Assessment of dating error for the clock (CL) and UCLN (UC) analyses of the simulated <i>ucln</i> data.

<p>All measures involve distance from the true node age, and are cumulative sums across all nodes. Height is the inferred node age. Lower and Higher regard the 95% HPD node age bounds. Nodes (%) indicates the percent of true node ages contained within the HPD interval. Error is the total error involved, equivalent to Low + High.</p

Results from a simulation comparing total difference between true and estimated ages for three random genes under a clock (RC) and UCLN (RU) and three genes chosen with SortaDate under a clock (SC) and UCLN (SU).

<p>Results are from 100 simulations of distinct parameter values. See details in the text.</p

The cumulative difference across all nodes in the height, lower 95% HPD, and higher 95% HPD of each node comparing the UCLN estimates to the strict clock estimates from the individual empirical dating analyses.

<p>A value lower than 0 results when the cumulative difference in the clock values of height or HPD are younger than the associated UCLN values.</p

Gene tree properties for the BIR, CAR, and CARY datasets.

<p>Left: relationship between root-to-tip variance and tree length for simulated (<i>clock</i> and <i>ucln</i>) and empirical (<i>data</i>) datasets. Each simulation condition consists of 100 simulated datasets. Contours represent densities, while grey dots represent raw empirical values. Right: tip-specific root-to-tip variance for empirical datasets. Here, 0 represents the mean root-to-tip across all genes and all lineages. Red dots indicate outgroup taxa.</p

Winnowing criteria used for sorting genes for use in divergence-time inference analyses.

<p>The order presented here is arbitrary.</p

A comparison of strict clock and UCLN estimates of node ages for the six curated empirical datasets.

<p>Bars represent 95% HPD intervals and overlay the UCLN maximum clade credibility tree.</p

Assessment of dating error for the clock (CL) and UCLN (UC) analyses of the simulated <i>clock</i> data.

<p>All measures involve distance from the true node age, and are cumulative sums across all nodes. Height is the inferred node age. Lower and Higher regard the 95% HPD node age bounds. Nodes (%) indicates the percent of true node ages contained within the HPD interval. Error is the total error involved, equivalent to Low + High.</p

A comparison of strict clock and UCLN estimates of node ages for the simulated <i>clock</i> and <i>ucln</i> datasets.

<p>Each simulation condition consists of three genes. Red and pink are scenarios where the generating and inference models are identical, while green and blue are where the models are mismatched. Bars represent 95% HPD intervals and overlay the true simulated tree.</p

Quartet Sampling Results/Data: Hinchliff and Smith 2014

A gzipped tar archive containing the input alignment and tree, and results the concatenated 200-replicate Quartet Sampling analyses for the Hinchliff and Smith 2014 study

Quartet Sampling Branch Replicate Simulations

A gzipped tar archive containing the results of the effect of number of replicates on QC values