Our research centers on five main topics: algae, evolution, macroecology, biodiversity and bioinformatics. Our aim is to be creative in combining two or more of these research fields in our projects. This usually leads to exciting new ideas that are fun to work on and keep those brain juices flowing.
Click the icons for more information about each topic.
Marine algae form the common denominator of the lab's research efforts. We are interested in various aspects of their diversity, evolution and macroecology.
Because we are just scraping the surface when it comes to our knowledge about algae, a considerable part of the work consists of exploratory studies of their biodiversity, ecology and evolutionary relationships. Once this basic information is available, we can go into more specific questions. The scope of our research is very broad. I encourage you to explore the various topics by clicking the icons above.
Eukaryotic algae have a very rich evolutionary history. They originated more than a billion years ago in a series of endosymbiosis events and have diversified in almost all imaginable directions.
We study many aspects of their evolutionary history. We study the evolutionary dynamics of their genes and genomes, for example because we want to find out why some species have one gene for a function while others have another for the same function (see paper), or because we want to investigate what happens to an alga's genome after it's been involved in an endosymbiosis event. And of course we study the evolution of genes to infer the phylogenetic history of the algae they are found in.
A recently started project aims to investigate how algae have evolved different preferences for trace elements like iron, zinc, copper etc. These trace elements are often limiting algal growth in the open ocean so it's important to find out how much different species need and how their needs have evolved.
A last exciting topic we like to work on is the question how biodiversity comes about from an evolutionary perspective. Biodiversity is essentially the result of three processes: speciation, extinction and dispersal. Studies of speciation and extinction are usually carried out by paleontologists, but phylogenies of extant species can also give clues about speciation-extinction dynamics in the past. We enjoy looking for associations between the rate of diversification and properties of the organisms in question, for example linking speciation to sea surface temperature to find out whether speciation happens more often in the tropics.
Macroecology deals with the relationships between organisms and their environment at large spatial scales. It deals with how organism's distributions and biodiversity relate to features of the environment such as sea surface temperature, nutrient load, etc.
An important aspect of our work in this area is ecological niche modeling or species distribution modeling, in which occurrence records of a species are related to the environmental conditions of those places and a model is built to relate the distribution of the species to the environment. This model can than be used to predict other places where the species can occur, either in the present, the past or the future (e.g. assuming climate change).
How many species are there on earth? How are they distributed? Do some places have more species than other places? Why is that so? And what causes underly biodiversity in the first place? These are the types of questions we try to answer in our biodiversity work. To do this, we first need to characterize which species there are and where they occur. This involves quite a bit of field work, mostly in places that have not been studied in enough detail. We use DNA sequences for species identification most of the time (you'll read why below).
For smaller algae, that approach doesn't quite cut it. Some diverse algal turfs like the one pictured on the left have several dozen species of small macroalgae and countless microscopic algae in just a few square inches. The same goes for all the phytoplankton growing in ocean water. You don't see most of those species in the field, and yet it's equally important, perhaps even more important because of their crucial role in many ecosystem processes, to understand their biodiversity and distribution. For example, one of the projects we're working on involves boring algae (yes, that's right, boring). These creatures bore through coral skeleton and have a crucial role in coral reef degradation. In order to better understand how many species of boring algae there are and whether or not each coral has its own set of boring algal species, we use environmental sequencing (metabarcoding), in which a sample containing many species is sequenced at once using high-throughput techniques.
When doing our research, we often discover new species or groups of species in which the boundaries between species are not clearly defined. In those cases, we sometimes choose to investigate those species boundaries in more detail. Algal species are most commonly defined using the morphological species concept. Unfortunately, morphological species delimitation tends to be problematic: because algae have fairly simple bodies and anatomies, there are relatively few characters in which closely related species can differ. As a consequence, some species boundaries are blurry. Additionally, morphologically simple organisms may be more prone to morphological convergence. Not surprisingly, explorations of alternative species concepts and information sources (e.g. crossing studies and DNA data) have lead to the collapse of morpho-taxonomic species boundaries. In a majority of cases, morphological species were found to contain multiple biological or phylogenetic species.
We use various approaches to combine morphological and DNA data in order to accurately pinpoint species boundaries. This often comes down to use DNA data to identify 'entities' that could be considered species and subsequently characterize these entities morphologically by analyzing morphometric datasets gathered from the sequenced specimens (see abstract). We are invesigating species boundaries in several algal groups using these and other techniques. We are increasingly using species delimitation algorithms that exploit the information in DNA data to delimit species in taxa where few other clues are available (e.g. when morphology is highly plastic: see abstract).
Computational tools are an essential part of converting raw results into meaningful results. So it is perfectly natural that they take a central place in everything we do, and a good understanding of what the software does behind the scenes is crucial to drawing meaningful conclusions.
Many aspects of our research involve phylogenetic analyses of DNA sequences. In the majority of cases, standard phylogenetic techniques are applied to examine patterns of diversification or address taxonomic or evolutionary questions. For our macroecological work, we often rely on species distribution models. This uses an entirely different set of computational tools like Maxent.
For most of the analyses that need to be done, we simply apply software that others have developed. But in many cases, the analysis needs to be taken a step further, and we need to write our own programs. For example, we're often dealing with large datasets that cannot easily be managed manually, and writing a small Perl or Python script can help with those sorts of tasks. For this and other reasons, students in the lab are encouraged to learn basic computer programming if they don't already know it. Acquiring some programming skills makes life a lot easier, you get to be a nerd, and it's a highly transferable skill, so what's not to like about it?
We are also interested in developing tools for molecular phylogenetics and niche modeling, and in testing the performance of analysis techniques We write software for new techniques that we develop. We test the performance of techniques with case studies and simulations.