Modelling Demographic Processes in Marked Populations: Proceedings of the EURING 2013 analytical meeting

Posted on November 27, 2014 by Samantha Ponton

By Charles M. Francis, Richard J. Barker, Evan G. Cooch

This joint Special Feature (published in MEE and the open access journal Ecology and Evolution) brings together a series of papers presented at the EURING 2013 technical conference that, collectively, cover many of the latest developments in the analysis of data from marked individuals to estimate demographic parameters, such as survival, recruitment, nest success, density, population size and movement.

The European Ringing Association (EURING) technical conferences were established to advance the field of ecological modelling by bringing together biologists with statistically challenging problems related to the analysis of data from marked animals and statisticians with the expertise to help develop appropriate models for analysis of those data. The initial impetus of the conferences was to develop improved methods for analysis of data derived from the millions of birds that have been ringed or otherwise uniquely marked since the early 20^th century in Europe and elsewhere in the world. Since then, these conferences have evolved to present leading edge statistical developments and applications relevant to many different types of work on marked animals, as well as other fields that benefit from mark-recapture type methodologies such as occupancy modelling.

The latest of these conferences, held in Athens, Georgia, USA, from April 28 to May 4 2013, continued the tradition of bringing together biologists and statisticians to advance the field. The papers presented, of which 31 are here included in the proceedings, covered a range of topics and included both development of new statistical approaches and application of established methods to specific biological data sets. The conference consisted of a mixture of plenary papers, presenting a broad overview of a topic, invited oral presentations and poster presentations.

The proceedings have been published in two journals, MEE and the open access journal Ecology and Evolution, and are collated in this Special Feature. The key themes represented in these proceedings include advances in statistical methods, spatially-referenced data, experimentation and hypothesis testing, integrating data from different sources, occupancy models, and future directions.

Click here to read the full Special Feature.

Laser scanning accurately ‘weighs’ trees

Posted on November 21, 2014 by Samantha Ponton

Below is a press release and video about the Methods paper, ‘Nondestructive estimates of above-ground biomass using terrestrial laser scanning‘, taken from UCL News:

Lidar point cloud from a scanned Eucalyptus tree (left) with colours correlating to point density (blue to red moving from high to low density). On the right is the reconstructed tree volume from which mass can be estimated.

A terrestrial laser scanning technique that allows the structure of vegetation to be 3D-mapped to the millimetre is more accurate in determining the biomass of trees and carbon stocks in forests than current methods, according to new research involving UCL.

The research paper, an international collaboration led by Wageningen University, is published today in Methods in Ecology and Evolution and demonstrates the technique in Australian forests.

The study authors believe it could be an important development in the monitoring of carbon stocks for worldwide climate policy-making. Both above-ground biomass and carbon stocks are important details for UN-REDD, the United Nations initiative on Reducing Emissions from Deforestation and forest Degradation that is striving to keep the destruction of forests in check and thereby preserve the uptake of carbon by trees.

Paper co-author Dr Mat Disney (UCL Geography) said: “This new paper shows how effectively we can now turn highly-accurate laser measurements, comprising millions of 3D laser points, into estimates of tree mass. Weighing trees is really hard – time Continue reading →

Seabirds’ plastic diet shows up in their feather oil

Posted on November 19, 2014 by Samantha Ponton

The amount of plastic a short-tailed shearwater has eaten can now be assessed by swabbing near its tail feathers. Credit: JJ Harrison (Creative commons)

BY CHRISTOPHER DOYLE
This article has been taken from ABC Environment.

Scientists have developed a new technique to assess how much plastic a seabird has eaten. It involves a quick massage and a cotton swab.

A TEAM OF AUSTRALIAN scientists has developed a new method for assessing how much plastic debris a seabird has eaten while foraging on the open ocean, leading to a better understanding of how human rubbish is affecting other species.

The scientists, from CSIRO’s Oceans and Atmosphere Flagship, say preening oil — the waxy substance used by seabirds to prevent their feathers from becoming waterlogged — can provide an indirect measure of plastic ingestion (findings published in MEE).

Click here to continue reading…

New Associate Editors

Posted on November 12, 2014 by Samantha Ponton

We’d like to welcome 4 new Associate Editors to the team! Patrick Jansen from Wageningen University, Nicolas Lecomte from Université de Moncton, John Reynolds from Simon Fraser University and Matt Schofield from the University of Otago. Read their profiles below to find out about their research interests:

Patrick Jansen

“I am an ecologist specializing in consumer-resource interactions, particularly those between predators and their prey and between herbivores and plants. My past research was mainly focused on seed dispersal by animals, my current research more broadly considers the roles of vertebrates in ecosystems. I am especially interested in how loss of species – for example due to overhunting – affects forest ecosystems. I am involved in the development of a variety of field techniques and analytical tools, such as for the measurement of seed dispersal and for the extraction of ecological information from camera-trap data.”

Nicolas Lecomte

“I am interested in the trophic dynamics of terrestrial ecosystems to better understand their functioning and sensitivity to perturbations, such as climatic change. My research seeks to develop empirical and theoretical models of species interactions and animal movements to predict species and food web changes in time and space. A special focus is placed on polar ecosystems using a combination of food web modelling and long-term population and ecosystem monitoring.”

John Reynolds

“I study aquatic ecology and conservation, with a current emphasis on land-terrestrial interactions. I also have ongoing interests in links between life histories and extinction risk, with comparative studies of marine and freshwater fishes. My fieldwork is based in the Great Bear Rainforest, a remote region along British Columbia’s central coast, where we are studying 50 pristine watersheds to understand ecological links between salmon and species ranging from riparian plants to birds.”

Matt Schofield

“My research involves developing statistical methodology and computation for ecological data. Much of my work has looked at statistical issues surrounding the estimation of demographic parameters of animal populations. In particular, it has focused on capture-recapture data and the importance of accounting for missing data. Examples include misidentification in non-invasive studies and incorporating covariate information.”

boral: R package for multivariate data analysis in Ecology

Posted on November 3, 2014 by Samantha Ponton

In this video Francis Hui introduces boral, a new R package he developed for Bayesian analysis of multivariate data in ecology. It uses Bayesian MCMC estimation to fit latent variable models for unconstrained ordination (read the MEE paper, Model-based approaches to unconstrained ordination, for details), and for multi-species inference while accounting for inter-species correlation:

Download boral from CRAN
Read the MEE paper Model-based approaches to unconstrained ordination

Solving the skewed sex ratio problem in science

Posted on October 31, 2014 by Samantha Ponton

Animal Ecology In Focus

In 2003 Milner-Gulland et al. wrote a paper on extreme adult sex ratios in saiga antelope. Males had become so rare in some years that the behavior of the system became dysfunctional and population performance suffered catastrophically. The only other environments where I know of heavily skewed adult sex ratios are university science faculties. Except here the skew is in the other direction, with females being rare. Social scientists have shown that skewed sex ratios in the workplace can negatively impact many performance metrics (e.g. Fenwick and Neal 2001).

Many scientists are rightly concerned by the paucity of women on the faculty of many science departments, and there has been much contemplation on the causes of attrition as more men progress from Ph.D. to post-doc to a faculty position to full professor than women. There are hypotheses proposed to explain this ranging from men being more likely than women to…

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Issue 5.10

Posted on October 30, 2014 by Samantha Ponton

Issue 5.10 is now online!

This month we include 4 freely available application articles:
– agTrend: A Bayesian approach for estimating trends of aggregated abundance
– MEMGENE: Spatial pattern detection in genetic distance data
– mizer: an R package for multispecies, trait-based and community size spectrum ecological modelling
– PyRate: a new program to estimate speciation and extinction rates from – incomplete fossil data

We also have 2 interesting open access papers, ‘Statistics for citizen science: extracting signals of change from noisy ecological data‘ by Nick Isaac et al. and ‘Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data‘ by Cuong Tang et al.

The cover image of this issue shows research diver Marine Guenzo using a diver-operated stereo-video system (stereo-DOV) to survey coral reef fish in Palau, Micronesia. Although SCUBA is commonly used to survey fish populations, the accompanying article, ‘Silent fish surveys: bubble-free diving highlights inaccuracies associated with SCUBA-based surveys in heavily fished areas ‘, highlights that the presence of bubbles produced by SCUBA can bias counts of reef fish. Using stereo-video techniques to survey the fish community inside and outside areas protected from fishing, the authors compared conventional SCUBA diving to a more advanced diving technique, the closed-circuit rebreather (CCR) which does not produce bubbles. The results show that especially in areas where reef fish are heavily targeted by fishing, SCUBA can underestimate the numbers of large fish, thereby overestimating the effectiveness of marine protected areas. Silent bubble-free diving is recommended to minimise the behaviour of reef fish towards divers.
Photo © Steve Lindfield.

To keep up to date with Methods newest content, have a look at our Accepted Articles and Early View articles, which will be included in forthcoming issues.

Open Access Week 2014

Posted on October 20, 2014 by Samantha Ponton

Once more Open Access Week has rolled around.

At MEE we operate a hybrid model: although we are a subscription journal, authors can choose to make their papers open access (for a price – sorry). Over the past year, 21 papers have been published as open access (listed here). They span the range of topics we cover, including citizen science, using cell phones, and asking people nicely to not vandalise your equipment.

There are several models for open access, and the Gold route – making the final version freely available – may not be for everyone. But we also let authors put pre-prints on the web (details here); this is an excellent way of getting more feedback on your manuscripts before a final version (there are other green OA models, but personally I think the preprint version has more advantages).

So, enjoy these papers, and next time you have a paper accepted by MEE – or indeed any other journal with a hybrid model – consider making it open access for all to read. You might be surprised: someone might read it.

Bob, Senior Editor

Graybill/ENVR 2014 – highlights, current trends and what’s next

Posted on October 2, 2014 by Samantha Ponton

In this video David Warton interviews the organisers of the “Modern Statistical Methods for Ecology” Graybill/ENVR Conference (Sept 7-10 2014, Fort Collins) – Alix Gitelman, Geof Givens, and Janine Illian. They discuss highlights of the conference, current trends in statistical ecology, and where the Graybill conference series (organised at Colorado State every year) is going next.

Noisy SCUBA bubbles scare fish(shh!)

Posted on September 29, 2014 by Samantha Ponton

Flickr (CC BY-SA 2.0)

A new Methods paper comparing SCUBA diving to bubble-free diving suggests that fish are deterred by the sound of SCUBA bubbles, particularly in heavily fished areas, which can result in potentially biased fish counts and research conclusions.

Steven Lindfield and colleagues from the University of Western Australia studied coral reef fish populations in Guam using two diving systems: the commonly used SCUBA equipment that produces bubbles, and a silent closed-circuit rebreather (CCR) that doesn’t produce bubbles.

To carry out the studies all divers used an underwater stereo-video system, and the footage was later used to figure out the number of fish present in the area, fish length and weight, and the minimum distance fish would allow a diver to approach before fleeing.

The findings show that within protected areas of water where no fishing occurs, fish surveys carried out by SCUBA divers and bubble-free divers produced similar results. However, in areas of water where fishing occurs, the bubble-free divers recorded 48% more species and up to 260% greater fish abundance, suggesting that they were able to sneak up on fish that usually shy away from SCUBA divers.

In their paper the authors state: “These results highlight the general importance of identifying all major sources of error associated with sampling populations in such variable environments. More specifically, it indicates how such errors can result in erroneous conclusions being drawn on the impacts of fishing and the effectiveness of marine protected areas (MPAs)”.

The paper can be found here: Lindfield, S. J., Harvey, E. S., McIlwain, J. L., Halford, A. R. (2014), Silent fish surveys: bubble-free diving highlights inaccuracies associated with SCUBA-based surveys in heavily fished areas. Methods in Ecology and Evolution. doi: 10.1111/2041-210X.12262

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