Dutch Bio-Acoustic conference

On Friday 11Oct, the Dutch Bio-Acoustic conference was organized. The gathering was held to share knowledge about the influence of acoustics on animal behavior. Scientist from VU Amsterdam, Leiden University, Wageningen University, Rijkswaterstaat, TNO, JASON, and VLIZ presented their results regarding noise pollution in the North Sea region (mostly underwater acoustics).

Olivier presented an overview of the SeabirdSound project under the scrutiny of the bio-acoustic experts. The talk was well received and opened fruitful discussions. This way, we like to thank RWS and the JOMOPANS project for organizing the conference, and we look forward to next year’s meeting!

Bio-logger

This week, I am precisely two years into the project! Besides this memorial milestone, we also finished one of the goals of our project! We finished the design of our logger for the upcoming fieldwork this January.

Last month I visited Dominique Fillipi, a well known and respected physicist who is specialized in developing Bio-loggers. Together with Dominique, I designed the “infrasound-sputnik”. This is the very first bio-logger, which besides tracking albatrosses, also can measure movement (acceleration), barometric pressure, differential pressure (infrasound), and wind speed/direction.

We worked on the hardware and software and did some first testing. We are all very excited and look forward to the outcome of the logger during the upcoming fieldwork.

Soon more updates on the logger!

Intense UK-France work trip (October-November 2018)

The Seabird Sound project is already in it’s second year and I’m still happy to be in this multidisciplinary team! (Have a look here if you’re getting lost with the many names in this text!). My role here is to develop and apply methods for movement analysis to contribute to a better understanding of seabird spatial behavior and how it is shaped by infrasound and meteorological conditions.

The seabird-ecology counterpart in the project is in Liverpool (Sam and Tommy) so we agreed that I would travel there to work with them. Since I had to make such a long trip from Fort Lauderdale, I decided to make the most of it, adding several destinations and working with as many people as possible.

This is a narrative of that month-and-a-half trip to Europe, by destination:

Chizé

The Centre d’Études Biologiques de Chizé (CEBC) is a CNRS lab is known for its research in marine mammals and seabirds, and for its scientific campaigns for data collection in faraway places like Kerguelen and Crozet islands. Sam, Tommy and I met in Chizé to discuss Tommy’s ideas for his paper on wind’s role on albatross behavior during foraging trips with Henri Weimerskirch. Henri has collected part of the data being analyzed and has worked with albatrosses for many years, so his feedback on Tommy’s findings was highly valuable. We also attended the outstanding PhD defense (viva) of Julien Collet, as Sam was a member of the jury, investigating strategies seabirds use to search and reach feeding areas. During this short but intense visit (2 days), I managed to squeeze in some time to finish a manuscript reviewing R packages and submitted it literally at the last minute: Not only was it the last day to submit the paper; we were also going to miss our train back to Paris if I didn’t finish on time. I made the quickest paper submission in my life so far (about 20-30 minutes) and I hope it will remain the quickest one.

Liverpool

This was the main destination of my trip. I was going to stay there for a bit more than two weeks so I had several tasks programmed for the journey.

The other postdocs of the project, Jeff and Ollie, joined Tommy and me at the University of Liverpool for the first week. We held meetings for just the four of us, to present our different topics of research to each other: introductions to our subjects, preliminary results and perspectives. I am very much familiar with Tommy’s research, as I play an active role in it. It was amazing to be able to learn from Ollie’s and Jeff’s own research.

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High and low pressure systems

At our request – or maybe just mine -, Ollie provided a great introductory talk to meteorology and its basic laws to help us understand how everything in meteorology is interconnected; thus also connected with infrasound. Jeff also gave an impressive introduction to hearing, and while it is hard to keep track of all the technical vocabulary, we enjoyed the presentation about auditory models and the anatomical comparison between terrestrial and aquatic bird species (read more about his research on this post). As I wanted to get more involved with the weather data analysis, Ollie shared a tutorial and gave me a script to download the ECMWF data, and we chatted about the links between atmospheric pressure and wind. It was all very helpful and I hope I can go visit him and Jelle at the Royal Netherlands Meteorological Institute soon!

During the second week, I focused more on working with Tommy to assess the effect of wind in albatross behavior during foraging trips via Hidden Markov modeling.

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Albatross track with inferred behaviors

There are at least two packages in R to implement Hidden Markov models (moveHMM and momentuHMM), making our tasks easier, but knowing how to parametrize the models and correctly interpret the results require understanding the intricacies of the methods as well as the ecology of the species. Together, a statistician and an ecologist, we’re trying to bring both components to the table for this piece of research—a manuscript should be ready in the next few months!

Working in Sam’s lab for a couple of weeks, I had the opportunity to participate in weekly lab meetings to discuss scientific articles and get to know a bit more about their research. I really felt like I was part of the lab during my stay, which is always a plus.

Avignon

After a long trip from Liverpool that took me the whole day, I arrived to Avignon for a workshop on SPDE (Stochastic Partial Differential Equations) modeling and INLA (Integrated Nested Laplace Approximation). I think that there is no need to say that this was a different scientific community than the seabird ecology department at the University of Liverpool.

inla
D. Allard, from RESSTE, introducing the SPDE workshop (picture taken by O. Gimenez)

The workshop was organized by the RESeau Statistiques pour données Spatio-TEmporelles (RESSTE) network and gathered a diverse public between applied (but quantitative) and theoretical researchers. Since I am considering using continuous time models for movement further in the HFSP project, I thought that learning an INLA approach would be handy for this. INLA can be a great solution to estimate parameters of complex models, and the organizers of the workshop provided a short introduction on how to express statistical models as SPDE that could be solved by INLA. Then, they showed the implementation of INLA in R (using R-INLA) with some examples of time series and spatial point processes. Some coauthors of the R-INLA and INLABRU packages were present and contributed to the seminars with their comments; that also made me realized that implementing INLA can be an incredibly difficult task for a model that has not been considered yet in the package. The seminars were complemented by the series of presentations from several participants on their research applying INLA.

Nantes

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View from my old flat in Nantes. I miss that.

After Avignon, I spent the weekend with some friends in Sète. Sète is a lovely small fishing city on the Mediterranean and one of the places I stayed in during my PhD. The weekend in Sète gave way to a three-week stay in Nantes. I did a previous postdoc at IFREMER in Nantes, and I was coming back this time to work on ‘old’ papers: one reviewing metrics to assess dyadic joint movement (now published in Movement Ecology) and one applying these metrics to several fleet movement data and learning about their collective behavior (almost ready to submit). My collaborators, which are not all from IFREMER, are quantitative researchers and founders of the trajectometry group Path Tool and analysIS (PathTIS). During my visit, we programmed meetings not only to discuss about the papers we needed to finish), but also to talk about my future projects to come again and collaborate on movement modeling papers.

Nantes was the last destination of this trip before heading back to Florida. All in all, I am very happy with all the work done and the scientific discussions. …And the wine, the food, the pubs, the funny conversations, the walks under the rain and the music. Thanks to everybody who welcomed me into their labs and cities, and the friends who hosted me. I had a blast and I hope to see you soon!

 

Fall Research Travels

It seems to be a good time to post a research update coming from the auditory physiology side of the project. I’m currently wrapping up a research trip to Europe, where I worked on multiple different components of the project with the other team members in the UK and Netherlands. Olivier and I also had a productive visit to a bird hearing expert earlier this week in Oldenburg, Germany.

I have been reviewing the scientific literature on low frequency hearing in birds, including the various experimental studies and hypothesized detection mechanisms. There are indeed many factors that can control the detection of low frequencies by birds. Sound vibrations move through the middle ear, inner ear, and auditory hair cells, ultimately becoming encoded into a neural signal at the end of the transmission line. At each of these levels, there are distinct structure-function relationships that will affect signal transmission. There is likely no single anatomical marker that will precisely reflect infrasonic hearing abilities, but the relevant anatomical parameters and how they might be expected to affect low frequency transmission is becoming clearer.

Multiple building blocks need to come together to pursue the big question, “do seabirds detect infrasound?”. One of these building blocks is a quantification of the large-scale patterns of auditory anatomy in seabirds. For this goal, I have been collecting microCT scans of seabird heads and skulls. In general, not a lot has been described on the auditory anatomy of seabirds.

The microCT images are quite cool to view and analyse. Below are microCT images of white-chinned petrel, Procellaria aequinoctialis (A). This species is commonly caught as bycatch from long-line fisheries vessels operating in South African waters, and that was my source for this particular specimen (thanks to folks at Capfish and BirdLife). You can even see a fish still in the throat and a bit of the hook apparatus on the lower right. Here are some additional images showing the reconstruction process for this technique. You can see clearly on this image the columella (middle ear bone of birds) and inner ear (B). After some analysis, the 3D models of specific components can be reconstructed (C,D).

One possible further application of the comparative microCT data is to use the 3D surface models to simulate acoustic transmission properties of the ear. This can be an option for animals for which direct hearing assessments are difficult, such as whales. The simulation models are then verified by direct vibrometric observation of middle ear. This technique might be a useful method for testing between the performance of different routes of acoustic stimulation. For example, the vibration transmission performance of the middle ear in tetrapod animals (including birds) generally declines towards low frequencies. Alternatively, sound at these very low frequencies might effectively couple to the whole body of the bird itself.

After some delay with getting permits  to collect seabird heads (partly due to restrictions related to the bird flu striking earlier in the year), we have the permissions we need and I hope to be examining many more species soon.4 in 1

SeabirdSound 2018 Workshop

From 14 till 17 May the first SeabirdSound workshop took place in Liverpool. The workshop focussed on infrasound and avian navigation and is part of the HFSP Project (investigating the role of infrasound in seabird navigation; it combines seabird ecology, physiology, infrasound soundscapes, and movement ecology in a comprehensive framework).

For the workshop, we brought together experts in all of these areas to share expertise and integrate ideas. In particular we were keen to discuss avian navigation in general with a focus on seabirds. By use of keynote presentations and engaging discussions, we developed an integrated framework around the use of infrasound in navigation and developed a begin for a review article around this subject. Follow the website for more news about this article.

We would like to thank all participants (alphabetic);

Simon Benhamou, Jakob Christensen-Dalsgaard, Annette Fayet, Jon Hagstrum, Christine Koppl, Emiel van Loon, Pascal Malkemper, Richard Phillips, Mark Prior, Pieter Smets and Yoshinari Yonehara.

And in particular Tommy Clay and Samantha Patrick for taking lead in organising!

 

EGU 2018 – Vienna

From 8 till 13 april the European Geosciences Union (EGU) organised the 2018 General Assembly in Vienna (Austria). During the assembly 4.776 oral, 11.128 poster, and 1.419 PICO presentations were given.

Jelle and Olivier represented the SeabirdSound team, both gave a poster presentation. Jelle presented his research about the Dutch Meteo-Tsunami of 29 May 2017. Olivier presented his studies on parameterising the CLEAN beamforming method on infrasound recordings.

Besides presenting, both participated many interesting presentations and short courses. It was an interesting week, good weather, good science and a good environment!

 

 

Master (MS) position in Movement Ecology at the University of Florida

We are seeking a motivated MS student to join our team in Florida, aiming at understanding how seabirds navigate and the role of infrasound in their movement. The MS thesis will follow one of two possible paths, requiring students with two distinct profiles: one in applied statistics/mathematics; and one in quantitative ecology. Applications are encouraged for both profiles, but only one student will be selected.

The Master’s program will consist of three semesters mainly dedicated to classwork during the first year and a second year exclusively dedicated to the Master’s thesis. This position will be completely supported for the two years (stipend + tuition) and the program is expected to start in fall 2018.

Classwork during the first two semesters will take place on the main UF campus in Gainesville. Research will be performed at Dr. Mathieu Basille’s lab, under the supervision of Dr. Basille and Dr. Rocio Joo. Dr. Basille’s lab is located at the University of Florida’s Fort Lauderdale Research and Education Center (FLREC), in Davie, Florida. Davie is a town within the large Miami metropolitan area in South Florida, just miles away from the Florida Everglades.

Full descriptionMasterAdvert-UF

!!please read the whole advertisement before sending your application!!

Please apply by sending an email including a cover letter describing your interest, experience and career goals, a CV, unofficial transcripts and GRE scores, and contact information for three references to Dr. Rocio Joo (rocio.joo@ufl.edu). Write “master application” as the email subject. Applications will be processed in the order they are received until April 15th or before if a suitable applicant is found.