Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias
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Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias. / Wang, Yong; Nielsen, Rasmus.
In: Molecular Ecology, Vol. 21, No. 4, 2012, p. 974-986.Research output: Contribution to journal › Journal article › Research › peer-review
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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
Y1 - 2012
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
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
VL - 21
SP - 974
EP - 986
JO - Molecular Ecology
JF - Molecular Ecology
SN - 0962-1083
IS - 4
ER -
ID: 222639348