Why Accurate Stable Isotope Discrimination Factors are so Important: A cautionary tale (involving kea)

Post provided by AMANDA GREER

Stable isotopes as a tool for ecologists

Our research into the foraging ecology of this cheeky parrot (kea: Nestor notabilis) prompted us to develop a simple method to establish discrimination factors © Andruis Pašukonis

Our research into the foraging ecology of this cheeky parrot (kea: Nestor notabilis) prompted us to develop a simple method to establish discrimination factors © Andruis Pašukonis

Isotopes are atoms that have the same number of protons and electrons but differ in their number of neutrons; they are lighter and heavier forms of the same element. Unlike radioactive isotopes, stable isotopes do not decay over time.

The ratio of heavy to light stable carbon (δ13C) and nitrogen (δ15N) isotopes in an animal’s tissues depend on its diet, although offset by a certain amount. This integration of δ13C and δ15N from an animal’s diet into its tissues allows ecologists to use stable isotope analysis to investigate a species’ present and historical diets, food-web structures, niche shifts,  migration patterns and more.   Continue reading

Issue 6.11

Issue 6.11 is now online!

The November issue of Methods is now online!

This month’s issue contains two Applications articles and one Open Access article, all of which are freely available.

mvMORPH: A package of multivariate phylogenetic comparative methods for the R statistical environment which allows fitting a range of multivariate evolutionary models under a maximum-likelihood criterion. Its use can be extended to any biological data set with one or multiple covarying continuous traits.

Low-cost soil CO2 efflux and point concentration sensing systems: The authors use commercially available, low-cost and low-power non-dispersive infrared (NDIR) CO2 sensors to develop a soil CO2 efflux system and a point CO2 concentration system. Their methods enable terrestrial ecologists to substantially improve the characterization of CO2 fluxes and concentrations in heterogeneous environments.

This month’s Open Access article comes from Jolyon Troscianko and Martin Stevens. In ‘Image calibration and analysis toolbox – a free software suite for objectively measuring reflectance, colour and pattern‘ they introduce a toolbox that can convert images to correspond to the visual system (cone-catch values) of a wide range of animals, enabling human and non-human visual systems to be modelled. The toolbox is freely available as an addition to the open source ImageJ software and will considerably enhance the appropriate use of digital cameras across multiple areas of biology. In particular, researchers aiming to quantify animal and plant visual signals will find this useful. This article received some media attention upon Early View publication over the summer. You can read the Press Release about it here.

Our November issue also features articles on Population Genetics, Macroevolution, Modelling species turnover, Abundance modelling, Measuring stress and much more. Continue reading

High-Res Camera Surveys of Wildlife Colonies: The advantages over traditional approaches

Post provided by ALISTAIR HOBDAY (senior principal research scientist, CSIRO Australia), Tim Lynch (senior research scientist, CSIRO, Australia) and Rachael Alderman (wildlife biologist, Tasmanian Department of Primary Industry, Parks, Water and Environment, Australia).

Cameras and wildlife monitoring

A Gigapan camera setup to record images of an albatross colony. ©Alistair Hobday

A Gigapan camera setup to record images of an albatross colony. ©Alistair Hobday

Behavioural and ecological research and monitoring of wildlife populations are based on collection of field data. Demographic data, such as breeding frequency, birth rates and juvenile survival, have been critical in understanding population trends for a wide range of species.

Photography has been extensively used by field biologists and ecologists to gather these data and they have been quick to take up improvements in this technology. Many field programmes today use photography either for primary data collection or the communication of results. Advances in digital photography, image storage and transmission, image processing software and web-based dissemination of images have been extremely rapid in recent years, offering ecologists and biologists a range of powerful tools.

Digital imagery has been captured from a wide range of platforms, each of which has various advantages and limitations for biological study. The most remote images are captured from satellite-based sensors, which have been used to assess population abundance of large animals, such as elephant seals, or locate colonies of emperor penguins. Cameras mounted on aircraft can also provide large-scale perspectives but both of these platforms suffer from high cost, operational limitations due to weather, and limited temporal replication. Recent use of drones, while cheaper, still requires a person to be close to the survey location and can only be used in short bursts, typically lasting less than 20 minutes.

Land-based cameras – or those fixed onto animals – can track behaviour closely, but have low sample size as data tends to be collected at the scale of individual or small groups. To improve replication, fleets of remote cameras can be used or multiple images stitched together post hoc to form a montage. However, this increases cost, either for hardware or labour to manually construct panoramas. To date all these camera systems have had limits to their spatial and/or temporal resolution and, therefore, to the number of individuals covered. This restricts biological study at the population level. Continue reading

Making the Most of Volunteer Data: Counting the birds and more…

Post provided by Rob Robinson

It’s 6am on a warm spring morning and I’m about to visit the second of my Breeding Bird Survey1 sites. Like 2,500 other volunteers in the UK, twice a year I get up early to record all the birds I see or hear on the two transects in my randomly selected 1km square. Each year I look forward to these mornings almost as much for the comparisons as the actual sightings. Will there be more or fewer sightings of our summer migrants this year? How will numbers in this rolling Norfolk farmland stack up against those I see in urban, central Norwich?

Dawn bird survey in arable farmland. © Rob Robinson/BTO

Dawn bird survey in arable farmland. © Rob Robinson/British Trust for Ornithology (BTO)

The importance of demography

But simply recording these changes is not enough; we need to understand why they occur if action is to be taken. This requires us to quantify the demographic rates (survival, productivity and movements) that underlie them, which in turn requires samples of marked individuals. Simply counting individuals is not enough. Continue reading

Accompanying Marine Mammals into the Abyss: The Benefits of Electronic Tag Data for Undersea Tracking

Post provided by Christophe Laplanche, Tiago Marques and Len Thomas

1km Deep

Most marine mammal species spend the majority of their lifetime at sea… underwater. Some species (like sperm whales, beaked whales, and elephant seals) can go routinely as deep as 1000m below sea level. To mammals like us, these incredible depths seem uninhabitable. It’s cold, dark, under high pressure (100kg/cm²) and 1km from air! Yet deep-diving marine mammals thrive there and have colonized every deep ocean on the planet. They have developed amazing capabilities for that purpose – including efficient swimming, an advanced auditory system, sonar (in some cases), thermal insulation, extreme breath holding abilities and resistance to high pressure.

How is that possible?

Spending most of their time at depth makes them quite difficult to study. And we have a lot of questions to ask them. How do they balance swimming cost versus food intake? Do they forage cooperatively, in groups? For those with sonar, how does it work? With increasing human activities (oil exploration, military sonar, sea transport, fishing etc.) an important new question arises: how do they cope with us?

Researchers tagging a Cuvier's beaked whale with a DTAG sound tag (soundtags.st-andrews.ac.uk) in the Ligurian Sea (© T. Pusser)

Researchers tagging a Cuvier’s beaked whale with a DTAG sound tag (soundtags.st-andrews.ac.uk) in the Ligurian Sea (© T. Pusser)

Continue reading

Progress and Future Directions for Passive Acoustic Monitoring: Listening Out for New Conservation Opportunities

Post provided by Ammie Kalan (Post-doctoral researcher at the Max Planck Institute for Evolutionary Anthropology, Department of Primatology)

A Primate Call in a Forest is like a ‘Needle in a Haystack’

An ARU powered by solar energy recording in the Taï national park, Côte d’Ivoire. ©Ammie Kalan

A solar-powered ARU recording in the Taï national park, Côte d’Ivoire.
©Ammie Kalan

Finding a call of a particular primate species within hours and hours of audio recordings of a forest is no easy task; like finding a ‘needle in a haystack’ so to speak. Automated acoustic monitoring relies on the ability of researchers to easily locate and isolate acoustic signals produced by species of interest from all other sources of noise in the forest, i.e. the background noise. This can be much harder than it sounds. Think about whenever you have to use any kind of voice recognition system: seeking out a quiet room will greatly improve the chances you are understood by the robot-like voice on the other end of the phone. If you ever set foot in a rainforest the first thing you’ll notice is that it is anything but quiet. In fact characterizing and quantifying soundscapes has become a marker for the complexity of the biodiversity present in a given environment.

Primate monitoring programmes can learn a great deal from cetacean research where Passive Acoustic Monitoring (PAM) is the norm (since individuals are rarely observable visually). Research on bats and birds can provide excellent examples to follow as well. Automated algorithm approaches including machine learning techniques, spectral cross-correlation, Gaussian mixture models, and random forests have been used in these fields to be able to detect and classify audio recordings using a trained automated system. Such automated approaches are often investigated for a single species but impressive across-taxa efforts have also been initiated within a framework of real-time acoustic monitoring. Implementing these in other research fields could lead to significant advances. Continue reading

The DOs and DON’Ts of Selecting Preferred Reviewers

Like many journals, Methods in Ecology and Evolution asks authors to submit a list of preferred reviewers along with their manuscript. This can be a difficult task and is often one that is overlooked or rushed when submitting. However, this list can be very important in the peer review process.

Why Do We Need Preferred Reviewers?

©Nic McPhee

©Nic McPhee

There are a number of reasons that we ask authors to provide preferred reviewers. These suggestions can be extremely useful in a number of situations. For example, if the Associate Editor is struggling to find referees for a paper, the preferred reviewers become a very valuable resource. Not only are they potential reviewers, but if they are unable to review the paper they can suggest other people who might be able to.

As Methods is a generalist journal, sometimes papers are submitted that do not fit perfectly into the areas of expertise of our Associate Editors. In cases such as these, the preferred reviewers can be a wonderful starting point for the reviewer search. Providing the Editors with a good list of experts in the subject (who they may not know off the top of their head) can make the peer review process quicker and easier for everyone involved.

While Editors are by no means required or obliged to choose the reviewers that authors suggest, the list can often be a source of inspiration. If the Editor chooses not to invite any of the preferred reviewers, they may use the suggestions to try to find people with similar expertise.

Providing a good list of preferred reviewers can speed up the peer review process and make it a much less stressful experience. So, what makes a preferred reviewer list good or bad? The DOs and DON’Ts below should help you to suggest the right reviewers for your paper. Continue reading

Issue 6.10

Issue 6.10 is now online!

The October issue of Methods is now online!

This month’s issue contains two Applications articles and one Open Access article, all of which are freely available.

letsR: A package for the R statistical computing environment, designed to handle and analyse macroecological data such as species’ geographic distributions and environmental variables. It also includes functions to obtain data on species’ habitat use, description year and current as well as temporal trends in conservation status.

Cleaning Oil from Seabirds: The authors assess the efficacy of sea water as an alternative to fresh water for cleaning oil from seabirds’ feathers. Results indicate that for oiled feathers, a sea water wash/rinse produced clean, low BAI/unclumped feathers with minimal particulate residue.

Stefano Canessa et al. provide this month’s only Open Access article. In ‘When do we need more data? A primer on calculating the value of information for applied ecologists‘ the authors guide readers through the calculation of Value of Information (VoI) using two case studies and illustrate the use of Bayesian updating to incorporate new information. Collecting information can require significant investments of resources; VoI analysis assists managers in deciding whether these investments are justified. The authors also wrote a blog post on VoI which you can find here.

Our October issue also features articles on Niche Modelling, Population Ecology, Spatial Ecology, Conservation, Monitoring and much more. Continue reading

New Associate Editors

Over the next few weeks we will be welcoming three new Associate Editors to Methods in Ecology and Evolution. Susan Johnston (University of Edinburgh, UK) became a member of the Associate Editor Board on Monday 5 October. She will be joined on 19 October by Natalie Cooper (Natural History Museum, London, UK) and finally by Luísa Carvalheiro (University of Brasília, Brazil) on 2 November. You can find out more about all three of our new Associate Editors below.

Susan Johnston

Susan Johnston“My research focuses on using genomic information to understand evolution in natural populations. I adapt mixed model approaches to determine the genetic architecture of interesting traits (e.g. estimating heritability, genome-wide association studies, outlier analyses) to examine its relationship with fitness or importance in local adaptation. I am interested in the potential of affordable genomics to answer evolutionary and ecological questions in wild systems, and how to deal with various statistical issues arising from such studies in small and/or structured populations.”

Susan’s most recently published article is ‘Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population‘, co-authored with T. Aykanat, P. Orell, E. Niemelä, J. Erkinaro and C.R. Primmer. The findings suggest that different evolutionary processes affect sub-populations of Atlantic salmon and that hybridization and subsequent selection may maintain low genetic differentiation without hindering adaptive divergence. This article was published in Molecular Ecology.

Natalie Cooper

Natalie Cooper“I am an evolutionary biologist, focusing mainly on macroevolution and macroecology. My interests include phylogenetic comparative methods, morphological evolution, using museum specimens in research, and integrating neontological and palaeontological data and approaches for understanding broad-scale patterns of biodiversity.”

Natalie has recently been published in Molecular Phylogenetics and Evolution (‘Effects of missing data on topological inference using a Total Evidence approach‘ with T. Guillerme) and in Evolution (‘Investigating evolutionary lag using the species-pairs evolutionary lag test (SPELT)‘ with C.L. Nunn). She was also a speaker at the Methods in Ecology and Evolution 5th Anniversary Symposium. Her presentation, ‘Limitations of Phylogenetic Comparative Methods‘, is freely available on YouTube.

Luísa Carvalheiro

Luisa Carvalheiro“My research focuses on community ecology & conservation. I have particular interest in the study of dynamics of biodiversity through time and space; and on the evaluation of how such biotic changes affect ecosystem functioning and ecosystem services, considering how the complex network of ecological interactions in which species are integrated mediates such changes.”

Earlier this year Luísa’s article ‘Susceptibility of pollinators to ongoing landscape changes depends on landscape history‘ (with J. Aguirre-Gutiérrez, J.C. Biesmeijer, E.E. van Loon, M. Reemer, and M.F. Wallis De Vries) was published in Diversity and Distributions. The article emphasizes the limited value of a one-size-fits-all biodiversity conservation measures and highlights the importance of considering landscape history when planning biodiversity conservation actions. This article is Open Access. Luísa was also the lead author of ‘The potential for indirect effects between co-flowering plants via shared pollinators depends on resource abundance, accessibility and relatedness‘ an Open Access article published in Ecology Letters last year.

We are thrilled to welcome Susan, Natalie and Luísa to the Associate Editor Board and we look forward to working with them over the coming years.

Issue 6.9

Issue 6.9 is now online!

The September issue of Methods is now online!

This month’s issue contains one Applications article and two Open Access articles, all of which are freely available.

POPART: An integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication-ready figure production. The package also provides a platform for the implementation and distribution of new network-based methods.

Michalis Vardakis et al. provide this month’s first Open Access article. In ‘Discrete choice modelling of natal dispersal: ‘Choosing’ where to breed from a finite set of available areas‘ the authors show how the dispersal discrete choice model can be used for analysing natal dispersal data in patchy environments given that the natal and the breeding area of the disperser are observed. This model can be used for any species or system that uses some form of discrete breeding location or a certain degree of discretization can be applied.

Our September issue also features articles on Animal Movement, Population Dynamics, Statistical Ecology, Biodiversity, Conservation Biology and much more. Continue reading