Assessing Sea Turtle Populations: Can We Get a Hand From Drones and Deep Learning?

Post provided by PATRICK GRAY

An olive ridley sea turtle in Ostional, Costa Rica. ©Vanessa Bézy.

Understanding animal movement and population size is a challenge for researchers studying any megafauna species. Sea turtles though, add a whole additional level of complexity. These wide-ranging, swift, charismatic animals spend much of their time underwater and in remote places. When trying to track down and count turtles, this obstacle to understanding population size becomes a full-on barricade.

Censusing these animals doesn’t just satisfy our scientific curiosity. It’s critical for understanding the consequences of unsound fishing practices, the benefits of conservation policy, and overall trends in population health for sea turtles, of which, six out of seven species range from vulnerable to critically endangered. Continue reading

Where do Animals Spend Their Time and Energy? Theory, Simulations and GPS Trackers Can Help Us Find Out

Post provided by MATT MALISHEV (@DARWINANDDAVIS)

 An adult sleepy lizard with a GPS tracker and body temperature logger strapped to her tail. ©Mike Bull.


An adult sleepy lizard with a GPS tracker and body temperature logger strapped to her tail. ©Mike Bull.

Changes in temperature and available food determine where and when animals move, reproduce, and survive. Our understanding of how environmental change impacts biodiversity and species survival is well-established at the landscape, country and global scales. But, we know less about what could happen at finer space and time scales, such as within habitats, where behavioural responses by animals are crucial for daily survival.

Simulating Movement and Daily Survival with Individual-Based Movement Models

Key questions at these scales are how the states of individuals (things like body temperature and nutritional condition) influence movement decisions in response to habitat change, and how these decisions relate to patchiness in microclimates and food. So we need tools to make reliable forecasts of how fine-scale habitat use will change under future environments. Individual-based movement simulation models are powerful tools for these kinds of studies. They let you construct habitats that vary in temperature and food conditions in both space and time and ask ‘what if’ questions. By populating these models with activity, behaviour, and movement data of animals, we can simulate different habitat conditions and predict how animals will respond to future change. Continue reading

Early Spring: Predicting Budburst with Genetics

Below is a press release about the Methods in Ecology and Evolution article ‘On the importance of accounting for intraspecific genomic relatedness in multi‐species studies‘ taken from the Université de Montréal.

Bud of American beech (Fagus grandifolia). ©Tim Savas

Researchers from Canada and the USA found that tree and shrub genetics can be used to produce more accurate predictions of when leaves will burst bud in the spring. Their study was published in Methods in Ecology and Evolution.

Although climate sceptics might find it hard to believe with this year’s endless snow and freezing temperatures, climate change is making warm, sunny early springs increasingly common. And that affects when trees start to leaf out. But how much?

Simon Joly, biology professor at Université de Montréal and Elizabeth Wolkovich, an ecology professor at University of British Columbia, showed that a plant’s genetics can be used to produce more accurate predictions of when its leaves will burst bud in spring. Continue reading

ViXeN: View eXtract aNnotate Multimedia Data

Post provided by KadaMbari Devarajan

At a time when data is everywhere, and data science is being talked about as the future in different fields, a method that produces huge amounts of multimedia data is camera-trapping. We need ways to manage these kinds of media data efficiently. ViXeN is an attempt to do just that.

Camera traps have been a game-changer for ecological studies, especially those involving mammals in the wild. This has resulted in an increasing amount of camera trap datasets. However, the tools to manage camera trap data tend to be very specific and customised for images. They typically come with stringent data organisation requirements. There’s a growing amount of multimedia datasets and a lack of tools that can manage several types of media data.

In ‘ViXeN: An open‐source package for managing multimedia data’ we try to fix this visible gap. Camera trap management is a very specific a use-case. We thought that the field was missing general-purpose tools, capable of handling a variety of media data and formats, that were also free and open source. ViXeN was born from this idea. It stands for View eXtract aNnotate (media data). The name is also an ode to the canids I was studying at the time which included two species of foxes.


Example camera trap video Continue reading

Scant Amounts of DNA Reveal Conservation Clues

Below is a press release about the Methods in Ecology and Evolution article ‘Empowering conservation practice with efficient and economical genotyping from poor quality samples‘ taken from the Stanford Woods Institute for the Environment.

Wild tiger in India. ©Prasenjeet Yadav

The challenges of collecting DNA samples directly from endangered species makes understanding and protecting them harder. A new approach promises cheap, rapid analysis of genetic clues in degraded and left-behind material, such as hair and commercial food products.

The key to solving a mystery is finding the right clues. Wildlife detectives aiming to protect endangered species have long been hobbled by the near impossibility of collecting DNA samples from rare and elusive animals. Continue reading

Editor Recommendation: Quantitative Evolutionary Patterns in Bipartite Networks

Post provided by ROB FRECKLETON

The study of interactions and their impacts on communities is a fundamental part of ecology. Much work has been done on measuring the interactions between species and their impacts on relative abundances of species. Progress has been made in understanding of the interactions at the ecological level, but we know that co-evolution is important in shaping the structure of communities in terms of the species that live there and their characteristics. Continue reading

Issue 10.5: Movement Ecology, Palaeobiology, Monitoring and More

The May issue of Methods is now online!

The May issue of Methods in Ecology and Evolution is absolutely packed! We’ve got a new ecoacoustics method from Metcalf et al. and a new inference and forecasting method from Cenci et al. There’s also a forum article on image analysis, and papers on physiology, palaeobiology, capture-recapture and much more. We’ve got SIX papers that are freely available to absolutely everyone this month too.

Find out a little more about the new issue of Methods in Ecology and Evolution (including details about what the diver is doing to the coral in the cover image) below. Continue reading

2018 Robert May Prize Winner: Laura Russo

The Robert May Prize is awarded annually for the best paper published in Methods in Ecology and Evolution by an Early Career Researcher. We’re delighted to announce that the 2018 winner is Laura Russo, for her article ‘Quantitative evolutionary patterns in bipartite networks: Vicariance, phylogenetic tracking or diffuse co‐evolution?‘.

Plant-pollinator interactions are often considered to be the textbook example of co-evolution. But specialised interactions between plants and pollinators are the exception, not the rule. Plants tend to be visited by many different putative pollinator species, and pollinating insects tend to visit many plant hosts. This means that diffuse co-evolution is a much more likely driver of speciation in these communities. So, the standard phylogenetic methods for evaluating co-evolution aren’t applicable in most plant-pollinator interactions. Also, many plant-pollinator communities involve insect species for which we do not yet have fully resolved phylogenies. Continue reading

Volunteer Ornithological Survey Shows Effects of Temperatures on Eurasian Jay Population

Below is a press release about the Methods in Ecology and Evolution article ‘Incorporating fine‐scale environmental heterogeneity into broad‐extent models‘ taken from the University of Southampton.

A study led by researchers at the University of Southampton has used data collected by volunteer bird watchers to study how the importance of wildlife habitat management depends on changing temperatures for British birds.

The team studied data from the British Trust for Ornithology’s Bird Atlas 2007 – 11 on the abundance of the Eurasian jay over the whole of Great Britain. The University of Southampton researchers focused on jays for this trial as they are a species of bird known to frequent a mixture of different natural environments. Continue reading

Introducing fishtree and fishtreeoflife.org

This post was originally published on Jonathan Chang’s blog.

In our recent publication (Rabosky et al. 2018) we assembled a huge phylogeny of ray-finned fishes: the most comprehensive to date! While all of our data are accessible via Dryad, we felt like we could go the extra mile to make it easy to repurpose and reuse our work. I’m pleased to report that this effort has resulted in two resources for the community: the Fish Tree of Life website, and the fishtree R package. The package is available on CRAN now, and you can install it with:

install.packages("fishtree")

The source is on GitHub in the repository jonchang/fishtree. The manuscript describing these resources has been published in Methods in Ecology and Evolution (Chang et al. 2019).

Continue reading