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Calibration types: F, fossil record; M, molecular clock; P, palaeogeographical or tectonic.
We chose the penalized likelihood algorithm since a likelihood ratio test, using constrained and unconstrained likelihood scores obtained from PAUP* [ 43], rejected the molecular clock (p <0.001).
The likelihood ratio test [ 91] conducted on the BI consensus tree in PAUP* [ 92] rejected a global molecular clock (P < 0.05) for the combined data set.
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Chi-square test was performed to estimate whether the four genes evolved according to the molecular clock model (P value>0.05).
The likelihood-ratio test performed with tree-puzzle 5.2 [ 32] rejected the strict molecular clock hypothesis (p < 0.05).
Our likelihood ratio test of the constancy of nucleotide substitution rate across lineages indicates that the present cpDNA data set rejects a constant molecular clock model (P = 4.06 × 10−20), and our phylogenetic trees (fig. 5 A ) show that Cryptomeria has an extremely longer branch than do the Pinaceae genera.
The difference between the likelihood values for the constrained and unconstrained phylogenies (δ = 2.8632) could not reject the molecular clock at the P = 0.95 level of significance (χ2 distribution P0.05 (2df) = 5.99147).
The null hypothesis of a molecular clock cannot be rejected (P = 1.00) using PAML package v4.445.
The null molecular clock hypothesis was rejected (P < 0.0001).
The null model of rate constancy (the molecular clock) was rejected at p < 0.001 (28 df).
No functional COG category was found particularly enriched for genes evolving under the molecular clock hypothesis (χ test, P value = 0.991).
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