Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias

TY - JOUR

T1 - Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias

AU - Wang, Yong

AU - Nielsen, Rasmus

PY - 2012/2/1

Y1 - 2012/2/1

N2 - The inference of population divergence times and branching patterns is of fundamental importance in many population genetic analyses. Many methods have been developed for estimating population divergence times, and recently, there has been particular attention towards genome-wide single-nucleotide polymorphisms (SNP) data. However, most SNP data have been affected by an ascertainment bias caused by the SNP selection and discovery protocols. Here, we present a modification of an existing maximum likelihood method that will allow approximately unbiased inferences when ascertainment is based on a set of outgroup populations. We also present a method for estimating trees from the asymmetric dissimilarity measures arising from pairwise divergence time estimation in population genetics. We evaluate the methods by simulations and by applying them to a large SNP data set of seven East Asian populations.

AB - The inference of population divergence times and branching patterns is of fundamental importance in many population genetic analyses. Many methods have been developed for estimating population divergence times, and recently, there has been particular attention towards genome-wide single-nucleotide polymorphisms (SNP) data. However, most SNP data have been affected by an ascertainment bias caused by the SNP selection and discovery protocols. Here, we present a modification of an existing maximum likelihood method that will allow approximately unbiased inferences when ascertainment is based on a set of outgroup populations. We also present a method for estimating trees from the asymmetric dissimilarity measures arising from pairwise divergence time estimation in population genetics. We evaluate the methods by simulations and by applying them to a large SNP data set of seven East Asian populations.

KW - ascertainment bias

KW - maximum likelihood

KW - phylogeny

KW - population divergence

UR - http://www.scopus.com/inward/record.url?scp=84856258105&partnerID=8YFLogxK

U2 - 10.1111/j.1365-294X.2011.05413.x

DO - 10.1111/j.1365-294X.2011.05413.x

M3 - Journal article

C2 - 22211450

AN - SCOPUS:84856258105

SN - 0962-1083

VL - 21

SP - 974

EP - 986

JO - Molecular Ecology

JF - Molecular Ecology

IS - 4

ER -