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. 2017 Jul 4;67(1):61–77. doi: 10.1093/sysbio/syx061

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© The Author(s) 2017. Published by Oxford University Press on behalf of the Systematic Biologists.

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Figure 2. — Posterior divergence time estimates from simulated data for different combinations of rate prior, calibration strategy and rate-drift model, when the clock is seriously violated. The tree shown is the true timetree. Horizontal bars represent the 95% highest posterior density (HPD) intervals for the six partition schemes. These are (from top to bottom): (i) concatenation (C), 1 single partition; (ii) codon positions (CP, 2 partitions); (iii) PartitionFinder (PF, variable partitions); (iv) gene (G, 50 partitions); (v) both gene and codon positions (GCP, 100 partitions); and (vi) ClockstaR (CS, variable partitions). The gap within the bar represents the posterior mean. The time estimates and their intervals are averages over the 100 replicates. IR independent-rates model, AR autocorrelated-rates model.

Inline graphic — Posterior divergence time estimates from simulated data for different combinations of rate prior, calibration strategy and rate-drift model, when the clock is seriously violated. The tree shown is the true timetree. Horizontal bars represent the 95% highest posterior density (HPD) intervals for the six partition schemes. These are (from top to bottom): (i) concatenation (C), 1 single partition; (ii) codon positions (CP, 2 partitions); (iii) PartitionFinder (PF, variable partitions); (iv) gene (G, 50 partitions); (v) both gene and codon positions (GCP, 100 partitions); and (vi) ClockstaR (CS, variable partitions). The gap within the bar represents the posterior mean. The time estimates and their intervals are averages over the 100 replicates. IR independent-rates model, AR autocorrelated-rates model.