focused on how to classify bats from acoustic data, with particular reference to ‘Acoustic identification of Mexican bats based on taxonomic and ecological constraints on call design‘ by Veronica Zamora‐Gutierrez et al. They also discuss Conservation 4.0!

We’ll have more of David’s interviews from the ISEC coming out over the next few weeks. Keep an eye out for them here and on the Methods in Ecology and Evolution YouTube channel.

Integrating Evolution and Ecology

©H. Zell

©H. Zell

The latest Methods in Ecology and Evolution Virtual Issue – ‘Integrating Evolution and Ecology‘ – is in honour of the late Isabelle Olivieri (1957-2016): an international, interdisciplinary and ground-breaking biologist. It was edited by Louise Johnson and James Bullock and features papers on topics she researched, and in many cases pioneered. But it might perhaps have been more difficult to find 15 Methods papers on areas outside of Isabelle’s research interests!

Isabelle was the first Professor of Population Genetics at Montpellier, a past President of the European Society for Evolutionary Biology (2007-2009), and a member of the European Molecular Biology Organization. She spanned subject boundaries as easily as she collaborated across geographical borders. Her publications range through metapopulation and dispersal ecology, host-parasite coevolution, life history, invasive species and conservation ecology. In keeping with this breadth of interests, she also combined theory easily with experiment, and worked with a wide range of study systems from mites to Medicago. Continue reading

The Manager’s Dilemma: Which Species to Monitor?

Post provided by Payal Bal and Jonathan Rhodes

The greater bilby (M.Lagotis). ©Save the Bilby Fund

The greater bilby (M.Lagotis). ©Save the Bilby Fund

Imagine you’re the manager of a national park. One that’s rich in endemic biodiversity found nowhere else on the planet. It’s under the influence of multiple human pressures causing irreversible declines in the biodiversity, possibly even leading to the extinction of some of the species. You’re working with a complex system of multiple species and threats, limited knowledge of which threats are causing the biggest declines and limited resources. How do you decide what course of action to take to conserve the biodiversity of the park? This is the dilemma faced by biodiversity managers across the globe.

In our recent paper, ‘Quantifying the value of monitoring species in multi‐species, multi‐threat systems’, we address this problem and propose a method using value of information (VOI) analysis. VOI estimates the benefit of monitoring for management decision-making. Specifically, it’s a valuation tool that can be used to disentangle the trade-offs in competing monitoring actions. It helps managers decide how to invest (or whether to invest) their money in monitoring actions when faced with imminent biodiversity declines and the urgency of efficient conservation action. Continue reading