Issue 6.7

Issue 6.7 is now online!

The July issue of Methods is now online!

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

fuzzySim: Binary similarity indices are widely used in ecology. This study proposes fuzzy versions of the binary similarity indices most commonly used in ecology, so that they can be directly applied to continuous (fuzzy) rather than binary occurrence values, producing more realistic similarity assessments. fuzzySim is an open source software package which is also available for R.

 Actave.net: A freely accessible, web-based analysis tool for complex activity data, actave.net provides cloud-based and automatic computation of daily aggregates of various activity parameters based on recorded immersion data. It provides maps and graphs for data exploration, download of processed data for modelling and statistical analysis, and tools for sharing results with other users.

Anna Sturrock et al. provide this month’s Open Access article. In ‘Quantifying physiological influences on otolith microchemistry‘ the authors test relationships between otolith chemistry and environmental and physiological variables. The influence of physiological factors on otolith composition was particularly evident in Sr/Ca ratios, the most widely used elemental marker in applied otolith microchemistry studies. This paper was reported on in the media recently. You can read more about it here.

Our July issue also features articles on Monitoring, Remote Sensing, Conservation, Genetics and three papers on Statistics. Continue reading

Statistics in Ecology and Environmental Monitoring: A Look Back at the SEEM 2015 Conference

Post provided by Dr Matt Schofield

Matt is an Associate Editor for Methods in Ecology and Evolution. He was the principle organiser of this year’s SEEM conference. His research interests include Bayesian inference and hierarchical modelling, computational methodology, ecological statistics and much more. Matt is based at the University of Otago.

A photo taken during a lunch break at the conference

A photo taken during a lunch break at the conference

The Statistics in Ecology and Environmental Monitoring (SEEM) conference was held in Queenstown, New Zealand on June 22-26, 2015. Queenstown is a resort town in the Southern Alps of New Zealand that looks out on Lake Wakatipu, surrounded by snow-capped mountains. The venue gave a chance to explore some of the natural beauty of New Zealand, with excursions to local ski fields, wineries and various hiking trails.

SEEM conferences have been organized by members of the Statistics group at the University of Otago since 1993. The first SEEM conference was held in Dunedin, New Zealand and conferences were then held regularly (every 3 years) until 2002. The last SEEM conference, in 2007, also served as the EURING (European Union for Bird Ringing) technical meeting. With nearly ten years passing since 2007, we had a smaller conference of around 50 attendees this year. There was an engaging atmosphere during the meeting and productive discussion followed each of the 40 talks. The SEEM 2015 meeting maintained the tradition of previous SEEM conferences with delegates from across a broad spectrum of statistical ecology coming together to discuss research. Continue reading

‘Bee soup’ could help understand declines and test remedies

Below is a press release about the Methods paper ‘High-throughput monitoring of wild bee diversity and abundance via mitogenomics‘ taken from the University of East Anglia:

It may sound counter-intuitive, but crushing up bees into a ‘DNA soup’ could help conservationists understand and even reverse their decline – according to University of East Anglia scientists.

Research published today in the journal Methods in Ecology and Evolution shows that collecting wild bees, extracting their DNA, and directly reading the DNA of the resultant ‘soup’ could finally make large-scale bee monitoring programmes feasible.

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©Mibby23 (click image to see original version)

This would allow conservationists to detect where and when bee species are being lost, and importantly, whether conservation interventions are working.

The UK’s National Pollinator Strategy outlines plans for a large-scale bee monitoring programme. Traditional monitoring involves pinning individual bees and identifying them under a microscope. But the number of bees needed to track populations reliably over the whole country makes traditional methods infeasible.

This new research shows how the process could become quicker, cheaper and more accurate. Continue reading

New Tool to Assess Effects of Powerful Man-Made Underwater Sounds

Below is a press release about the Methods paper ‘An interim framework for assessing the population consequences of disturbance‘ taken from the University of St Andrews:

A team of scientists from the University of St Andrews has developed a new desktop tool for assessing the impact of noise from human disturbance, such as offshore wind development on marine mammal populations.

PCOD_PR_imageThe team, led by Prof. John Harwood, have developed the interim Population Consequences of Disturbance (PCoD) framework for assessing the consequences of human induced noise disturbance on animal populations. The study was published yesterday in the journal Methods in Ecology and Evolution.

Changes in natural patterns of animal behaviour and physiology resulting from animals being disturbed may alter the conservation status of a population if the activity affects the ability of individuals to survive, breed or grow. However, information to forecast population-level consequences of such changes is often lacking. The project team developed an interim framework to assess impacts when empirical information is sparse. Crucially, the model shows how daily effects of being disturbed, which are often straightforward to estimate, can be scaled to the duration of disturbance and to multiple sources of disturbance.

“We have developed a novel framework that can be used to broadly forecast the consequences of anthropogenic disturbance on animal populations, which in principal can be applied to a range of marine and terrestrial species and different types of disturbance.” – Dr Stephanie King

One important application for the interim PCoD framework is in the marine industry. Many industries use practices that involve the generation of underwater noise. These include shipping, oil and gas exploration, defence activities and port, harbour and renewable energy construction. Continue reading

Advances in Phylogenetic Methods – The Applications Papers

Original Image ©PLOS One Phylogeny

Original Image ©PLOS One Phylogeny

Timed to coincide with Evolution 2015, we have released a new Virtual Issue on Phylogenetic Methods. All of the articles in this Virtual Issue will be freely available for a limited period.

On Friday, we gave some more information about the research articles in this Virtual Issue. In this post, we will be focusing on the Applications papers.

Applications papers introduce new tools for research, which provide practitioners with an important source of information and background on the tools they use. In this Virtual Issue we have highlighted the newest Applications papers that describe how phylogenetic methods are contributing to the fields of ecology and evolution. These include tools with aims as diverse as phylogenetic tree reconstruction and analysing phylogenetic diversity in communities. All Applications papers, not just those in the Virtual Issue, are free to access.

You can see a little more information on each of the Applications Papers below.

Continue reading

Virtual Issue: Advances in Phylogenetic Methods

Original Image ©PLOS One Phylogeny

Original Image ©PLOS One Phylogeny

Timed to coincide with Evolution 2015, we have released a new Virtual Issue on Phylogenetic Methods. All of the articles in this Virtual Issue will be freely available for a limited period.

An understanding of the tree of life contributes to many facets of biology. This Virtual Issue has assembled studies that showcase the breadth of the utility of phylogenetic trees, including phylogenetic beta diversity, trait evolution, diversification, biodiversity studies, phylogenetic signal, biogeography, ecosystem functioning, and host-pathogen dynamics.

The Research papers included are excellent examples of new ways that phylogenies can be applied to central questions in ecology, evolution and biodiversity, such as measuring niche conservatism, trait evolution and diversification rates. The issue also has articles on barcoding methods, which increasingly are used to understand phylogenetic and functional diversity.

You can see a little more information on each of the articles below.

Continue reading

The Methods in Ecology and Evolution 5th Anniversary Impact Factor

Thomson-Reuters have just released this year’s Impact Factors. The Methods in Ecology and Evolution Impact Factor is now an astounding 6.554, up from a truly dismal 5.322 last year. We now have enough years of Impact Factors to make it worthwhile drawing a graph.

Zoooom!

The Methods in Ecology and Evolution Impact Factor goes up and up (…except when it doesn’t).

This puts us ninth in Ecology, and we would be fifth in Evolutionary Biology if Thomson-Reuters thought we published stuff in Evolutionary Biology. We would also be top in Statistics and Substance Abuse if we could get ourselves into either of those categories. Continue reading

Issue 6.6

Issue 6.6 is now online!

The June issue of Methods is now online!

This month’s issue contains one Applications article and one Open Access article.

VirtualCom: A simple and readily usable tool that will help to resolve theoretical and methodological issues in community ecology. VirtualCom simulates the evolution of the pool of regionally occurring species, the process-based assembly of native communities and the invasion of novel species into native communities. One of the authors of this Application is the 2014 Robert May Young Investigator Prize Winner, Laure Gallien.

Calibrating animal-borne proximity loggers, this month’s only Open Access article, comes from Christian Rutz et al. The authors calibrated a recently developed digital proximity-logging system (‘Encounternet’) for deployment on a wild population of New Caledonian crows. They show that, using signal-strength information only, it is possible to assign crow encounters reliably to predefined distance classes, enabling powerful analyses of social dynamics. Their study demonstrates that well-calibrated proximity-logging systems can be used to chart social associations of free-ranging animals over a range of biologically meaningful distances.

Our June issue also features articles on Phylogenetic MethodsPhysiological Ecology, Biomonitoring and Conservation, Species Distribution Monitoring and Bioinformatics. Continue reading

What fish ears can tell us about sex, surveillance and sustainability

Below is a press release about the Methods paper, ‘Quantifying physiological influences on otolith microchemistry, from the University of Southampton:

Dr Anna Sturrock blood sampling plaice ©Anna Sturrock

Dr Anna Sturrock blood sampling plaice ©Anna Sturrock

Scientists at the University of Southampton have found a way to pry into the private lives of fish – by looking in their ears!

By studying ear stones in fish, which act as tiny data recorders, scientists can now reveal migration patterns and even provide insights into their sex life.

Managing fish stocks in a sustainable way is a major challenge facing scientists, conservationists, policy makers and fishermen. To get the best results, accurate information about the movements of fish in the wild is needed but gathering this information is extremely difficult. Continue reading

In Defence of Satellite Data: The Perfect Companion to Ground-Based Research

Post provided by Dr Nathalie Pettorelli

Nathalie is an Institute Research Fellow at the Zoological Society of London. She heads the Environmental Monitoring and Conservation Modelling (EMCM) team and her main research involves assessing and predicting the impacts of global environmental change on biodiversity and ecosystem services. Nathalie was one of the presenters at the UK half of the Methods in Ecology and Evolution 5th Anniversary Symposium in April. You can watch her talk, ‘Harnessing the Potential of Satellite Remote Research’ here.

If there is one question I hear over and over again, it’s this: “why, oh why, do you use satellite data instead of ground-based data in your research?” People seem to think that I believe satellite data are better than ground-based data. Do I not value fieldwork? Do I not trust ground-based data? My answer to all of this is: you’ll never catch me preaching that satellite remote sensing can solve the entire data collection gap in ecological monitoring.

I use satellite data because a lot of my work happens at relatively large spatial and temporal scales, targets regions where ground-based data are simply unavailable or extremely difficult to gather and relies on being able to access data that have been collected in a systematic and scalable manner.

Yes, satellite-based techniques can address spatial and temporal domains inaccessible to traditional, on-the-ground, approaches, but I am the first to acknowledge that satellite remote sensing cannot match the accuracy, precision and thematic richness of in-situ measurement and monitoring.

©Clare Duncan

The New Generation of Ecologists in Action: Clare Duncan conducting field measurements in the Philippines to be combined with satellite remote sensing information to monitor ecosystem services delivery. ©Clare Duncan

In spite of this, data collected on the ground are currently difficult to use for mapping and predicting regional or global changes in the spatio-temporal distribution of biodiversity (a problem for those of us trying to tackle these kinds of issues). Ground-based data can also be expensive and tend to come from a single annual time period. This makes it difficult to gather information on temporal changes and phenology. Continue reading