Comparisons of treeModel.rootHeight estimates by BEAST with different SNP calls and different numbers of genomes.

Abstract

<p>A. Distribution of numbers of estimates of rootHeight as a percentage of all estimates in BEAST analyses according to the best model in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134435#pone.0134435.t001" target="_blank">Table 1</a>. The numbers were from samples taken every 1000 steps over a total of 200 million steps (4 genomes) or 50 million steps (73 genomes), after excluding the first 10 million steps as burn-in. Mean values of rootHeight are indicated next to arrows. Inset, different scale for values of rootHeight over 500 years. B. Representation of the individual rootHeight values for each sample over the last 40 million steps. Pettengill, 4 genomes: uses the SNP calls calculated by Pettingill [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134435#pone.0134435.ref015" target="_blank">15</a>]; Zhou, 4 genomes: uses the SNP calls for the same four genomes extracted from the core genomes in Zhou <i>et al</i>., [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134435#pone.0134435.ref009" target="_blank">9</a>]; Zhou 73 genomes, uses the core genome SNPs from all 73 genomes in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0134435#pone.0134435.ref009" target="_blank">9</a>].</p