Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias
Research output: Contribution to journal › Journal article › Research › peer-review
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.
Original language | English |
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Journal | Molecular Ecology |
Volume | 21 |
Issue number | 4 |
Pages (from-to) | 974-986 |
Number of pages | 13 |
ISSN | 0962-1083 |
DOIs | |
Publication status | Published - 2012 |
Externally published | Yes |
- ascertainment bias, maximum likelihood, phylogeny, population divergence
Research areas
ID: 222639348