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Table 2 Summary of results

From: Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary

Recon. method Simulation MAPE (%) Topo. error HPD width (%) Gamma statistic Sister pair analysis
BEAST 2 (UCLN) Unlinked 6.3–30.9 0–14 43–29 − 1.46–1.09 None
  Continuous 6.7–30.3 0–16 35–605 − 1.52–0.20 None
  Punctuated 8.8–80.4 0–8 42–154 − 2.16–3.92 Negative
PAML (ACLN) Unlinked 11.4–192.1 Fixed 62–178 − 5.32–9.77 Positive
  Continuous 9.4–188.0 Fixed 57–151 − 5.15–6.25 Positive
  Punctuated 15.4–438.9 Fixed 73–327 − 8.4–2.99 Positive
PAML (UCLN) Unlinked 22.7–245.2 Fixed 49–263 − 6.53–7.51 Positive
  Continuous 26.2–227.5 Fixed 49–379 − 6.246.65 Positive
  Punctuated 18.1–535.4 Fixed 102–301 − 8.43–4.83 Positive
  1. Summary of reconstructed tree characteristics. Trees simulated under three models: Unlinked, Continuous, and Punctuated. Molecular dates were then reconstructed using three different methods: BEAST 2 (uncorrelated lognormal model, UCLN), PAML (autocorrelated lognormal model, ACLN), and PAML (UCLN). For each reconstructed tree we calculated median absolute % error of node ages (MAPE %), topological error (Topo. Error) by number of true bipartitions not reconstructed, and uncertainty by mean highest posterior density interval width as a percentage of reconstructed node age (HPD width %). We compared the gamma statistics of the reconstructed trees to the simulated trees and used sister pair analysis to test if we can detect the positive correlation between speciation rate in the reconstructed trees (None = no significant correlation)