Evaluating the ability of the pairwise joint site frequency spectrum to co-estimate selection and demography.

ABSTRACT: The ability to infer the parameters of positive selection from genomic data has many important implications, from identifying drug-resistance mutations in viruses to increasing crop yield by genetically integrating favorable alleles. Although it has been well-described that selection and demography may result in similar patterns of diversity, the ability to jointly estimate these two processes has remained elusive. Here, we use simulation to explore the utility of the joint site frequency spectrum to estimate selection and demography simultaneously, including developing an extension of the previously proposed Jaatha program (Mathew et al., 2013). We evaluate both complete and incomplete selective sweeps under an isolation-with-migration model with and without population size change (both p

SUBMITTER: Mathew LA 

PROVIDER: S-EPMC4538300 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature