Research

I am broadly interested in evolution, adaptation, and population genetics. Adaptation by natural selection is the driving force behind phenotypic change. If we wish to understand adaptation we need to understand how natural selection works on phenotypic variation and how does new phenotypic variation arise by mutation. A complete theory of evolution must have these two components (Hartl and Taubes 1998). In the past, great effort has been made to understand how selection works and now population genetics theory can give us a reasonably detailed understanding of this process. However, until recently the theory of mutation was somewhat ignored, probably partly because of the empirical difficulties of studying beneficial mutations. Even though it was none other than Fisher who presented the first model adaptation (Fisher 1930), now called the Fisher’s geometric model, which was later improved and extended by many authors.

Specifically, I am interested in how different extrinsic and intrinsic factors can influence the paths evolution can take. By intrinsic factors I mean the properties of the genetic networks that are the basis of phenotypic traits. How does the genetic architecture of the trait under selection affect adaptation? Will different genetic architectures constrain adaptation? If we know the genetic network that underlies the development of some phenotypic trait, can we predict what the genetic basis of adaptation will be? Can we say something about what types of mutations we expect to contribute to adaptation? What are the relative contributions of regulatory changes versus protein coding, gene and genome duplications, or even epigenetic changes?

Another question is how do extrinsic factors, that is ecology, affect adaptation. Often when we think of adaptation we model a sudden environmental change that the population has to adapt to. However, in the real world environments often change gradually, environments will fluctuate and environmental changes are probably autocorrelated. How does adaptation change when the environment changes in different ways?

I study these questions using both models and experiments. Currently my experimental work is focusing on evolution experiments with microbes. At the moment the microbe of choice is the filamentous fungus Neurospora crassa. I think experimental evolution is great for testing different hypotheses about evolution. When I have to work large multicellular organisms (i. e. macrobes) I use population and quantitative genetics.

Current and past projects

Role of epigenetics in phenotypic plasticity and adaptation

Currently I am doing a post-doc funded by the Academy of Finland in collaboration with Tarmo Ketola investigating what is the role of epigenetic changes in phenotypic plasticity. Phenotypic plasticity means that a single genotype can produce many different phenotypes depending on the environment. Organisms must respond to their environment all the time by changing their physiology, and development. They accomplish this by regulating the expression of their genes. Transcription factors are ultimately responsible for turning genes on or off. However, epigenetic changes can affect the binding of TFs and thus gene expression and phenotypic plasticity. What is interesting is that in cases some plastic changes are inherited by the next generation and epigenetic changes seem to be responsible in some cases. I’m interested in the role epigenetic changes in phenotypic plasticity and possible subsequent effects on evolutionary adaptation. I’m using the fungus Neurospora to investigate these questions experimentally.

See: Kronholm et al. 2016. Epigenetic control of phenotypic plasticity in the filamentous fungus Neurospora crassa. G3 6: 4009-4022

The role of epigenetics in adaptation

I did a post-doc with Sinead Collins in Edinburgh working on the (possible) role of epigenetics in adaptation. In recent years advances in molecular biology have revealed that there is more to heredity than just DNA sequence. Some organisms decorate their DNA by doing all sorts of modifications to it. Mostly these changes are reset between generations, but in some cases these modifications can be inherited by the offspring. First, one might think that this won’t make any difference for evolution as the theory is not dependent in any way on the chemical basis of heredity. Indeed, the foundations of modern evolutionary theory were in place before we even knew that it was DNA that carried genetic information or how genes worked. Yet, there is the possibility that epigenetic changes have some properties that are sufficiently different from changes in DNA sequence changes, so that epigenetic changes would alter adaptive outcomes. We tested this hypothesis using models and experiments.

See: Kronholm & Collins 2016. Epigenetic mutations can both help and hinder adaptive evolution. Molecular Ecology 25: 1856-1868

Kronholm et al. 2017. Epigenetic and genetic contributions to adaptation in Chlamydomonas. Molecular Biology and Evolution 34: 2285-2306

Local adaptation in seed dormancy in the plant Arabidopsis thaliana

In my doctoral work I studied the population genetics of seed dormancy in the plant Arabidopsis thaliana. The goal was to examine if populations of A. thaliana were locally adapted for seed dormancy, a trait that is ecologically very important for plants, and what is the genetic basis of local adaptation. We did find some evidence for local adaptation and we found that the gene Delay of Germination 1, a previously found quantitative trait locus, showed a signature of local adaptation and phenotypic variation in seed dormancy was associated with different DOG1 alleles in the populations we examined.

See: Kronholm et al. 2012. Genetic basis of adaptation in Arabidopsis thaliana: local adaptation at the seed dormancy QTL DOG1. Evolution 66: 2287-2302

References

Fisher, R. A. 1930. The genetical theory of natural selection. Clarendon Press, Oxford.

Hartl, D. L. & Taubes, C. 1998. Towards a theory of evolutionary adaptation. Genetica 102/103: 525-533