After one year as a SciEx postdoctoral fellow in the population ecology and the amphibian conservation biology groups, Raluca Bancila returns to Romania.
We greatly enjoyed having Raluca as a member of our groups and wish her all the best for her future.
Our collaboration will continue!
I, Mollie, am organizing a workshop here at the University of Zurich. I’ve recruited two experts to come help me teach: Hans Skaug (Dept of Mathematics, Univ of Bergen) and Kasper Kristensen (Dept of Applied Maths and Comp Sci, Technical Univ of Denmark). We’ll teach researchers from diverse fields how to fit state-space models via maximum likelihood estimation using the Laplace approximation to integrate out latent variables and automatic differentiation to calculate gradients. This is much faster than Bayesian methods.
These methods are implemented in AD Model Builder and a new R package called TMB. Currently, the course organizers are trying to decide if we should teach both, or only TMB. There are costs and benefits to being early adopters of new software. For example, several years ago, when the user base of ADMB was expanding beyond fisheries stock assessment, we found several bugs that weren’t exposed until people started trying different types of models and different computational platforms. We don’t want to expose students to these issues. On the other hand, learning one new program (rather than two) in a three day workshop might be preferable for some participants. Plus, most ecologists already use R, so learning the package TMB might be slightly easier for them than learning to use ADMB through the R2admb interface. TMB is more streamlined than ADMB because it had ADMB as an example and took advantage of existing free and open source C++ libraries. Whatever we decide to do, we’ll make sure the class exercises and examples are fully debugged before the workshop. Maybe I’ll use my lab mates’ computers as Guinea pigs.
The course will take place September 1-3, followed by 2 days of developing the TMB package and applications. We still have some openings for participants. Applications are due August 1.
More information can be found at the course website
https://sites.google.com/site/uzhstatespaceworkshop/
The workshop is funded by a GRC Grant from the University of Zurich.
“Thank you”, I whispered in a soft voice while driving by the rayon and plating factories surrounding Lake Orta. “Thank you for giving me a PhD”.
The wastewater of those factories polluted the lake with copper and ammonium sulphate from approaching the mid-nineteen hundreds until the end of the last century. This history of pollution makes Lake Orta an interesting ecosystem to study, and sets the perfect stage for my PhD: the life-history responses of the rotifer Brachionus calyciflorus to past environmental changes (i.e. industrial pollution) and the underlying eco-evolutionary processes.
To study this, I (try to) resurrect rotifers from up to 80 year old lake sediments that contain their resting eggs, and compare the performance of these rotifers under different experimental treatments. As I have had some difficulties getting resting eggs from the post-pollution conditions, I decided to go to Lake Orta to get the most recent Brachionus calyciflorus: the ones that are currently swimming around.
Together with Diego Fontaneto of the ‘Istituto per lo Studio degli Ecosistemi’, I drove around the lake, and found five spots to easily enter the lake to collect zooplankton with a plankton net. This net made of fine nylon mesh is pulled through the water horizontally and the animals are captured in a vial at the bottom of the net.
A quick look together with Diego revealed that we captured tons of animals, but probably no Brachionus. A more thorough look together with our summer research assistant Conor Waldock confirmed this suspicion, but we have still some bottles of water to go through, so we keep on hoping. And otherwise, our hope lies in the sediment samples of Lake Orta that I also brought back from the trip.
The reason why we didn’t find any Brachionus in our water samples? Probably because the water was still too cold due to the relatively bad summer, and there have been no big algae blooms yet of which Brachionus could profit. I guess this means I have to go back next month to again sample Italian ice cream… Ehm, Lake Orta I mean.
‘Think hard and dig deep, without being canalized by the ideas of others published in literature. Not very often do you get a chance like this offered to you. Take the challenge.’ And all the students participating in the Guarda Evolutionary Biology course took the dare set by Dieter Ebert, Sebastian Bonhoeffer, David Queller, and Joan Strassmann.
In the idyllic Swiss village of Guarda, twenty-eight MSc/PhD-students interested in evolutionary biology were selected for a week of isolation, and given time to devote themselves to writing a grant proposal on any question they thought was worthwhile pursuing. The only requirements were that you had to collaborate in a group of 4-5 students, and choose a topic that was not related to your field of research at all. Oh, and you were not allowed to look for information in books or on the Internet: it was only tolerated to use the creativity of your own mind, the mind of your fellow students, and of the faculty members.
In just 15 working hours, the first draft of the grant proposal (including idea, hypotheses, and well-thought out experiment) had to be handed in. The faculty members granted every group 20 minutes to undergo their severe but justified feedback on the proposal. Six working hours after this feedback, the revised version had to be handed in, which got another feedback round. Five hours after this round, the final version and a presentation had to be ready. On top of that, there was an armchair lecture by one of the faculty members every evening, and you were (happily) obliged to offer all of them a hand cooked dinner during one of the days in the week.
This has been one of the most inspiring courses I ever took that has brought me back to basic scientific thinking: What is an interesting and important question in (evolutionary) biology? How would you solve that question? Is your hypothetical experiment really answering that question? Does working within a group of complete strangers full of enthusiasm facilitates the brainstorming, discussing and writing-up process, or do you might have to learn a lot in how to successfully listen, be open-minded, and collaborate?
After this highly motivating and encouraging course (e.g. why not embrace serendipity in your scientific work?), we got home extremely exhausted, to find out that the project we proposed was at the moment being presented at the big Evolution meeting in North Carolina: how mutualistic interactions could alter the dynamics of natural selection. I think that’s what you call Zeitgeist.
Welcome back to the Natural Reserve of La Grande Sassière where the second field season on alpine marmots started 3 weeks ago. Whereas last year at the same period there was deep snow (1m40), we arrived in an almost snow-free area.
As some of you enjoyed the mild winter, it seems that the marmots did too. Survival rate of the juveniles has never been that good: we already caught 90% of them! Even the lightest one, that was 165g last year survived: it is now 900g and it is running and playing all around with its 4 brothers and sisters!
To deal with energy limitation, individuals have to adjust their energy balance (energy acquisition vs. energy expenditure) to maintain their homeostasis and maximize their fitness. Among all mechanisms, thermoregulation represents the highest energetic cost in endotherms. My research project focus on the role of hibernation in the life history of the marmot. To understand how hibernation patterns are adjusted to environmental conditions, we are following the body temperature of 33 individuals since May last year with loggers placed in the intra-abdominal cavity. We already caught 20 of them. Cannot wait to download the data from these loggers! Some preliminary results below… Looks great, does not it!
Have a look to our blog in 3 weeks to know how the field session ended, and come back in few months to know more about the mechanisms underlying critical trait-demography relationships of the Alpine Marmot!
‘Don’t feign to be stupid.’ This well-chosen phrase of Marc Kéry introduced some of our group members to the world of Bayesian Statistics (where the use of your previous knowledge on the parameter you’re interested in, the prior distribution, plays a role). Together with Michael Schaub, Marc taught the inspiring course entitled ‘Bayesian population analysis using WinBUGS’ based on the book of the same name.
I was impressed by how they managed to cover almost the whole book within 5 days: starting with a gentle introduction to the analysis of distribution, abundance and population dynamics using a Bayesian framework, followed by an introduction to the software WinBUGS and implementation of mixed models in it, and finishing with some examples of the implementation of Integrated Population Models in WinBUGS. Lectures were alternated with useful exercises.
I think all the participants are after this course better trained in making a balanced decision whether they want to make use of the full knowledge they have, or use the veil of stupidity to make big discoveries (Schwartz, 2008).
Well, sometimes it is about fathers and sons, but sometimes it is also about sisters and unrelated males to find each other and settle down…
Three months after the beginning of our fieldwork we finally recorded our first long-range dispersal event. Following aggressive eviction from the natal group, a dispersing coalition of five subordinate females joined a group of unrelated roving males and left the core study area. The newly- formed group went undetected for several weeks until Nino found one of the coalition members (VLF152) …back on the reserve where she was captured and collared 5 weeks before. Interestingly enough she wasn’t with any of her original coalition partners and instead paired up with two newly evicted sisters.
But where were the other four sisters? Did the coalition simply split or did the other die? Or did they settled down somewhere with the males? But if so, why did VLF152 “return home” instead or remaining within them? Is this because, even within the new group, she was occupying a low rank and had therefore no chance of reproducing (for only one female, the dominant female, reproduces within a group)? We are currently trying to find the other four females to answer some of our questions. Knowing the where about of VLF152 – information that we can remotely download from her GPS collar – should help in this task since we can restrict our search radius.
This dispersal event adds to the previously collared individuals. At present, three dispersal coalitions returned to the natal group, one female returned to the natal group after her coalition partner got hit by a car but got evicted again, three coalitions are still dispersing and one single disperser got predated by a raptor. We thus recorded two cases of dispersal-related mortality. These movement data will allow us to investigate the influence that individual traits (e.g. age, size) but also the environment and the social spatial context (i.e. the distribution of territorial groups) have on dispersal patterns and dispersal success (survival rate and settlement likelihood).
!!! Merry Christmas from us all and a successful 2014 !!!
This Tuesday, Dr. Gabriele Cozzi gave a public talk at the Zurich Zoological Society about his PhD work on wild dogs, hyenas and lions in Botswana, and in collaboration with the University of Zurich and the Botswana Predator Conservation Trust :
“Mit Katzen (nicht) kommunizieren: ein Hundeleben”
“In (no) communication with cats: A dog’s life”
At the end of his talk, Gabriele received the prestigious Price for Nature and Environmental Protection (2013) in recognition of his contribution to wildlife conservation in Africa. Congratulations to Gabriele for this well-deserved award!
Sometimes Science is nothing more than checking assumptions. This holds true whether you are a theoretical biologist (e.g. checking model assumptions), experimental biologist (e.g. checking assumptions of experimental design), or just love doing statistics (as we all do). During the first weeks of my PhD, I found out that I perhaps needed to check the basic assumption my supervisor has about me: that I would be able to let eggs hatch in the lab. Until now, I have been unable to let the desired rotifer eggs hatch, but I can proudly announce that since five days we have some pets in our office: Triops! These crustaceans are considered ‘living fossils’, and just as the rotifers I’m investigating, their eggs can remain in a state of diapause for a prolonged period of time.
Assumption “I have the capacity to let resting eggs hatch under laboratory conditions”: Check!
Pfieuw
A rare opportunity for a group & affiliates photo. Taken during the apero following my inaugural talk, the reason why I am dressed like a bible salesman.
