TY - JOUR

T1 - Perfect simulation of population genetic models with selection.

AU - Fearnhead, P.

PY - 2001

Y1 - 2001

N2 - We consider using the ancestral selection graph (ASG) to simulate samples from population genetic models with selection. Currently the use of the ASG to simulate samples is limited. This is because the computational requirement for simulating samples increases exponentially with the selection rate and also due to needing to simulate a sample of size one from the population at equilibrium. For the only case where the distribution of a sample of size one is known, that of parent-independent mutations, more efficient simulation algorithms exist. We will show that by applying the idea of coupling from the past to the ASG, samples can be simulated from a general K-allele model without knowledge of the distribution of a sample of size one. Furthermore, the computation involved in generating such samples appears to be less than that of simulating the ASG until its ultimate ancestor. In particular, in the case of genic selection with parent-independent mutations, the computational requirement increases only quadratically with the selection rate. The algorithm is demonstrated by simulating samples at a microsatellite locus.

AB - We consider using the ancestral selection graph (ASG) to simulate samples from population genetic models with selection. Currently the use of the ASG to simulate samples is limited. This is because the computational requirement for simulating samples increases exponentially with the selection rate and also due to needing to simulate a sample of size one from the population at equilibrium. For the only case where the distribution of a sample of size one is known, that of parent-independent mutations, more efficient simulation algorithms exist. We will show that by applying the idea of coupling from the past to the ASG, samples can be simulated from a general K-allele model without knowledge of the distribution of a sample of size one. Furthermore, the computation involved in generating such samples appears to be less than that of simulating the ASG until its ultimate ancestor. In particular, in the case of genic selection with parent-independent mutations, the computational requirement increases only quadratically with the selection rate. The algorithm is demonstrated by simulating samples at a microsatellite locus.

KW - ancestral selection graph

KW - coalescent

KW - coupling from the past

KW - diploid selection

KW - genic selection

KW - genealogical processes

KW - microsatellites

KW - Wright–Fisher model

U2 - 10.1006/tpbi.2001.1514

DO - 10.1006/tpbi.2001.1514

M3 - Journal article

VL - 59

SP - 263

EP - 279

JO - Theoretical Population Biology

JF - Theoretical Population Biology

SN - 1096-0325

IS - 4

ER -