Efficient pedigree recording for fast population genetics simulation.

ABSTRACT: In this paper we describe how to efficiently record the entire genetic history of a population in forwards-time, individual-based population genetics simulations with arbitrary breeding models, population structure and demography. This approach dramatically reduces the computational burden of tracking individual genomes by allowing us to simulate only those loci that may affect reproduction (those having non-neutral variants). The genetic history of the population is recorded as a succinct tree sequence as introduced in the software package msprime, on which neutral mutations can be quickly placed afterwards. Recording the results of each breeding event requires storage that grows linearly with time, but there is a great deal of redundancy in this information. We solve this storage problem

SUBMITTER: Kelleher J 

PROVIDER: S-EPMC6233923 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature