Importance sampling for the infinite sites model

TY - JOUR

T1 - Importance sampling for the infinite sites model

AU - Hobolth, Asger

AU - Uyenoyama, Marcy K.

AU - Wiuf, Carsten

PY - 2008/1/1

Y1 - 2008/1/1

N2 - Importance sampling or Markov Chain Monte Carlo sampling is required for state-of-the-art statistical analysis of population genetics data. The applicability of these sampling-based inference techniques depends crucially on the proposal distribution. In this paper, we discuss importance sampling for the infinite sites model. The infinite sites assumption is attractive because it constraints the number of possible genealogies, thereby allowing for the analysis of larger data sets. We recall the Griffiths-Tavaré and Stephens-Donnelly proposals and emphasize the relation between the latter proposal and exact sampling from the infinite alleles model. We also introduce a new proposal that takes knowledge of the ancestral state into account. The new proposal is derived from a new result on exact sampling from a single site. The methods are illustrated on simulated data sets and the data considered in Griffiths and Tavaré (1994).

AB - Importance sampling or Markov Chain Monte Carlo sampling is required for state-of-the-art statistical analysis of population genetics data. The applicability of these sampling-based inference techniques depends crucially on the proposal distribution. In this paper, we discuss importance sampling for the infinite sites model. The infinite sites assumption is attractive because it constraints the number of possible genealogies, thereby allowing for the analysis of larger data sets. We recall the Griffiths-Tavaré and Stephens-Donnelly proposals and emphasize the relation between the latter proposal and exact sampling from the infinite alleles model. We also introduce a new proposal that takes knowledge of the ancestral state into account. The new proposal is derived from a new result on exact sampling from a single site. The methods are illustrated on simulated data sets and the data considered in Griffiths and Tavaré (1994).

KW - Ancestral inference

KW - Coalescent

KW - Importance sampling

KW - Infinite sites

UR - http://www.scopus.com/inward/record.url?scp=55549095994&partnerID=8YFLogxK

U2 - 10.2202/1544-6115.1400

DO - 10.2202/1544-6115.1400

M3 - Journal article

C2 - 18976228

AN - SCOPUS:55549095994

SN - 1544-6115

VL - 7

JO - Statistical Applications in Genetics and Molecular Biology

JF - Statistical Applications in Genetics and Molecular Biology

IS - 1

M1 - 32

ER -