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Table 1 Age estimates for the six nodes subtending a fossil calibration (FC)

From: Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating

Fossil calibration strategy Prior HME MLE (SS) ESS (logL) BF Cycad stem (FC1) Dioon stem (FC2) Bowenia stem (FC3) Lepidozamia stem (FC4) Cycad crown (FC5) Encephalarteae stem (FC6)
min. age 265.1 Ma min. age 56 Ma min. age 33.9 Ma min. age 33.9 Ma min. age 235 Ma min. age 72.1 Ma
Traditional fossil dataset Birth-death −26343.61 −26828.83 2451 26.7 316.6 [269.5-363.3] 140 [90-192.9] 116.3 [76.7-160.8] 38.1 [33.9-50.9] 257.2 [184.3-337.5] 129.2 [84.3-180.2]
Yule −26330.62 −26855.49 3835 295.7 [265.1-350.1] 206.4 [161.2-258.2] 170.3 [130.8-216.3] 68 [41.7-100.4] 277.2 [231-344.9] 190.4 [146.9-240.2]
New fossil dataset Birth-death −26343.36 −26825.04 2076 36.3 323.2 [273.9-364.6] 156.1 [107-207.9] 129.7 [88.7-174.3] 39.1 [33.9-55] 274.5 [235-332.4] 144.5 [97.7-192.5]
Yule −26331.16 −26861.34 1361 296.9 [265.1-351.7] 203.5 [158.6-253.6] 169.5 [129.4-214.2] 67.8 [40.6-102] 280.1 [235.6-334.8] 188 [143.6-235.6]
  1. Absolute ages and their credibility intervals were obtained for the two pairs of Bayesian calibration strategies, using either the Yule or the birth-death model as branching process prior.
  2. Values are the median ages and 95% Highest Posterior Density (HPD). We denote HME: harmonic mean estimate; MLE (SS): marginal likelihood, estimated with the stepping-stone sampling; ESS: effective sample size; BF: Bayes factor (BF), computed as the difference between the MLE of the birth-death and the Yule prior. A positive value indicates support for the birth-death prior.