In this study, we use msprime software for coalescent simulation of large-scale DNA-sequence variation, to generate the ancestry of genetic sequences sampled from the population. We also generate some hypothetical phenotypes for individuals carrying these sequences by using additive trait models. The resulting phenotypes can be associated to the ancestral trees in various ways to check if we can identify the genomic regions harbouring trait variants. We compare our results from associating phenotypes and ancestral trees to results from standard single-variant approaches that associate phenotypes to genotypes, such as Fisher’s exact test.

Keywords
Coalescent, ancestral tree, msprime software, Population genetics, Phenotype and ancestral-tree association, distance matrices