@phdthesis{11388,
  abstract     = {In evolve and resequence experiments, a population is sequenced, subjected to selection and
then sequenced again, so that genetic changes before and after selection can be observed at
the genetic level. Here, I use these studies to better understand the genetic basis of complex
traits - traits which depend on more than a few genes.
In the first chapter, I discuss the first evolve and resequence experiment, in which a population
of mice, the so-called "Longshanks" mice, were selected for tibia length while their body mass
was kept constant. The full pedigree is known. We observed a selection response on all
chromosomes and used the infinitesimal model with linkage, a model which assumes an infinite
number of genes with infinitesimally small effect sizes, as a null model. Results implied a very
polygenic basis with a few loci of major effect standing out and changing in parallel. There
was large variability between the different chromosomes in this study, probably due to LD.
In chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency
based summary statistic, giving an equation based on the initial allele frequencies, average
pairwise LD, and the first four moments of the haplotype block copy number distribution. I
describe this distribution by referring back to the founder generation. I then demonstrate
how to infer selection via a maximum likelihood scheme on the example of a single locus and
discuss how to extend this to more realistic scenarios.
In chapter three, I discuss the second evolve and resequence experiment, in which a small
population of Drosophila melanogaster was selected for increased pupal case size over 6
generations. The experiment was highly replicated with 27 lines selected within family and a
known pedigree. We observed a phenotypic selection response of over one standard deviation.
I describe the patterns in allele frequency data, including allele frequency changes and patterns
of heterozygosity, and give ideas for future work.},
  author       = {Belohlavy, Stefanie},
  isbn         = {978-3-99078-018-3},
  pages        = {98},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The genetic basis of complex traits studied via analysis of evolve and resequence experiments}},
  doi          = {10.15479/at:ista:11388},
  year         = {2022},
}