Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family

Table 4 Model comparisons of global vs local clocks using the baseml module of PAML

Model	M0	M1	M2	M3
Description	Global Clock	Jasmineae (local) vs M0	Jasmineae and Ligustrinae (each local) vs M1	Jasmineae, Oleeae, Forsythieae, and Ligustrinae (each local) vs M2
No. parameters	188	189	190	192
No. branch parameters	0	1	2	4
AICc	397616.0097	393910.5308	393526.1902	393391.5477
—log_eL	198619.36	196765.6138	196572.4365	196503.1014
Λ	Na	3707.492572	386.354476	138.670312
df	Na	1	1	2
P-value/ Bonferroni corrected	Na	*/*	*/*	*/*
Clade rate parameters (relative	Na	Jas = 5.58123	Jas = 6.98256	Jas = 4.90304
to background rate of 1)			Lig = 2.29322	Lig = 1.61560
				Ole = 0.70533
				For = 0.42790

No. parameters, the total number of free parameters for a particular model
No. branch parameters, number of clades defined to evolve by a local clock
—log_eL, the likelihood of the data, given the model
AICc, corrected Akaike Information, AICc = -2(log_eL) + 2K(n/(n-K-1)) and log_eL is the likelihood function, n is the number of sites in the alignment, and K is the number of free model parameters
Λ, the chi-square distributed, Λ = 2 * the difference in log_eL between two models
df, degree of freedom, df = the difference in no. parameters between two models
P value, significance of log likelihood ratio test comparing fit of two models (including after Bonferroni correction where P = α/m, and m is the number of branch parameters)
Na, not applicable
***P < 0.001; Jas = Jasmineae; Lig = Ligustrinae; Ole = Oleeae; For = Forsythieae

ISSN: 1741-7007