Solving the Midpoint Melee: Introducing New Methods for Plant Cover Classes

Post provided by KATHI IRVINE and TOM RODHOUSE

Collecting ordinal data. ©NPS

Or better yet, this post could be named ‘Our Cathartic Journey to Convince Ecologists to STOP Using the Midpoint Values for Analysing Plant Cover Classes’. Our work picks up where another recent post (Stuck between Zero and One) and Methods in Ecology and Evolution article (‘Analysing continuous proportions in ecology and evolution’) by Douma and Weedon left off. They introduced the benefits of using beta and Dirichlet regression. We’re going to tackle the sticky wicket of ordinal data. So, what should you do if you assign a range (like 0.2 to 0.3) instead of record a value (like 0.22) for a continuous proportion?

What is Ordinal Data?

It’s probably a good idea to start by defining the type of data we’re talking about. The best example is from plant surveys. Biologists visually assess the percentage of a pre-defined area covered by a certain plant species. They then record a ‘cover class value’ as an estimate of abundance. Each cover class value corresponds to the percentage of the area that is taken up by the plant in question (e.g., record a 0 for 0%, record a 1 for >0-5%, record a 2 for >5-25%, …, record a 6 for >95%). Continue reading

Researchers Develop Tools to Help Manage Seagrass Survival

Below is a press release about the Methods in Ecology and Evolution article ‘Analysing the dynamics and relative influence of variables affecting ecosystem responses using functional PCA and boosted trees: a seagrass case study‘ taken from Queensland University of Technology.

©Paul Asman and Jill Lenoble

A new QUT-led study has developed a statistical toolbox to help avoid seagrass loss which provides shelter, food and oxygen to fish and at-risk species like dugongs and green turtles. Seagrasses are a critical habitat that have been declining rapidly globally.

The research has been published in Methods in Ecology and Evolution describing key monitoring and management designs to maximise seagrass resilience to human activities. They will help to better inform seagrass dredging operations and development of coastal areas.

Led by statistical data researcher and lecturer Dr Paul Wu, from QUT’s School of Mathematical Sciences, the study identified and analysed factors that drove variations in a global seagrass dredging case study. Continue reading

Making Tags Less of a Drag: Optimising Biologging Devices with Computational Fluid Dynamics

Post provided by WILLIAM KAY

Drag and Biologging Devices

A harbour seal tagged with a biologging device. ©Dr Abbo van Neer

A harbour seal tagged with a biologging device. ©Dr Abbo van Neer

Michael Phelps is one of the most decorated Olympic athletes of all time and the world’s fastest swimmer. And yet, he could swim faster. Wearing the Speedo LZR Racer supersuit Michael Phelps could reduce his hydrodynamic drag, or water resistance, by upwards of 40%. That could increase his swim speed by more than 4%! In competition, that’s the difference between silver and gold. But, if Phelps forgot to remove his “drag socks” – cumbersome footwear designed to increase water resistance for strength training – his speed would be dramatically reduced. He’d be lucky to walk away with bronze!

Professional swimmers have adapted to the use of performance enhancing technologies to decrease their drag, but that’s nothing compared to the adaptations made by wild animals. Creatures in the marine environment have evolved incredible adaptations to decrease drag, such as extreme streamlining in marine mammals and seabirds. This allows them to move underwater as quickly and efficiently as possible. Seals, for example, are pretty ungainly on land, but in the water they’re sleek and rapid. They have a body shape designed to maximise speed while swimming.

When we study marine animals we often use tracking devices, which can be attached using harnesses, glue, or suction-cups. These ‘biologging devices‘, or tags, are similar to Fitbits. Attaching them to animals allows us to record, amongst other things, all of the animal’s movements and behaviours. This information is crucial to understanding their ecology and for improving their conservation management. Continue reading

Bringing Movement Ecologists and Remote Sensing Experts Together: Seeing the World through Each Other’s Eyes with rsMove

Post provided by RUBEN REMELGADO

“Man must rise above Earth to the top of the atmosphere and beyond, for only then will he fully understand the world in which he lives” – Socrates (469-399 BC)

Since the launch of the first Landsat mission in 1972, several new earth observation satellites made their way into Earth’s orbit. As of 2018, UNOOSA recorded an impressive 1980 active satellites. Of those, 661 were dedicated to earth observation. These numbers show how widespread the use of remote sensing technologies has become.

As space agencies recognised the scientific and economic value of satellite data, they made it open access. By doing so, they gave the scientific community the means to develop a growing variety of spatially explicit – and often temporally dynamic – data products on both the land and the atmosphere. Over the years, those of us studying movement ecology have greatly profited from it. Continue reading

Issue 10.9: Phenotypes, Species Interactions, Biodiversity and More

The September issue of Methods is now online!

We’ve got another brilliant issue of Methods in Ecology and Evolution out today. In another bumper 250 page offering, you’ll find articles on identifying waterbird hotspots, identity metrics, capture-recapture methods (and the alternative close-kin mark-recpature) and way more.

Don’t have a subscription to the journal? No need to worry – this month’s issue has TEN articles that are free to access for absolutely anyone. You can find out about all 10 below.

Keep reading for a little more information on the September issue of Methods in Ecology and Evolution. Continue reading

Finding the Links between Prey and Microplastics

Below is a press release about the Methods in Ecology and Evolution article ‘What goes in, must come out: Combining scat‐based molecular diet analysis and quantification of ingested microplastics in a marine top predator‘ taken from Plymouth Marine Laboratory.

Wild grey seals. By Philip Newman, Natural Resources Wales

A brand new method has been developed by scientists at Plymouth Marine Laboratory (PML) and the University of Exeter, in collaboration with Abertay University and Greenpeace Research Laboratories, to investigate links between top predator diets and the amount of microplastic they consume through their prey. It offers potential insights into the exposure of animals in the ocean and on land to microplastics.

An estimated 9.6-25.4 million tonnes of plastic will enter the sea annually by 2025.  Microplastics in particular have been found on the highest mountains and in the deepest seas. New techniques are needed to trace, investigate and analyse this growing concern. Continue reading

Atlantis: A Model for Biophysical, Economic and Social Elements of Marine Ecosystems

Post provided by ASTA AUDZIJONYTE, Heidi Pethybridge, Javier Porobic, Rebecca Gorton, Isaac Kaplan, and Elizabeth A. Fulton

Increased Demands on a Crowded Ocean

Multiple demands on, and uses of, the ocean. ©Frank Shepherd

The ocean was once a limitless frontier, primed for exploitation of fish and other marine life. Today, a scan of the coastline (in our case off Australia and the US) shows an ocean landscape dotted with aquaculture pens, wind farms, eco-tours, and oil rigs, as well as commercial and recreational fishing boats. This presents marine and maritime managers with the huge challenge of balancing competing social, conservation, and economic objectives. Trade-offs arise even from success stories. For example, seal and sea lion populations are recovering from centuries of hunting, which is great. But now they’re preying heavily on economically valuable species like salmon and cod, creating potential tensions between fisheries and conservation communities. Ecosystem-based management is one way that we can start to address these trade-offs. Continue reading

Thermal Images in R


Why use Thermal Images?

Temperature is important in ecology. Rising global temperatures have pushed ecologists and conservationists to better understand how temperature influences species’ risk of extinction under climate change. There’s been an increasing drive to measure temperature at the scale that individual organisms actually experience it. This is made possible by advances in technology.

Enter: the thermal camera. Unlike the tiny dataloggers that revolutionised thermal ecology in the past decade or so, thermal images capture surface temperature, not atmospheric temperature. Surface temperature may be as (if not more) relevant for organisms that are very small or flat, or thermoregulate via direct contact with the surface. Invertebrates and herps are two great examples of these types of organisms – and together make up a huge proportion of terrestrial biodiversity. Also, while dataloggers can achieve impressive temporal extent and resolution, they can’t easily capture temperature variation in space.

Like dataloggers, thermal cameras are becoming increasingly affordable and practical. The FLIR One smartphone attachment, for example, weighs in at 34.5 g and costs around ~US$300. For that, you get 4,800 spatially explicit temperature measurements at the click of a button. But without guidelines and tools, the eager thermal photographer runs the risk of accumulating thousands of images with no idea of what to do with them. So we created the R package ThermStats. This package simplifies the processing of data from FLIR thermal images and facilitates analyses of other gridded temperature data too. Continue reading

Speeding Up Systematic Reviews: This New Method for Automated Keyword Selection Will Save You Time

Post provided by ELIZA GRAMES

The number of studies published every year in ecology and evolutionary biology has increased rapidly over the past few decades. Each new study contributes more to what we know about a topic, adding nuance and complexity that helps improve our understanding of the natural world. To make sense of this wealth of evidence and get closer to a complete picture of the world, researchers are increasingly turning to systematic review methods as a way to synthesise this information.

What is a Systematic Review?

Systematic reviews, first developed in public health fields, take an experimental design approach to reviewing the literature. They treat the search for primary studies as a transparent and reproducible data gathering process. The rigorous methods used in systematic reviews make them a trusted form of evidence synthesis. Researchers use them to summarise the state of knowledge on a topic and make policy and practice recommendations. Continue reading