Table 3.

Analysis of Covariance

Response variable	Covariate	Taxonomic depth	Pooled regressiond	Homogeneity of slopes among classese	Homogeneity of intercepts among classesf
dNa	Protein expression level	Genus	0.349	n.a.	n.a.
		Order	0.001**	0.15	3.5 × 10−6 **
		Class	0.009**	0.6	1.01 × 10−7 **
		Phylum	0.23	n.a.	n.a.
Protein distanceb	Protein expression level	Genus	0.23	n.a.	n.a.
		Order	0.009*	0.602	1.01 × 10−7**
		Class	0.049*	0.54	3.22 × 10−6**
		Phylum	1.29 × 10−4**	0.08	3.63 × 10−7**
dNa	CAI	Genus	0.76	n.a.	n.a.
		Order	9.73 × 10−11**	0.62	3.1 × 10−30 **
		Class	1.14 × 10−27**	0.25	4.37 × 10−16 **
		Phylum	3.26 × 10−13 **	0.56	1.42 × 10−15 **
Protein distancec	CAI	Genus	0.37	n.a.	n.a.
		Order	9.73 × 10−11 **	0.63	3.1 × 10−30 **
		Class	1.14 × 10−27 **	0.26	4.37 × 10−16 **
		Phylum	3.26 × 10−19 **	0.56	1.42 × 10−15 **

Note.—The ANCOVA test and its underlying assumptions (Zar 1999). The analysis in each taxonomic depth was performed using a single representative genome while maximizing the sample size for the test. The best linear models were obtained when both responses and covariates were transformed logarithmically. Note that the pooled regression hypothesis was rejected in all combinations at the genus depth. This may be due to the small range of rates measured within the Escherichia genomes.

^aRepresentative genomes: Genus: E. coli BW2952; Order: Klebsiella oxytoca E718; Class: Aeromonas hydrophila ATCC 7966; Phylum: Burkholderia pseudomallei K96243.

^bRepresentative genomes: Genus: E. coli SE15; Order: Klebsiella pneumoniae NTUH_K2044; Class: A. hyrophila ATCC_7966; Phylum: B. pseudomallei K96243.

^cRepresentative genomes: Genus: E. coli K12_W3110; Order: Shigella nonnei 53G; Class: A. hyrophila ML09_119; Phylum: Burkholderia sp. 383.

^dP value of an F-test with the null hypothesis H₀: the response and covariate variables are linearly correlated.

^eP value of an F-test for equality of slopes among the classes.

^fP value of an F-test for equality of intercepts among the classes.

*P value < 0.05.

**P value <0.01.