This week’s PhDetails is with Isolde van Riemsdijk who does her PhD at the Naturalis Biodiversity Centre in the Netherlands. I first met Isolde last year at the PEB meeting in Buttermere which was a really lovely small conference/workshop where the topic is the use of bioinformatics in evolutionary biology and have bumped into her at various conferences since including PopGroup earlier this year (I wrote about both of these conferences in an earlier blog post HERE!
Isolde did her BSc and MSc at Wageningen University (the Netherlands). During her masters she did a research project on time calibration of tropical plant phylogenetic trees at the Biosystematics group with Prof. Lars Chatrou at Wageningen University, and a research project on ZooMS in archaeological bone fragments at BioArch, with Prof. Matthew Collins, York University (UK). Both projects were about 6 months. After this masters she did a research project with Prof. Katja Nowick at Leipzig University (Germany) on bioinformatic tools for detection of SNPs and inversions in genomes. During the project in Leipzig, Isolde applied for her current PhD at Naturalis Biodiversity Center in Leiden, The Netherlands. During her PhD Isolde also went to join the Shaffer laboratory with Prof. Bradley Shaffer at the University of California, in Los Angeles, to set up a RAD sequencing project for half a year.
Isolde did her BSc and MSc at Wageningen University (the Netherlands). During her masters she did a research project on time calibration of tropical plant phylogenetic trees at the Biosystematics group with Prof. Lars Chatrou at Wageningen University, and a research project on ZooMS in archaeological bone fragments at BioArch, with Prof. Matthew Collins, York University (UK). Both projects were about 6 months. After this masters she did a research project with Prof. Katja Nowick at Leipzig University (Germany) on bioinformatic tools for detection of SNPs and inversions in genomes. During the project in Leipzig, Isolde applied for her current PhD at Naturalis Biodiversity Center in Leiden, The Netherlands. During her PhD Isolde also went to join the Shaffer laboratory with Prof. Bradley Shaffer at the University of California, in Los Angeles, to set up a RAD sequencing project for half a year.
What is your favourite band/musical artist pre 1980?
Nina Simone.
Favourite band/musical artist post 1980?
Yann Tiersen.
Favourite movie?
I recently saw Mortal Engines, which was awesome!
Do you listen to podcasts?
I have tried to listen to podcasts, but the only one I listened to with dedication was on the Dutch education system “opgejaagd” (transl. rushed). The Dutch education system has a big emphasis on performance during exams, starting already around the age of 5. The podcast looked at how this impacts child development, and the impact it has on their parents experience with day care and school etc. The journalist who made the podcast really did her research, and included interviews with a lot of experts on education.
Where do you study and who are your supervisors?
Naturalis Biodiversity Center, my supervisors are Dr. Ben Wielstra and Dr. Pim (J.W.) Arntzen, and my promotor is Prof. Menno Schilthuizen.
What year of your PhD are you in?
The fourth year!
O-o
Who’s giving you the money – and for how long?
The Netherlands Organisation for Scientific Research (NWO), for four years, which is the normal length of a PhD trajectory in the Netherlands.
Do you have any publications – if so where?
Yes! The two publications on the banded newt (genus Ommatotriton), and the one on the common and spined toad (genus Bufo) are PhD projects. I have some more in the pipeline, including some cool projects by our students! You can find my publications on google scholar: https://scholar.google.nl/citations?user=inA6psoAAAAJ&hl=nl&inst=2536098262531718533&oi=ao
Did you do a masters – where was it and was it about?
Yes, in the Netherlands most people who do a Bachelors at University also do a Masters. I did my 2-year Masters in Biology at Wageningen University. I also took some courses at the University of Utrecht, and I went to the University of York (UK) for one of my research projects.
Do you do fieldwork? What is the best fieldwork you have ever done and what made it great?
I did only a little bit of fieldwork. Most of the samples were already gathered by my supervisors, which has as an advantage that the stage of trial-and-error of finding the right spot for making transects had already been passed. The best fieldwork I did was during a course in the south of France, near Tigouleix, organised by EPMAC. During this course I’ve learned a lot about the local amphibians and reptiles and their habitat.
How many PhDs did you apply for – what were you looking for?
I think maybe four, but none of the earlier PhDs were fitting as well with my interests as the one I’m now doing. I was looking to do something on evolution, where I would be able to learn new stuff as well as apply the experience I had from previous research projects. I was very excited to get this opportunity.
What is the most bodged piece of equipment you have had to use during labwork – did it work?
A big plate centrifuge with a lid with one broken hinge. You had to hold the lid with two hands when opening or closing it. The lid was heavy, so it was quite inconvenient.
What one piece of advice would you give to a masters student applying to PhDs now?
Visit labs and do multiple science projects during/after your masters, so that you know which research groups you like, what kind of stuff you like to do. And people get to know you, too. At the moment I applied for my current PhD position, I was working on a research project at the University of Leipzig, with Prof. Katja Nowick and her group. I think that really contributed to getting the position.
How often do you meet with your supervisors?
In average over the past 3.5 years I’d say once every two weeks. We never had regular meetings, and whenever I need to ask something small I can just ask (one of my supervisors is in the same office). We make appointments for longer meetings.
What supervisor traits are important to you?
Didactic skills, patience, and being able to switch supervision style to the person in front of you. Different people need different things.
What do you think are the worst supervisor traits?
Not being aware of bad traits, or not acting on their bad traits. It’s OK to have things you are bad at, everybody has their imperfections, but I think as a supervisor, you can make sure that there are alternative solutions if those become an issue, so the student doesn’t suffer from the negative impact of the supervisors’ shortcomings.
In one sentence what is your PhD about?
The genetic dynamics of moving hybrid zones in amphibians
What has been your academic highlight of the last year?
Having Nico Bierne (whom I've never met) make a GIF about my recent publication on moving hybrid zones
What has been your academic highlight of the last year?
Having Nico Bierne (whom I've never met) make a GIF about my recent publication on moving hybrid zones
Now that I know how to gif I did a gif to illustrate the expectation of this very interesting paper #HybridZonesAreCool— Nico Bierne (@nbierne) January 9, 2019
Testing an hypothesis of hybrid zone movement for toads in France - van Riemsdijk - Molecular Ecologyhttps://t.co/v5mtYYvWi7 pic.twitter.com/nL0rh6Pl36
Have you had an academic lowpoint of the last year – if so what happened?
I was super enthusiastic about a research project I wanted to set up, but it being the last year of my PhD it was decided we were not going to pursue the topic anymore. It made total sense but still was a bit disappointing from my point of view.
Who has been your academic role model/inspiration and why?
I think all my PI’s contributed to who I am now; all the groups I worked in had their good aspects, and I take them as inspiration to what type of person I would like to be.
Which academic idol/scientist have you met?
Prof. Katja Nowick, Prof. Roger Butlin, … and so many more!
Which academic idol/scientist would you most like to meet?
I guess Nico Bierne, partly because of the GIF he made. And so many others. I think we have many great scientists working in the field of evolutionary biology.
Do you have a favourite paper?
Ravinet et al. 2017, this paper really helped me to get a grip on the literature concerning barrier effects between species. (Rishi: Someone else wrote a great comment on this paper and I'm slightly biased but if you want to check that out its HERE)
What has been your favourite conference so far – why?
The PEB conference in Buttermere, because I met a lot of interesting people there, and I learned a lot from both the talks and workshops, the location was amazing.
What hours do you typically work?
Most of my PhD 9:00h – 17:30h, Monday to Friday. If needed, I adapt my schedule. I’ve noticed I’ve worked a lot the last few months, so after I’ve finished my thesis, I really want to slow down a bit.
How do you avoid procrastinating?
Whenever I really can’t focus anymore on the work at hand, I try to find some easy, preferably fun, task that I need to do anyway, like editing a figure. However, I find that when you relax your brain for a bit, you can have the best ideas. So taking a break in my opinion also counts as avoiding procrastinating.
What motivates you in your day to day PhD life?
Sequencing technologies have really pushed back the boundaries of what questions we can answer in evolutionary biology. I’m really excited to be part of this new era, where it becomes increasingly important to be able to handle and analyse large quantities of data, and be able to interpret them in a sound way. In addition, I really like the diversity of doing a PhD; you are involved in all steps of the research, more so then when you are doing a project during your masters.
What do you do when you’re not working – how do you balance it with your PhD?
I go swimming at a local swimming pool each week. Doing stuff with friends and family, read books, go hiking.
What essential tool hardware/software could you not do your PhD without?
R (but also python/bash/C++/eidos/… so probably “Stackoverflow” would be more appropriate)
If a genie could grant you one wish to help with your PhD what would you wish for?
A bigger server (more cores, I have 8 now)!
What would be your dream job?
Being part of a diverse research group, preferably focussed on amphibian population genetics, a big server, and a walk-in help desk at the IT department, where you can go with all your server related problems.
Where do you see yourself in 5 years?
Who says dreams don’t come true? I hope to be working with some enthusiastic people on amphibian population genomics.
One word to sum up your future in academia: cloudy-with-a-fair-chance-of-sunshine
What do you want to achieve outside of academia in the coming year?
I would like to make more music, maybe join a group again.
What would you like to work on in the future?
I would really like to continue working in hybrid zone research, preferably in amphibians and reptiles.
Do you have a favourite organism?
I really like kingfishers. Those birds bring along a bit of magic, whenever you see them.
Are there any social interactions/meetings which have enhanced your PhD experience?
I’ve ran the journal club of our group for a couple of years, which was loads of fun. We even published a comment on a paper based on a journal club session. The group meetings at the Shaffer laboratory in Los Angeles were exceptional, we would sometimes discuss someone’s work for about two hours! This was very intense, but also gave a good boost, as people were genuinely interested, asked loads of questions, and gave good advice on how to continue your work.
If you could change one thing about your group/department structure what would it be?
During the whole of my PhD, the Naturalis research building has been closed due to construction and refurbishing, and the Naturalis scientists are located in different buildings across Leiden. This made it kind of hard for people from different groups to mingle and stay connected. Later this year, the new building will open. I think this will really improve the connectedness in the institute!
What major question in your subject area is yet to be addressed – why is it important and why isn’t anyone addressing it?
Within amphibian and reptile species, a lot of questions regarding evolution on the genome level are still unanswered. Sequencing whole genomes is still difficult for such large and weird genomes, especially since not so many reference genomes are available, either. So I’m really excited to see what new technologies will contribute to our knowledge of amphibian and reptile evolution.
Nice to see what (and how) you are doing Isolde!
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