Table 1. Likelihood ratio test between the neighbor-dependent and hybrid models of metabolic evolution.

Pathway map	Neighbor-dependent model		Hybrid model		LH ratio
	()	Log LH	()	Log LH
Glycolysis/Gluconeogenesis	(2.6177, 0.4229)	−76.53	(0.4989, 0.1598, 0.2152)	−63.47	26.13
Pentose phosphate pathway	(0.5680, 0.7144)	−60.13	(0.4762, 0.2953, 0.4259)	−53.42	13.41
Lysine degradation	(0.0127, 1.0780)	−59.43	(0.0063, 0.2926, 0.0159)	−52.40	14.05
Histidine metabolism	(0.7669, 0.3895)	−54.22	(0.1852, 0.1643, 0.1370)	−47.28	13.89
Phenylalanine metabolism	(1.1035, 0.6856)	−62.40	(1.0299, 1.0297, 0.0038)	−49.91	24.97
Pyruvate metabolism	(0.1648, 0.5656)	−88.64	(0.0897, 0.1913, 0.1194)	−81.74	13.81

The maximum likelihood estimates (MLEs) of the parameter values (: insertion rate, : deletion rate and : neighbor dependence probability), maximum log-likelihoods, likelihood (LH) ratios, and the -values for different pathway maps in P. fluorescens Pf0-1 used in this analysis. The MLEs were obtained using the Gibbs sampler described by Mithani et al. [9] by evolving the networks from P. fluorescens Pf-5 to P. fluorescens Pf0-1. The equilibrium probability of a network was used as the likelihood of observing the network. The low -values for all the pathway maps suggest a better fit for the hybrid model compared to the neighbor-dependent model.