A major goal in evolutionary biology is to understand which processes shape genetic diversity observed in natural populations. Classic population genetic theory provides a solid mathematical framework to study genetic variation and predict efficacy of natural selection relative to drift in equilibrium conditions, for example under constant population size. However, the majority of natural populations often experience large size fluctuations that make prediction less straightforward.

            The main purpose of this project is to test how extreme fluctuations in population size of outbreaking species affect the dynamics of neutral and adaptive genetic variation. Many pests experience epidemic outbreaks characterized by sudden changes in population size, often spanning orders of magnitude. Such outbreaks are known from ecological studies of closely monitored species of economic importance. However, little is known about how genetic variation changes during outbreak cycles. Specifically, the rate of adaptive evolution during relatively short periods of large population size remains unknown.

This can be studied in species which experience extreme fluctuations of population size, such as spruce bark beetle (Ips typographus). 

Spruce bark beetle is the most destructive pest of Norway spruce forests because under specific conditions (e.g. storms) populations may outbreak, causing mass mortalities of spruce stands. We are comparing populations of spruce bark beetle that have experienced frequent, recent outbreaks and populations that did not experience outbreaks in the recent past. By combining existing knowledge on biology and ecology of the species with newly generated, large-scale genomic data, we address specific questions about the relationship between genome-wide variation and fluctuating effective population size: How outbreaks affect species genetic structure? Are adaptations in frequently outbreaking populations mainly driven by soft sweeps? How demographic history of the spruce bark beetle and historical fluctuations of effective population size over time affect current patterns of neutral and adaptive variation and many more. 

We have several ongoing projects where we use the data we have recently generated:

  1. Genetic structure and genome wide variation in spruce bark beetle. I this project Anastasiia is analyzing high coverage data from 250 individuals from 18 populations across species range. She is looking into SNP variation as well as trying to understand chromosomal rearrangements discovered within the species. In collaboration with Fredrick Schlyter, Martin Andersson.
  2. Demographic history inference. In this project Piotr is using whole genome datasets and advanced inference methods to reconstruct spruce bark beetle demographic history.
  3. Genetic structure in the Carpathians and Apennines. Julia is looking in more details into the genetic structure of spruce bark beetle from two mountain ranges at the southern border of species distribution.
  4. Within species variation of spruce bark beetle microbiome. Julia is using whole genome data sets to fish for sequences that belong to microbiota associated with spruce bark beetle.
  5. Linkage map reconstruction, recombination rate and mutation rate estimation. This is a collaborative project with Fredrick Schlyter, Martin Andersson and Dineshkumar Kandasamy. Anastasiia is looking into pedigree data to estimate crucial parameters – recombination and mutation rate.
  6. MORE to come 😊

The project is funded by the Polish National Science Centre (NCN) SONATA BIS grant.