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. 2017 Mar 6;66(5):823–842. doi: 10.1093/sysbio/syw119

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© The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com

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Figure 8. — a) The MAP species tree (also the majority-rule consensus species tree) produced in the BPP analysis of the simulated dataset Sim1-Matching of Giarla and Esselstyn (2015). Posterior probabilities for nodes are shown as percentages, whereas those not shown are 100%. Branches are drawn to reflect the posterior means of the node ages (s), which are shown next to the nodes (with the true values in parentheses, ), whereas the node bars indicate the 95% highest posterior density (HPD) intervals. The number of sequences per species per locus is in the parentheses after each species name. This tree is also the species tree that Giarla and Esselstyn (2015) inferred from the UCE data and is the true species tree used to generate the three simulated datasets (Sim1, Sim2, and Sim3x). b) and c) Two alternative species trees ( and ) with high posterior probabilities in the BPP analysis of the UCE dataset. appears to be the MAP tree, and the posterior means of s for modern and ancestral populations on are shown in square brackets (). The 95% HPD intervals of node ages in and , shown as node bars, are shorter than those in , probably because there are 919 loci in the UCE dataset and 500 in Sim1. Note that and differ by an NNI move around node 1, whereas and differ by another NNI move around node 2.

Inline graphic — a) The MAP species tree (also the majority-rule consensus species tree) produced in the BPP analysis of the simulated dataset Sim1-Matching of Giarla and Esselstyn (2015). Posterior probabilities for nodes are shown as percentages, whereas those not shown are 100%. Branches are drawn to reflect the posterior means of the node ages (s), which are shown next to the nodes (with the true values in parentheses, ), whereas the node bars indicate the 95% highest posterior density (HPD) intervals. The number of sequences per species per locus is in the parentheses after each species name. This tree is also the species tree that Giarla and Esselstyn (2015) inferred from the UCE data and is the true species tree used to generate the three simulated datasets (Sim1, Sim2, and Sim3x). b) and c) Two alternative species trees ( and ) with high posterior probabilities in the BPP analysis of the UCE dataset. appears to be the MAP tree, and the posterior means of s for modern and ancestral populations on are shown in square brackets (). The 95% HPD intervals of node ages in and , shown as node bars, are shorter than those in , probably because there are 919 loci in the UCE dataset and 500 in Sim1. Note that and differ by an NNI move around node 1, whereas and differ by another NNI move around node 2.