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.
Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:10.15479/at:ista:11388
Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis of evolve and resequence experiments. ISTA. https://doi.org/10.15479/at:ista:11388
Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” ISTA, 2022. https://doi.org/10.15479/at:ista:11388.
S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” ISTA, 2022.
Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. ISTA.
Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments. ISTA, 2022, doi:10.15479/at:ista:11388.
All files available under the following license(s):
Creative Commons Attribution 4.0 International Public License (CC-BY 4.0):
thesis_sb_final_pdfa.pdf 8.25 MB
Embargo End Date
thesis_sb_final.zip 7.09 KB
Material in ISTA:
Part of this Dissertation