Efficient pedigree recording for fast population genetics simulation

Kelleher J, KR Thornton, J Ashander, PL Ralph 2018 PLoS Computational Biology DOI 10.1371/journal.pcbi.1006581

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  • We describe a way to record all of the gene-trees along a segment of genome, as well as how genetic material is passed down through the pedigree, during a forwards-time population genetic simulation.
  • To make effective use of this information, we describe both efficient storage methods for this embellished pedigree as well as a way to remove all information that is irrelevant to the genetic history of a given set of individuals, which dramatically reduces the required amount of storage space.
  • Storing this information allows us to produce whole-genome sequence from simulations of large populations in which we have not explicitly recorded new genomic mutations; we find that this results in computational run times of up to 50 times faster than simulations forced to explicitly carry along that information.