Over the Christmas break I couldn’t resit playing around with some detailed stickleback photos I took for one of our experiments, and created my first full-size non-academic poster! It just arrived and I am very excited about the result:
My first non-academic poster: an array of close-up photos of 33 experimental sticklebacks.
The poster shows the 33 individual sticklebacks that we used for an experiment in which we investigated consistent individual differences. As is clear from the poster, despite the fish being size-matched for the experiments, the fish have a beautiful range of colour and shading patterns. Let’s see if I’ll continue doing this for all my future experiments..!
This is a repost of an article I was invited to write for the Academic Life Histories Blog, a great collection of articles about navigating academia. See it here.
I always knew in the back of my mind I wanted to have children. However, I never really thought about when that would be. About halfway through my PhD that started to change. Work was progressing well and I was really enjoying the freedom of being able to dive deep into my own research interests. I was fortunate to have my own scholarship and a great supervisor who gave me all the freedom I wanted but was also there for me for long chats about science and academia. I was making my own plans and working according to my own schedule, which wasn’t exactly always nine to five. After some time, I suddenly started to realise that these conditions were actually pretty ideal for having a child and that, as I wanted to have children anyway at some point, why wait?
Towards the end of my third year as a PhD student my son was born. As I was doing my doctorate in the UK, that unfortunately also meant that I only had a few months of funding left. I took a couple weeks of paternity leave and, when my son was about five weeks old, flew with my family to Southern Germany for a job interview. I was lucky to get offered a postdoc position. I still had my PhD to finish though…
The last couple days Shaun Killen and Lucy Cotgrove from the University of Glasgow visited me in Konstanz to work together on a couple of exciting projects. Shaun and I started collaborating about a year ago to bridge the fields of animal physiology, animal personality, and collective behaviour.
With help of a Zukunftskolleg mentorship grant, we recently started writing an opinion paper on the topic, as well as analysing an exciting experiment with Lucy on the role of individual differences in metabolic rate on collective movement dynamics of schooling fish.Read further…
Today is the start of a new research period for me. I was very lucky to be awarded both a von Humboldt postdoctoral fellowship as well as a Zukunfstkolleg fellowship. These fellowships will give me the freedom to fully develop and pursue my own research ideas and set up my own interdisciplinary research program.
The next couple years I will aim to set up a unified framework for investigating the link between consistent behavioural variation, the emergence of collective properties, group functioning, and ultimately individual fitness and between-group dynamics. I will employ a combination of detailed laboratory experiments, field surveys, and computational modelling to study consistent behavioural phenotypes and collective behaviour of three-spined sticklebacks (Gasterosteus aculeatus).
By developing this framework and fully bridging the gap between the fields of Animal Personality and Collective Behaviour, I aim for this project to yield crucial new insights into the ecological and evolutionary implications of consistent behavioural phenotypes and the evolution of sociality.
As a scientist, I think it is important to contribute to the community. One of the ways I have been doing this the last couple years is by reviewing a fair share of papers (currently 44 reviews for 20 different journals). Even if I am busy I try to accept review invitations if I think I can give a proper assessment of the paper.
I have recently decided to join Publons to have an actual official log of my reviewing activity. After adding my whole backlog of reviews it is now as simple as a simple as forwarding an email to Publons to keep track of my reviews. I think it is great scientists get credit or their reviewing and editorial contributions and think that potentially a website like Publons may help provide further incentive for academics to keep fulfilling this important job.
Today after work I went snorkeling with some friends from work. We decided to start near the heart of Konstanz and swim down the Seerhein for about one and a half kilometer. I must say people looked a bit surprised to see three guys walking in wetsuit across the street. Although the water was not as clear as I hoped we still managed to see a couple groups of huge Carp, a number of single adult Pike of 1m+ at about 5-8m depth on the river floor, and some huge stickleback schools swimming in the shallows.
A huge Carp, my friend Ziga, and a large adult Pike somewhere in the green of the Seerhein
The last few weeks I delved into learning , a code language for more aesthetically pleasing article writing, especially in terms of mathematical formulas. As my research has increasingly been focused on the mechanisms underlying collective behaviour, for which I do a lot of mathematical computations, such an advanced yet simple text-editor is very helpful and overcomes the many pains I have with MS word!
It was quite a steep learning curve, but I managed to write my first paper with it last week. The great thing is that it is also possible to use in wordpress (which I used to create this website). It is also the standard language for drafting preprint articles, which is increasingly suggested and done in the biological sciences, thus a very relevant skill to learn.
Last week I was in Catalunya visiting friends and family and some undistracted paper writing. Catalunya, where my wife grew up, is an amazing place and feels like a second home to me. With the Mediterranean sea and the Pyrenean mountains within half an hour’s drive, there is always a lot to explore.
Hiking up the beautiful Gorge of Sadernes, Catalunya.
During some recent trips, I went hiking in the Pyrenean foothills and discovered schools of Mediterranean barbel (Barbus meridionalis). They seemed to be separate populations living in semi-isolated pools of a small mountain river. This species of Barbus is only native to a small area in and around the Eastern Pyrenees. Sadly, in recent years its numbers have plummeted with 30% (source: IUCN), highlighting an urgent need to better understand their ecology and vulnerabilities.
A shoal of Mediterranean barbel foraging on limestone rocks.
The last few months I have been working hard on the sophisticated new experimental set-ups in the lab with which we will be able to get high spatial and temporal resolution tracking of large schools of fish, in tanks that are up to 3x3m in size!
To get highly accurate spatial data of the fish we need to correct for the distortion of the camera lens, which almost all lenses have to some extent. I just finished the script (in Python) that enables us to undistort the image from a camera using functions in opencv based on a video of a moving checkerboard.
Me calibrating a camera with a checkerboard pattern, with colours showing the output of my python script, with a school of 1000 moderlieschen in the background :)
It works pretty well already, even with non-optimal videos. Next step will be to stitch the videos of multiple linked camera’s.
Recently I started a couple experiments related to parasite infection of Sticklebacks with Schistocephalus, a tapeworm with a fascinating life cycle that requires three separate host species. Our experiments focus on how the parasite affect the fish’s movements, its social interactions and positioning, collective behaviour, and survival in the context of predation.
Today, when moving fish around for experiments, I noticed one particularly bulged individual that, instead of a the smooth elongated body had the body shape of a brick! A clear sign of Schistocephalus infection. We put it down and measured its body weight, both before and after opening up its stomach cavity. What we found was not one, not two, not three, but four individual flatworms with a total weight of 55% of that of the fish! Incredibly how the fish could actually survive with such an immense parasite load.
Three-spined stickleback before and after removing four Schistocephalus worms
Went out again with the boat yesterday to catch sticklebacks. A cold but beautiful day. At first we couldn’t find them where I saw them last week, but soon enough it was clear they were still there but just very well camouflaged against the pebbled background!
With the three of us we managed to catch about 300 of them in half an hour by wading through the shallow waters. Most of the fish are likely 1st-years, but we also caught a couple older individuals that were huge, close to 10 cm!
After mooring the boat, we moved all fish to a large social housing tank at the Limnological institute where they will undergo a anti-parasite treatment for a couple weeks. After that I will move them to our fish lab at the University of Konstanz as well as to outside mesocosms. There they will ‘participate’ in a range of my behavioural experiments focused on individual differences in collective behaviour.
The past summer, I successfully completed a motorboat course to enable me to drive a motorboat on the Bodensee, required for my ongoing research on fish collective behaviour. I got my “Sportbootführershein” in the post a couple weeks ago, and finally this weekend was able to ‘take the boat out’.
In the cold rainy weather of early November, I set-off with with a good friend on one of the motorboots from the Limnological Institute. The water was considerably clearer than during the summer, providing a visibility of just over 5 meters. It was beautiful being out on the water. However, in the first hour almost being out, we still hadn’t seen our first fish!
We navigated around the island of Mainau, and started exploring the very shallow areas near the mainland. I was a bit annoyed I hadn’t seen any fish yet, let alone any sticklebacks, but when we decided to cross under the bridge leading to Mainau we suddenly found thousands of them!
The water was so shallow that it was necessary to take the motor out, and continue by oars. But this also meant we could observe the swarming fish from very close. Despite sticklebacks being very abundant in the Bodensee, in the autumn and early winter most of them move to deeper waters, likely following the movements of their invertebrate prey. These remaining fish were apparently some of the last ones remaining in the shallows, likely seeking shelter in the shadow of bridge, and I was therefore very happy to have found them.
We spent about half an hour observing their movements and behaviour and I got some good ideas to come back for some more quantitative field measures of their group sizes and compositions. After that we decided to go for a quick snorkel before going back to the harbour.
With my freediving wetsuit, the 11 degrees C actually still felt very comfortable, and I was enjoying the relatively clear waters of the lake. The Bodensee has a very interesting geology, with relatively shallow water on its edges that can suddenly drop almost vertically tens and tens of meters into the deep.
We only snorkeled a bit above a drop-off near the harbour to check our wetsuits and the visisbility, which both passed our expectations. I therefore can’t wait to go back again and take the boat out the lake to catch wild individuals for my experiments, get some more quantitative observations of the sticklebacks and their predators, and explore underwater.
Last weekend I went exploring the streams and lakes in the countryside near Konstanz to search for Moderlischen and determine the possibilities for doing fieldwork to investigate group movement dynamics and composition in the wild.
I was able to find them in some tiny streams leading to a small lake, showcasing some nice examples of collective shelter use and leadership and exploration of the stream, see the video below. Looking forward to starting exploring possibilities to start some actual field work on these populations.
For my new research projects on the role of individuality in collective movements and decision making at the University of Konstanz, I have been getting new sticklebacks from the Bodensee. Last weekend I went to see them together with my 10mo son! I think it was the first time he actually ever saw moving fish. Although I showed him fish in aquaria before, he was too young to react to them, but this time he was amazed by the large school of fish swimming back and forth. The sticklebacks from the lake were absolutely huge, I estimate up to about 9cm, much bigger than the ones I ever saw in Cambridge and the ones in the ponds near the University here. I hope to go on a trip soon to observe the collective behaviour of the sticklebacks in lake Konstanz, the ponds, and streams in the area to set-up some exciting experiments on the population-specific differences of this amazing species.
Here showing my excited son a school of Moderlieschen
My research is currently centred around understanding the role of consistent behavioural differences in the collective movements and functioning of animal groups. In particular, I assay large numbers of stickleback fish on various personality traits and expose them in groups to different ecological scenario’s. I have written custom tracking software in Python using the OpenCV library to be able to accurately track the position of individual fish in the freely-moving schools.
Today I wanted to share a simple visual that highlights the detailed individual-based tracking of a small fish school over time. Each fish is represented by a different colour, with the arrow showing its vectorized movement, with larger arrows indicating a higher speed. The video is centred around the vector of the group as a whole to better visualize the structure of the group over time. Lines indicate the smallest polygon encompassing all individuals and Individual Centre Distances. The moving axes indicate the relative speed of the group in a large circular arena.
In this short section of a 30-min long experimental trial it is clear that the group speed, cohesion, and structure fluctuate over time. At the same time, individuals also maintain to some extent their positions relative to the group centre, such as the green and yellow individual clearly having a stronger pulling power on the movements of the group as a whole.
I used RaspberryPi computers to film the fish, custom Python tracking scripts to acquire individual X,Y coordinates for each individual in the group, R to process the tracking data and acquire movement characteristics, and R with ffmpeg to create the visual.
I have been trying to improve my drawing skills to better illustrate how my sticklebacks behave and in what way personalities matter in collective behaviour. I still have a far way to go but this is my latest quick sketch that shows four sticklebacks with different morphologies. When I get more time on my hands after I hand in I will try to get some more elaborate drawings done!
Just over three years ago I was standing up to my waist in cold water, somewhere in the vicinity of Cambridge. I was catching sticklebacks for the first experiments of my PhD. Now, 37 months later, I am in the final stages of writing-up and will actually hand in my thesis in ten days time! During this last chapter of my PhD, I have also become a dad and am actually writing this with my 5 month-old son in the carrier on my chest. Luckily, after a nice walk with our dog in the cold autumn air, he has fallen vast asleep.
If it wasn’t for all funding falling away at the 3 year mark, one and a half month ago, I would be continuing with some additional exciting data chapters of which I already got the data. However, with five data chapters, two of which are published and two have been accepted, I have enough exciting work to talk about. In the months to come, I will be wrapping up a lot of small and large stickleback projects that I have done over the years and that have not made it into my thesis, besides some nice collaborative studies, and will continue with further experiments on the link between personality and collective behaviour as a Postdoc!
I have been taking quite a lot of photos and videos of the sticklebacks recently for public engagement and wanted to share this large close-up photo with you. Although it is a three-spine stickleback, it actually only has two spines, a feature that is common amongst this species.
My article on Clareity and the Clareity symposium in the autumn edition of Clare News
With the start of the new academic year 2014-2015, my role as Graduate Research officer of the Graduate committee of Clare College (and Clareity President) has ended. It was a wonderful and diverse year. Next to organising a series of evening seminars where Clare graduates present their work and discuss topics in the humanities or natural sciences, and a full-day research symposium, I set-up a new umbrella organisation with the aim to increase the interdisciplinary discussion at Clare. Read further…
Throughout the animal kingdom, individuals have been found to behave consistently different from one another over time or across different contexts. This is now mostly referred to as “animal personality”. As part of my PhD I want to understand what role such personality traits play in the structuring and functioning of social groups, i.e. in collective behaviour.
Today I am running an experiment to investigate the consistency of risk-taking behaviour, also known as the boldness personality trait. I work with three-spined sticklebacks that I caught in wild streams near Cambridge. The three-spined stickleback is a wonderful little fish that is not only easy to work with and keep in the lab but a model system for collective behaviour and animal personality.
Topview of the boldness tank with left the deep covered area that leads to an increasingly shallow area on the other side. You can see a fish and its trajectory in the toplane
This is a snippet of my late-evening train of thought on blogging and the start of a more personal and open style of blogging I’d like to embrace.
I really enjoy blogging. From the moment I created my nature blog mudfooted.com back in 2009. However, over the last years I have discovered again and again it is challenging to find the right balance with self-criticism and careful considerations to actually publish my ideas. It often takes considerable time to properly research background information before publishing new posts. Furthermore, having high standards to deliver interesting/fascinating/in-depth/popular content makes it hard to actually publish those drafts waiting in my ideas folder.
Often I wear a thick winter coat when working in my lab but today I forgot it.. Just on a day when I have to spent 12 hours in the lab..
Although most people will probably be enjoying another warm and sunny summer day (unless you live in Britain), I will be in my underground fish lab for 12 consecutive hours. It is about 11 degrees Celsius down here to keep the water housing the hundreds of sticklebacks nice and cool so they won’t get into breeding state and show the associated changes in territorial/mating behaviour. I am however feeling a bit chilly as well as I forgot my coat today.. By typing this I hope at least my hands and fingers will warm-up a bit.
Everyone knows that our personality plays a large role in daily life, from our need for adventure and our desire to hang out with friends, to our discipline in work and our compassion with others. But when we talk about personalities in animals, or non-human animals as I like to say, many may feel it is different. Although most people use personality related terms when talking about our pets, the majority of people may still believe personality is a uniquely human characteristic. The interesting thing is, personalities exist throughout the animal kingdom!
Until about ten years ago researchers talked about the behaviour of animals in general terms, ignoring the behavioural variation between individuals because it was considered ‘noise around the mean’. However, during the last ten years, more and more researches have shown that personalities exist in a wide range of species. From birds to bees, all species so far investigated show that individuals often behave very different from one another and do so consistently throughout their lives in a similar way like we do ourselves. For example, some individuals might be bolder or more aggressive while others are more sociable and tend to follow others. Read further…
This is the first blog post on my academic website JolleJolles.com. Although I have already been running my own nature and science blog Mudfooted.com for the past four years, I felt a need for a more personal view on science and the academic world and really like to increase the engage more with the public about my own research!
This blog will present my personal view of interesting new findings from the behavioural ecology literature and beyond, additional information, photos and videos about my own research, and my personal opinions and experiences of academia. If you like to be amazed by our wonderful natural world and read about the most recent fascinating scientific discoveries, please go and visit my other blog Mudfooted.com!