ArticleMolecular ecology2012
Estimating population divergence time and phylogeny from single-nucleotide polymorphisms data with outgroup ascertainment bias.
Article in Molecular ecology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Genomic history of early dogs in Europe.Nature · 2026Article
- The Population History of Domestic Sheep Revealed by Paleogenomes.Molecular biology and evolution · 2024Article
- Modeling of African population history using f-statistics is biased when applying all previously proposed SNP ascertainment schemes.PLoS genetics · 2023Article
- Regularized sequence-context mutational trees capture variation in mutation rates across the human genome.PLoS genetics · 2023Article
- Modeling of African population history usingbioRxiv : the preprint server for biology · 2023Article
- SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle.Genetics, selection, evolution : GSE · 2021Article
- Article
- SNP-Discovery by RAD-Sequencing in a Germplasm Collection of Wild and Cultivated Grapevines (V. vinifera L.).PloS one · 2017Article
- How do SNP ascertainment schemes and population demographics affect inferences about population history?BMC genomics · 2015Article
- New World cattle show ancestry from multiple independent domestication events.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls.PloS one · 2013Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
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.
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