Category: Methods papers

Methods papers

What About Winter? Accounting for the Snow Season When We Simulate Climate Warming

Post provided by Rebecca Sanders-DeMott and Pamela Templer

Processes that occur in winter are a significant component of annual carbon and nutrient cycles. ©Travel Stock Photos
Processes that occur in winter are a significant component of annual carbon and nutrient cycles. ©Travel Stock Photos

The climate is changing throughout the globe with consequences for the biogeochemical processes and ecological relationships that drive ecosystems. Scientists have been conducting manipulative experiments to determine the effect of climate warming on ecosystems for several decades. These experiments allow us to observe ecosystem responses before the climate changes occur and have yielded invaluable insight that has expanded our understanding of the natural world.

There is a wide range of creative approaches to mimicking climate warming that have been used, for example open-topped chambers which passively heat small areas of soil and small stature plants (like the ITEX global network), burying heating cables in the soil to directly increase soil temperatures (e.g. Harvard Forest experiments), infrared heating lamps (like Jasper Ridge), or even large scale chambers that can encompass taller stature plants like trees and actively warm the air (like the SPRUCE experiment). The focus of much of these inquiries has been on changes that occur during the growing season, when biological activity is at its peak. Continue reading “What About Winter? Accounting for the Snow Season When We Simulate Climate Warming”

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Lab Methods, Methods papers, Photo Post

Scales, Slime and Dragon(fly) Wings? Investigating the Surfaces of Organisms

Post provided by Dylan Wainwright Our recent Methods in Ecology and Evolution paper – ‘Imaging biological surface topography in situ and in vivo‘ – shows how to use gel-based profilometry to image various biological surfaces. To start you need to press a gel into a surface of interest. The bottom surface of the gel is coated in a paint to create an impression of the surface that has standard optical … Continue reading Scales, Slime and Dragon(fly) Wings? Investigating the Surfaces of Organisms

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Methods papers, Online extras

How Can We Quantify the Strength of Migratory Connectivity?

Technological advancements in the past 20 years or so have spurred rapid growth in the study of migratory connectivity (the linkage of individuals and populations between seasons of the annual cycle). A new article in Methods in Ecology and Evolution provides methods to help make quantitative comparisons of migratory connectivity across studies, data types, and taxa to better understand the causes and consequences of the seasonal distributions … Continue reading How Can We Quantify the Strength of Migratory Connectivity?

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Methods papers, Online extras

Improved and Harmless Demethylation Method for Ecological Epigenetic Experiments

In a new Methods in Ecology and Evolution video, Javier Puy outlines a new method of experimental plant DNA demethylation for ecological epigenetic experiments. While the traditionally-used approach causes underdeveloped root systems and high mortality of treated plants, this new one overcomes the unwanted effects while maintaining the demethylation efficiency. The authors demonstrate its application for ecological epigenetic experiments: testing transgenerational effects of plant–plant competition. … Continue reading Improved and Harmless Demethylation Method for Ecological Epigenetic Experiments

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Methods papers, Online extras

Animal Behaviour through a Virtual Lens

Motion vision is an important source of information for many animals. It facilitates an animal’s movement through an environment, as well as being essential for locating prey and detecting predators. However, information on the conditions for motion vision in natural environments is limited. To address this, Bian et al. have developed an innovative approach that combines novel field techniques with tools from 3D animation to … Continue reading Animal Behaviour through a Virtual Lens

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Conservation and management, Evolution, Methods papers

Sticking Together or Drifting Apart? Quantifying the Strength of Migratory Connectivity

Post provided by Emily Cohen

Red Knot migratory connectivity is studied with tracking technologies and color band resighting. © Tim Romano
Red Knot migratory connectivity is studied with tracking technologies and colour band resighting. © Tim Romano

The seasonal long-distance migration of all kinds of animals – from whales to dragonflies to amphibians to birds – is as astonishing a feat as it is mysterious and this is an especially exciting time to study migratory animals. In the past 20 years, rapidly advancing technologies  – from tracking devices, to stable isotopes in tissues, to genomics and analytical techniques for the analysis of ring re-encounter databases – mean that it’s now possible to follow many animals throughout the year and solve many of the mysteries of migration.

What is Migratory Connectivity?

One of the many important things we’re now able to measure is migratory connectivity, the connections of migratory individuals and populations between seasons. There are really two components of migratory connectivity:

  1. Linking the geography of where individuals and populations occur between seasons.
  2. The extent, or strength, of co-occurrence of individuals and populations between seasons.

Continue reading “Sticking Together or Drifting Apart? Quantifying the Strength of Migratory Connectivity”

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Evolution, Methods papers

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

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Lab Methods, Methods papers

Animation Meets Biology: Shedding New Light on Animal Behaviour

Below is a press release about the Methods paper ‘Integrating evolutionary biology with digital arts to quantify ecological constraints on vision-based behaviour‘ taken from the La Trobe University.

Ctenophorus fionni (Peninsula Dragon), male push up display - Copyright Jose Ramos, La Trobe University
Ctenophorus fionni (Peninsula Dragon), male push up display. © Jose Ramos, La Trobe University

Many animals rely on movement to find prey and avoid predators. Movement is also an essential component of the territorial displays of lizards, comprising tail, limb, head and whole-body movements.

For the first time, digital animation has been used as a research tool to examine how the effectiveness of a lizard’s territorial display varies across ecological environments and conditions. The new research was published today in the journal Methods in Ecology and Evolution.

A team from La Trobe University’s School of Life Sciences, led by Dr Richard Peters, worked with academics from Monash University’s Faculty of IT to create, using 3D animation, a series of varied environmental settings and weather conditions, comprising different plant environments and wind conditions, to quantify how lizard displays are affected by this variation. Continue reading “Animation Meets Biology: Shedding New Light on Animal Behaviour”

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Methods papers, Virtual Issues

Microbial Methods Virtual Issue

The BES Microbial Ecology Special Interest Group is running a workshop today (Thursday 2 November) on Novel Tools for Microbial Ecology. To compliment this workshop, Xavier Harrison has edited a Virtual Issue of the best Methods in Ecology and Evolution articles on advances in methods of studying microbial evolution and ecology from the past few years.

Advances in Next-Generation Sequencing (NGS) technology now allow us to study associations between hosts and their microbial communities in unprecedented detail. However, studies investigating host-microbe interactions in the field of ecology and evolution are dominated by 16S and ITS amplicon sequencing. While amplicon sequencing is a useful tool for describing microbial community composition, it is limited in its ability to quantify the function(s) performed by members of those communities. Characterising function is vital to understanding how microbes and their hosts interact, and consequently whether those interactions are adaptive for, or detrimental to, the host. The articles in this Virtual Issue cover a broad suite of approaches that allow us to study host-microbe and microbe-microbe interactions in novel ways.

All of the articles in the Microbial Methods Virtual Issue will be freely available for the next two months. You can find out a little more about each one below. Continue reading “Microbial Methods Virtual Issue”

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Conservation and management, Methods papers

Midwater Ocean Communities: Sounds Like Siphonophore Soup

Post provided by Roland Proud

How do we know how many fish there are in the ocean? 1000, 1 billion, 1000 billion? We can’t catch them all and count – that’s not practical. Nor can we make observations from Earth-orbiting satellites – light does not penetrate far into the ocean. What we can use is sound.

Sound travels well in water (faster and further than it does in air), so we can use scientific SONAR (echosounders) to produce sound waves and record backscatter from organisms and communities. This provides information concerning their biomass, distribution and behaviour. A recent study used echoes from the mesopelagic zone (200 – 1,000m) to predict global mesopelagic fish biomass to be between 11 and 15 billion tonnes (that’s a lot), suggesting that mesopelagic fish communities could potentially provide global food security.

Mesopelagic Biogeography

In a recent paper, we (the Pelagic Ecology Research Group, PERG at the University of St Andrews) divided the global ocean up into regions based on the properties of echoes from the mesopelagic zone (see below).

10 mesopelagic classes are shown for the open-ocean, echo intensity (a proxy for biomass) increases from blue to red. Coastal zones excluded. Longhurst provinces overlaid. Shapefile here. Proud et al. (2017)
10 mesopelagic classes are shown for the open-ocean, echo intensity (a proxy for biomass) increases from blue to red. Coastal zones excluded. Longhurst provinces overlaid. Shapefile here. Proud et al. (2017)

Continue reading “Midwater Ocean Communities: Sounds Like Siphonophore Soup”

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