Getting Every Last Bit Out of Dives: Data Abstraction On-board Telemetry Tags

Post provided by THEONI PHOTOPOULOU, MIKE FEDAK, LEN THOMAS and JASON MATTHIOPOULOS

Animal Telemetry for Air-breathing Divers

CTD-SRDL Tags

CTD-SRDL telemetry tags being primed for deployment. ©Theoni Photopoulou

Nowadays animal telemetry tags for air-breathing divers come in all shapes and sizes. In four short decades tags for diving animals have gone from prototypes like the one built by Jerry Kooyman for deployment on Weddell seals – which consisted of a kitchen timer and a roll of graph paper – to a multitude of sophisticated electronic devices, fit for just about any animal or purpose you can think of.

All this progress has meant we can collect more information than ever before and do so remotely. Nevertheless, the lives of most divers remain a well-kept secret. For tags that transmit what they collect (as opposed to those that store data until they’re retrieved), the transmission stage is usually the bottleneck. This has driven the development of energy and time efficient software and data processing.

For a tag like the conductivity-temperature-depth Satellite Relay Data Logger (CTD-SRDL) built by the Sea Mammal Research Unit Instrumentation Group at the University of St Andrews – which was designed to spend months at sea – the problem boils down to one thing. Data are collected at a high resolution on-board the tag amounting to 100kB daily, but only 1kB of this information (at best) can be transmitted to the ground station. Therefore in preparation for transmission, the data need to be chosen carefully, compacted and fitted into several satellite messages of fixed size to ensure that enough useful information is received. Each satellite message can hold up to 248bits of information. To give an idea of how limiting this is, consider that this sentence would (without compaction) take up 896bits! Continue reading

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On the Tail of Reintroduced Canada Lynx: Leveraging Archival Telemetry Data to Model Animal Movement

Post provided by FRANCES E. BUDERMAN

Animal Movement

218 Canada lynx were reintroduced to the San Juan Mountains between 1999 and 2006 with VHF/Argos collars. © Colorado Parks and Wildlife

218 Canada lynx were reintroduced to the San Juan Mountains between 1999 and 2006 with VHF/Argos collars. © Colorado Parks and Wildlife

Animal movement is a driving factor underlying many ecological processes including disease transmission, extinction risk and range shifts. Understanding why, when and how animals traverse a landscape can provide much needed information for landscape-level conservation and management practices.

The theoretical underpinnings for modelling animal movement were developed about seventy years ago. Technological developments followed, with radio-collars initially deployed on large mammals such as grizzly bears and elk. We can now monitor animal movement of a wide variety of species, including those as small as a honeybee, at an unprecedented temporal and spatial scale.

However, location-based data sets are often time consuming and costly to collect. For many species, especially those that are rare and elusive, pre-existing data sets may be the only viable data source to inform management decisions. Continue reading

Recently accepted articles

We have been very busy in the past couple of weeks and we have a whole range of recently accepted articles:

  • A novel digital telemetry system for tracking wild animals: a field test for studying mate choice in a lekking tropical bird
    Dan Mennill, Stéphanie Doucet, Kara-Anne Ward, Dugan Maynard, Brian Otis and John Burt
  • A general theory of multimetric indices and their properties
    Donald Schoolmaster, James Grace and E. Schweiger
  • Beyond sensitivity: nonlinear perturbation analysis of transient dynamics
    Iain Stott, Dave Hodgson, and Stuart Townley
  • A two-phase sampling design for increasing detection of rare species in occupancy surveys
    Krishna Pacifici, Robert Dorazio and Michael Conroy
  • Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
    Douglas Yu, Yingiu Ji, Brent Emerson, Xiaoyang Wang, Chengxi Ye, Chunyan Yang and Zhaoli Ding
  • How to measure and test phylogenetic signal
    Tamara Münkemüller, Sébastien Lavergne, Bruno Bzeznik, Stéphane Dray, Thibaut Jombart, Katja Schiffers and Wilfried Thuiller
  • Statistical evaluation of parameters estimating autocorrelation and individual heterogeneity in longitudinal studies
    Sandra Hamel, Nigel Yoccoz and Jean-Michel Gaillard
  • jPopGen Suite: population genetics analysis of DNA polymorphism from nucleotide sequences with errors
    Xiaoming Liu

They will be soon available on Early View.

Network analyses of animal movement

Determining how animals move within their environment is a fundamental knowledge that contributes to effective management and conservation.

In our latest video, David Jacoby and Edd Brooks explain how their paper brings together two disparate and rapid advancing fields: biotelemetry and social networking analyses.

In a paper recently published in Methods, David, Edd and colleagues Darren Croft and David Sims, demonstrate some of the descriptive and quantitative approaches for determining how an animal’s movement interconnects home range habitats. David and colleagues describe the novel application of network analyses to electronic tag data whereby nodes represent locations and edges between nodes, the movements of individuals. They consider both local and global network properties from an
animal movement perspective and simulate the effects of node disruption as a proxy for habitat disturbance.

Network theory is a well-established theoretical framework and its integration into the fast
developing field of animal movement and telemetry might improve significantly how we interpret animal space use from electronically recorded data.

Related

2011 top cited papers – part 3

Welcome to part 3 of our review of the most highly cited papers published by Methods in Ecology and Evolution in 2011. In case you missed them, here are part 1 and part 2 of this series.

Population monitoring and management

Climate change

Evolutionary ecology and phylogenomics

A year of podcasts and videos

We have been uploading videos and podcasts for a year now – these have proved really popular, both with authors and readers of the journal. I thought I would just take this opportunity to highlight some of the online content that is supporting articles from the first 3 issues:

Our podcasts include:-

We also have video interviews with our authors, including:

What we are hoping to do is to maximise the utility of our published papers for readers, as well as ensure that the methods we publish reach as wide an audience as possible. Please do give feedback on any of our content, and we are always open for suggestions for new ways to promote new methods!

Issue 2 is now online

Issue 2 of Methods in Ecology and Evolution is now online, the table of contents is here.  In this issue there are 14 new papers on:

  • Statistical methods
  • Monitoring & modelling plant populations
  • Telemetry
  • Entomology
  • Modelling wildlife disease
  • Building databases of life-history traits
  • GIS methods

One innovation is that we now have a correspondence site:

http://www.respond2articles.com/mee/

From here you can send in correspondence about papers, as well as view other correspondence. We think that this is a really useful feature for a journal devoted to methods: corresp0ndence between authors and readers will be a useful resource, allowing discussion of techniques, refinement of methods, ironing out of problems as well as further suggestions for developments.  We encourage readers and authors to use this to discuss papers. The site is fully moderated so all material appearing should be constructive and useful to all.

The methods digest for the last month will be appearing soon:- delayed largely as a consequence of volcano ash.

Finally do check out the latest podcasts and videos, they are being updated all the time. The very latest video is an interview with Aaron Ellison from his field site!

 

Methods Digest – March 2010

The first thing to point out this month is that issue 1 of the journal is now online here. To accompany the issue we have a podcast and a videocast. There is also now a  journal correspondence site to host feedback and discussion of published papers, more on this soon.

The one day journal launch symposium is accepting bookings, with a good response so far. However places are still available, and the booking form is here.

We hope that Methods in Ecology and Evolution will be listed on ISI as soon as possible – if you have 2 minutes to spare we would be really grateful if you would fill out the nomination form. This will help us get noticed by them.

To begin this month’s round up of recent methods papers, Ecological Monographs has a paper  by James Grace and colleagues on structural equation modelling. In this paper they outline how meta-models can be used to aid the translation of theory into SEMs.

In Ecological Applications, Lester Yuan describes how observational data and propensity scores can be used to estimate the effects of excessive nutrients on stream invertebrates.

In Ecology Fitsum Abadi and colleagues perform an analysis of the performance of integrated population models, particularly focussing on the issue of independence of data. Pierre Legendre et al. look at how ‘space-for-time’ experiments can be analysed in the absence of replication. Toby Patterson et al. look at how state space methods can be used to correct telemetry data and the limits to this approach. Etienne Laliberté & Pierre Legendre present a new approach for measuring functional diversity, along with R code.

Richard P. Brown and Ziheng Yang in Systematic Biology look at the problem of dating shallow phylogenies with relaxed clocks using Bayesian methods. Jeremy Brown et al. discuss the problem of very long branch length estimates in trees generated using Bayesian methods, compared with ML alternatives. R. Alexander Pyron presents a Likelihood method for assessing molecular divergence time estimates with the placement of fossils.

In Ecology Letters Colleen Webb et al. present a new approach to develop trait based theory for predicting community composition and ecosystem function.

The latest issue of the Journal of Applied Ecology has a section on ‘Modelling Distributions’. This includes methods papers on the use of proxy-based methods for mapping ecosystem services,  estimating individual survival using occupancy data, estimation of immigration rates using integrated population models, and the ability of habitat suitability models to predict the recovery of threatened species.

In the American Naturalist Bart Haegeman and Rampal Etienne look at the relationship between entropy maxization and species distributions.

Thanks to Rua Mordecai for pointing out an interesting paper in the Auk by Jason Riddle and colleagues on incorporating estimates of prior detections in estimating occupancy, abundance and probability of detection.

Please let me know if there are any papers that could be featured in the next month’s digest update.


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Allometry, statistics, telemetry and physiology – new papers online

Four more papers have gone online this month and we are close to being able to put together the first issue of the journal!

In the first new paper to be published Adrian Barnett and colleagues present a comparison of methods for selecting the correct variance structure for longitudinal data. This is likely to be of considerable interest as it is a paper about how to fit the most appropriate description of non-independence in ecological time series data. The approach is illustrated with an analysis of the effects of forest fragementation in a 15-year data set on bird species richness.

Can Hui et al. look at the problem of fitting and predicting allometric relationships. They introduce a new way to measure bias in prediction and show that this is effective in improving predictions.

A new model by Thomas Brey can be used to estimate rates of respiration by invertebrates. The aim of this approach is to allow rapid and easy estimation of estimates of respiration rates. To facilitate the use of this model, a simple to use Excel spreadsheet can be downloaded here to accompany the paper.

Finally for now, Claudio Signer and colleagues describe a new Telemetry system for estimating heart rate, body temperature and locomotor activity in ruminants. This system has been used on Alpine Ibex to provide continuous measurements for up to 2 years.

Title of articles are posted here as soon as they are accepted. Updates on journal developments and new papers are also published on Twitter and Facebook, do join us!