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 determine how habitat structure, weather and motion vision influence animal behaviour. Their project focuses on Australia’s charismatic dragon lizards, and will place the animals’ motion displays in a visual-ecological context. The application of this approach goes well beyond this topic and the authors suggest the motion graphic technologies is a valuable tool for investigating the visual ecology of animals in a range of environments and at different spatial and temporal scales.

This video is based on the article ‘Integrating evolutionary biology with digital arts to quantify ecological constraints on vision-based behaviour by Bian et al.

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Two More New Associate Editors

Today we are welcoming two more Associate Editors to the Methods in Ecology and Evolution who were invited to work with the journal following our open call earlier this year. Jessica Royles joins from the University of Cambridge, UK and Simon Blomberg is coming to us from the University of Queensland, Australia. You can find out more about both of them below.

Simon Blomberg

“I am a statistician who started out as a lizard demographer. I am interested in all applications of statistics in evolutionary biology and systematics. It is my passion to see that good science gets done by everybody, and sound statistical methods are essential to reach that goal. My research involves the application of stochastic process models (predominantly Itoh diffusions) to the macroevolution of quantitative traits. I believe that evolution can be described by beautiful mathematics but theory must be tested with data. I have published widely on phylogenetic comparative methods. I use Bayesian methods, data augmentation, regularisation and other modern and traditional statistical methods. I am interested in how to treat missing data. I still like lizards. Also jazz.”

Simon has been working on stochastic process models for a couple of years. His most recent article ‘Beyond Brownian motion and the Ornstein-Uhlenbeck process: Stochastic diffusion models for the evolution of quantitative characters‘ is now available on BioRxiv and he would welcome comments on it from the Methods community.

Jessica Royles

“I am interested in the impact of climate change on plant physiology and specialise in using stable isotopes as environmental markers. Having worked in Antarctica I have strong interests in polar biology, high latitude peatlands and fieldwork techniques. My current work focusses on  temperate bryophytes and I am interested in using techniques including gas exchange and chlorophyll fluorescence at different spatial scales to link the leaf level to the ecosystem level.”

Jessica’s most recently published article – ‘Widespread Biological Response to Rapid Warming on the Antarctic Peninsula‘ – describes how she and her co-authors used moss cores to study Antarctic warming due to climate change. The article builds on her previous paper ‘Plants and Soil Microbes Respond to Recent Warming on the Antarctic Peninsula‘. Jessica is currently working on a Moss Ecophysiology project which aims to investigate the value of mosses as tools to understand past climate.

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

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.

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Issue 8.11

Issue 8.11 is now online!

The November issue of Methods is now online!

This extra large issue contains seven Applications articles and three Open Access articles. These five papers are freely available to everyone, no subscription required.

 LSCorridors: LandScape Corridors considers stochastic variation, species perception and landscape influence on organisms in the design of ecological corridors. It lets you simulate corridors for species with different requirements and considers that species perceive the surrounding landscape in different ways.

 HistMapR: HistMapR contains a number of functions that can be used to semi-automatically digitize historical land use according to a map’s colours. Digitization is fast, and agreement with manually digitized maps of around 80–90% meets common targets for image classification. This manuscript has a companion video and was recommended by Associate Editor Sarah Goslee.

 vortexR: An R package to automate the analysis and visualisation of outputs from the population viability modelling software Vortex. vortexR facilitates collating Vortex output files, data visualisation and basic analyses (e.g. pairwise comparisons of scenarios), as well as providing more advanced statistics.

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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

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

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.

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

New Associate Editors

Today we are welcoming seven new people to the Methods in Ecology and Evolution Associate Editor Board. All of these new Associate Editors were invited to join the Board following our open call for applications a couple of months ago. You can find out more about them below.

Karen Bacon

Karen Bacon

Karen Bacon

“I am a plant ecologist and palaeoecologist with interests that span the present day to the Mesozoic. My particular interests include plant–atmosphere interactions, fossil plant taphonomy, mass extinctions, stable isotope ecology, and Anthropocene ecology. My current work focuses on the development of plant-based proxies to improve interpretations of plant responses to past environmental change and investigating plant functional traits that lead to success across environmental upheaval events in both the fossil record and present day.”

Torbjørn Ergon

Torbjørn Ergon

“I am a population/evolutionary ecologist with wide interests. My research has mostly been focused on variation in life-history traits and demographic rates within populations, and I have a strong interest in statistical modelling in this field. As an associate editor of Methods in Ecology and Evolution, I hope to promote novel papers that pay close attention to ecological/evolutionary theory in addition to study design and statistical modelling.” Continue reading

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)

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