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Squeezing out the last egg

Annual fishes of the genus Nothobranchius are endemic to temporary ponds. When exposed nonlethally to a predation risk, their reproductive efforts are increased, likely to reproduce as much as possible before being predated upon.

This experiment was done by Arnout Grégoir, who recently defended his PhD. We are learning more about the interesting life histories of these remarkable vertebrates, that, in terms of certain life history aspects, have more in common with aquatic invertebrates than  fish.

The paper is out now in Ecology & Evolution.

 

Aridity promotes bet hedging

In a new paper Tom Pinceel shows that crustaceans from ephemeral water bodies have different egg hatching frequencies depending on local climatic conditions. If the climate is harsher and less predictable, a lower percentage of eggs hatches after rains. This ensures that more long lived eggs are left that may grow during future conditions!

The work has been published in  Oecologia

 

Figuring out why species are threatened

In a new paper, Falko Buschke tried to test whether  vertebrates that differ in conservation status differ in to what extent their ranges can be predicted by spatial and environmental gradients. It turns out there are no strong differences. Instead, models to predict the ranges of the most threatened species perform much worse than models for least concern species. Also, response to broad environmental gradients could not distinguish endangered, threatened or least concern species.  This suggests that we may underestimate extinction risk of species if we would try to assess this based on reliance on specific environmental conditions.

The paper is out in Biodiversity & Conservation

Mossing around

Mosses are more than just plants, for a wild variety of tiny animals, moss patches are veritable jungles. Yet, few animal ecologists have ventured into this world (but see and see). We did a first field survey to study spatial variation in biodiversity on moss islands that form on tree trunks. It was a small project that formed the BSc thesis of Mario Driesen and under supervision of Hendrik Trekels. In this pilot study we wanted to test whether typical island biogeography principles apply to moss islands. Despite the insular structure, small scale variation in isolation and island size don’t seem to matter for biodiversity. Canopy cover was the most important environmental variable. However, overall, we conclude that invertebrate composition in moss patches may not only depend on local patch conditions, in a particular moss species. It also depended on the presence of other moss species in the direct vicinity which can be dispersal sources of other species.

The work has been published in Acta Oecologica

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A moss island in the Sonian forest

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Mario in the field (albeit not in the Sonian forest)

Meeting with the STURN working group

sTURN Working Group: Does time drive space? Building a mechanistic linkage between spatial and temporal turnover in metacommunities

Bram recently met up with an international selection of ecologists in Leipzig to develop new ways to study metacommunity dynamics and gave a lecture at the German Centre for Integrative Biodiversity Research (iDiv) https://www.idiv.de/

Welcome Joren

Joren Snoeks finished his MSc thesis at KULeuven and joins us to study the ecological and evolutionary role of ancient granite inselbergs in landscapes. Besides from his PhD, Joren will also teach a number of practicals in our BSc program.

Opinion: What type of PhD student should you be if you want to stay in Academia?

More and more people are getting PhD degrees while, at the same time, the number of permanent academic positions seems to remain relatively constant at best, if not decreasing. A consequence of this is that natural selection among PhD students is increasing. This results in problems that range from psychological issues such as burn outs and depression to unethical behavior and scientific fraud. When I look back at the diversity of PhD students I have known during my – still relatively short – career, the dormant taxonomist in me pointed out that many of them could be classified into a set of categories based on the predominant strategy they used to complete their PhD. I only consider strategies that could lead to a successfully defended PhD at a proper university, not PhD’s you buy on the internet or obtain at universities with very low academic standards.

Here, I introduce ten different strategies that can be used to complete a PhD. You could consider them archetypes or perhaps better as stereotypes. Many strategies of people I knew or know, however, show affinities to more than one of the categories I present. Although hopelessly simplistic, I believe this caricature might expose a number of problems that are inherent with current PhD systems. I will discuss some advantages and disadvantages of a certain strategy with respect to obtaining funding for a prolonged stay in academia over short (post doc) and longer (tenure) time scales. Clearly, the success of different strategies will depend on your institution and on the research culture of the place where you work. Such discrepancies are highlighted to some extent where they could apply. However, this text is clearly insufficient to cover subtle differences in research culture among universities, faculties and research groups in different continents. Evidently, I am also biased by the departments in which I have worked or visited and from the stories of the people I know. I also have never hired new professors, so my knowledge of the internal cuisine of hiring committees is necessarily limited. I will approach this from the perspective of someone who obtained his PhD in a time with fierce competition for post docs and fixed positions, a situation that is likely to be familiar to many.

  1. The pioneer: although it is no doubt intellectually stimulating, breaking new ground and starting up a totally new project on a topic for which there is little or no available expertise or background information in the lab, remains tricky. Chances are your initial assumptions were wrong and you will certainly need a lot of tinkering to develop protocols and procedures that help you to get where you want to be. Worst case scenario is that your initial idea turns out to be totally wrong. Too bad nobody was there to warn you. On the other hand, you might be doing one of these high risk, high gain projects and the resulting Nature or Science publication could be your golden ticket to a tenured position. Overall, science could not exist without pioneers so it is a very honorable endeavor. However, it can be frustrating to see that others who possibly put much less effort into something less risky (bulk producers) might find it easier to get a post doc when the funding agencies fail to see the importance of your groundbreaking work and only count papers.

Likely to stay in Academia? Often not  (unfortunately)

  1. The specialist: you could decide to dedicate all your time to mastering a certain skill that nobody else in the lab has and certainly not your promoter. You advertise the technique and try to make sure it is something everyone will need or something your promoter will want to include in all his new projects. Your contributions to the work of others will generate a lot of 2nd, 3rd and 13th authorships. As long as you make sure that you are the only one who can do this, your job will be safe. Most biology labs will have a go-to-person for statistical issues, a bio-informatician and this-one-person who can use the whatchamacallit machine. You could aspire to be any of these people. A downside is that your position will be weaker as soon as your favorite programming language, molecular technique or machine gets out of fashion or becomes obsolete. Specialists always have to be on the tips of their toes and make sure they are still up to date with the latest new thing. Someone else could be hired who can do all you did and even more. It can also be risky to train younger members of the lab in the subject that you know best. In the short term, specialists have a good chance to stay on board. They will get plenty of co-authorships from their customers and as long as you cannot be missed, the boss will do anything he/she can to keep you on board. However, when considering people for tenure faculties may decide it is too risky to invest in a one-trick-pony and might go for a more generalist profile with a more diverse set of useful traits. People might think you are only good at one particular element of doing research – your specialty – and that there is a trade off with your skills in other dimensions such as the creative process of research, group management, teaching and writing. Some specialists are more likely to get hired than others depending on the latest needs or fashion. Every biology department in the world is looking for bio informaticians. Few are looking for the world taxonomic expert of the intestinal parasites of earthworms.

Likely to stay in Academia? Yes, but maybe not in the long run.

  1. The golden boy/girl. This is a strategy that, generally, cannot simply be adopted by choice. You grow into it, or are propelled into it. Popularized by Jorge Cham’s PhD comics, many supervisors would seem to have one student for whom everything seems to work out and can’t do anything wrong. As scientists, we know that this set of positive observations that surround a specific subject can result from any or a combination of different processes. Some golden boys or girls may just be overall better than the rest of the lot at doing their job and this can justify their status. In this case it helps to be the best at something the professor particularly values. Problems arise when the merits of the golden one do not warrant such a status. Luck can be important, but only over the short term. In the long run and over many events chance effects tend to disappear. So although an initial lucky shot might give you a golden aura, this is likely to fade over time. Another reason could be that you simply remind your supervisor of himself or another person he/she cares or cared about (given that your supervisor actually has emotions). You might simply get along well, listen to the same music or become friends. This might be a positive experience for the two of you, but beware that this special relationship might be despised by everyone else in the department and friendships can go sour very easily due to the unpreventable promoter-student tensions that emerge towards the end of a PhD. Worse is the situation in corrupt systems where having the same ethnicity, gender or political views, being related, attractive or a love interest of the professor or another person of power in the research group results into privileges over others. Unfortunately such situations exist in many parts of the world. Being the golden one always helps to stay in academia when your supervisor can afford to keep you, but the envy of others can sometimes prevent effective collaborations.

Likely to stay in Academia? Yes

  1. Generalist.

Trying different things and emerging yourself in different fields may help you to make the links that specialists did not see. The result of this can be important papers of synthesis. On the other hand, you might also end up writing reasonably good papers in different fields while never reaching the absolute top specialist journals because you lack the tricks the specialist knows. A way to compensate for this is to surround yourself with specialists to help you. Knowing a bit of everything is convenient when you have to teach bachelor level introductory courses. On the other hand, being specialized will earn you the right (or the task) to teach difficult highly specialised MSc courses.

I believe generalists tend to struggle in the short term. Their CV’s may be interpreted as lacking clear focus by some funding agencies. Therefore, they probably should explain very well how everything fits together in their applications. Trying many things is ok… but it must be going somewhere. In the long term, generalists often thrive when surrounded by the right people. Hiring committees may appreciate their flexibility and experience. They are also less likely to get bogged down because their field is no longer or simply not a hot topic.

Likely to stay in Academia? Not in the short run, can be beneficial in the long run

  1. The harvester

The harvester is the worst nightmare of the pioneer. It is the PhD student that comes in in the final stages of a long project and scores a big paper. Standing on the shoulders of all the pioneers who came before, the harvester puts the cherry on the cake and scores the long awaited home run. This big score will almost guarantee a post doc, but might also induce jealousy in hard working colleagues scraping together results. Clearly it is great to be a harvester so you might be on the lookout for those projects. However, the fact that the end goal has been laid out long before might make such projects less exciting. And scoring a big paper will surely be more rewarding if it was your idea all along.

Likely to stay in Academia? Yes, very much so!

  1. The risk avoider /bulk producer

If you don’t like risk it can be tempting to become a bulk producer. Many funding agencies did or are still counting papers rather than taking into account the value of individual contributions. Whether SCI impact factors are a reliable indicator of quality is another discussion (surely the scaling is non linear). Many funding agencies and faculties worldwide still count or at least have different criteria of what they consider as valuable contribution to the field. As such, for many PhD students it will be a good idea to not just focus on high risk projects but publish low hanging fruit. A downside of this is that without a breakthrough paper you might not convince people to give you a faculty position. It is also not intellectually stimulating to work on topics of which the expected outcome of endeavors will be quite obvious.

Likely to stay in Academia? Yes, possibly not in the long run

  1. The networker

Very few researchers excel in all elements that can contribute to a successful PhD. Therefore, surrounding yourself with others with complementary expertise is generally rewarding. It may lead to papers with many co-authors which may be frowned upon in some countries. An individualist may get these prestigious single author papers… but generally those papers also tend to be reviewed heavily by colleagues that are simply not in the author list. I doubt few true individualists survive in Academia. Bad networking practices include trading authorships or setting up (unspoken) deals with friendly reviewers (to scratch each other’s backs).

Likely to stay in Academia? Yes, but networking alone is not enough

  1. The principalist

The archetype of the ideal PhD student is probably that of the one that does not run off with efforts of other people’s work, never cuts corners and always prefers quality over quantity.  Doing this can be very rewarding and I think most students strive to adhere to these strict principles. Yet, throughout the PhD, you might be confronted with harvesters, bulk producers, networkers and risk avoiders and change your strategy when you notice that these other strategies are more effective.

Likely to stay in Academia? Yes, but not always

  1. The drone

Authoritarian promoters with a clear vision of what they want can sometimes decide to hire PhD students to literally do their bidding and perform their research by proxy. Some people start a PhD and the experiments they have to do are already written up by the promoter before they even started. While this relationship is great for the promoter who can see his inclusive fitness increase due to an army of drones, a PhD candidate may learn very little except from the practical skills related to performing protocols. Few people would say that the safety of having such clear goals would outweigh the intellectual desert of being a cheap lab technician. Due to interesting fiscal deals for PhD students, it is in many parts of Europe at least, much cheaper to hire a PhD student than a technician. Long term chances for drones to stay in Academia are slim because they have not been involved in essential steps of the research process and hence lack the crucial experience of thinking up hypotheses and experimental designs.

Likely to stay in Academia? No

  1. The Fraud

I’ll devote little space to those that choose to cut corners and commit minor or major actions of fraud. Just about everyone would agree that anyone who deliberately (or out of ignorance) slows down the process of scientific progress by selling unreliable or outright fake results has no place in this domain. However, detecting culprits can be difficult and fraud may remain undetected for quite some time. Open access to datasets can help as well as the rigorous review process in top journals. Over time, chances to get caught should increase and I doubt many can continue to publish for years to come.

Likely to stay in Academia? Yes, but not in the long run

Discussion

Thus far, I have considered PhD students and their strategies as independent and did not consider that these strategies have to be able to coexist in a research group:  I neglected the ecology. Which strategies are compatible and which are not? Clearly – as game theory showed us – the success of one strategy will also depend on the strategy of others. With many pioneers, a harvester can thrive. But a harvester needs pioneers to be successful. Harvesters can in many cases turn out to be parasites i.e. individuals that engage in relationships with others from which they only benefit.  In other cases, when the original collectors of the data or the pioneers already left academia or when the harvester used an original perspective to make more of data that were lying around it would be better to describe the relationship as commensalism. To some extent a variety of strategies makes sense and can be beneficial for a research group when some strategies are complementary.  However, I believe many funding agencies for post doctoral grants favor a certain type of research and publication strategy.  They are selecting for a particular type of academic (sometimes bulk producer, sometimes based on a few outlier publications) while academia may benefit from a larger diversity of different academic profiles.

Most of all, I think there is a need for alternative futures as many promoters believe that the academic path is the only path worth pursuing (possibly because it is the only path they know). We need to project alternative careers for people with PhDs. Inform companies about the added value of hiring someone with a PhD or post doc level experience. Currently many companies often don’t  know why they should hire a PhD, certainly not if this means they have to pay this person a larger salary. I think many people from academia assume that having a PhD proves that a person can do independent work, solve problems and is proficient in interpreting, analysing and writing up information. This, however, is not well known to people outside of academia and as we highlighted above: there are many ways to get a PhD using totally different skill sets. The person you want to hire might have been a good networker, who needed help from others to do his analyses but did not contribute much to the huge list of papers he is co authoring.  Take away his network and the person might not be able to independently do what you are hiring him/her for. You might be hiring a harvester with a lot of papers who might struggle in a new role as a pioneer to set up a new project from scratch.

Clearly, having a PhD can mean many things and people with PhDs can have totally different trait sets. Not all of these traits are also useful to strengthen a research group and warrant a prolonged stay in Academia. For a hiring committee it can be challenging to find out which trait set a person developed and used to get his/her PhD and this may require more than a quick glance on a person’s CV and a brief interview.

Joining the Inselberg Research Initiative

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I visited the University of Rostock to consult with some of the world’s leading experts on the ecology of isolated mountain habitats known as inselbergs. We’ll be joining forces for a number of future projects combining insights from plants and animals to better understand how these enigmatic landscape features survived through the ages and how their biota interact with the landscape matrix around them.

https://www.botanik.uni-rostock.de/forschung/inselberg-research-initiative/what-are-inselbergs/

Using X rays to look inside zooplankton resting eggs

Zooplankton dormant eggs are time capsules that can transport offspring to distant futures. However, after decades of study we still don’t know very well how this mechanism has evolved and how it works from a mechanistic point of view.

In new paper, Tom and I decided to use the VUB’s micro CT scanner to have a look at the internal structures of zooplankton resting eggs. Why would we want to? Well, in the past, the only way to look inside them was to freeze dry them, cut them and look at them with a scanning electrone microscope. This means that you’d have to kill the embryo and that the procedure might result in artefacts. You might see structures that don’t look that way in real life. Given that we are doing a lot of experiments on the evolutionary importance of differential hatching from resting eggs we were really keen to have a look at exactly what’s going on inside these eggs before they decide to hatch.

This pilot experiment showed that the method can yield useful images although the resolution is less than SEM. In addition it turns out that the embryos in the eggs also don’t seem to suffer too much from the X rays and most of them still hatch afterwards. More information, is likely to follow as soon as we can start to link embryonic and egg traits to the hatching behavior of eggs.

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3D reconstructions of resting eggs obtained via X ray scanning. Top left: a cyst of the fairy shrimp Branschipodopsis wolfi, Top right: a cyst of the tadpole shrimp Triops. Bottom: an ephippium with two resting eggs of the water flea Daphnia magna.

Modeling the sensitivity to climate change

In a new paper out in Scientific Reports, we use a matrix population model to test how sensitive populations of fairy shrimps are to changes in climate. The stepwise modeling procedure allows to calculate the long term population growth as a measure of fitness. If it is positive, the population will survive, if it is negative it will not. It does this by calculating, for each generation, how many eggs would be produced based on known life history traits of the species and a measure of environmental quality of the inundation (in this case represented by inundation length).

For most species it is very difficult to know how they would respond to changes in climate. However, for our fairy shrimp we have a lot of background information that allows us to make educated guesses about which life history traits could be important. We know for this species that it requires a specific amount of time to reproduce which is related to how long a pool can hold water and on the conditions they need to hatch. We also know how much eggs they can produce per day, how many eggs hatch during each inundation etc…

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Population of the fairy shrimp Branchipodopsis wolfi in a temporary rock pool on a mountaintop in South Africa

The length of these inundations is one environmental parameter (of many) that will change under changing climates. But it is an important one that is directly linked to fitness. Shorter inundations means less inundations that are long enough for reproduction.

We were – and are – still ignorant about how these species will respond to these changes. However, the model does allow us to test which life history traits could be important to maintain long term survival of the populations. As such it shows which traits could help populations to survive.

One of the conclusions of the study is that, when inundations are short, it would be beneficial to make sure that a lower fraction of eggs would hatch during a given inundation. Such a mechanism could be an example of a risk spreading theory that is consistent with predictions of evolutionary bet hedging theory.

It is still a simplistic model, so it does not tell us how things will go in the future. It does not capture tradeoffs among life history traits nor the evolutionary potential of the populations.  Yet, it still narrows down the range of possible future scenarios of these populations by showing what the consequences for population survival would be if populations could respond adaptively or plastically and change there life history traits.