Table S4.

Metrics of phylogenetic signal for fitness effect of each introduced mutation

Phylogeny	Mutation/growth rate	Pagel’s λ (P value)*	Blomberg’s K (P value)	I, Moran (P value)	Cmean, Abouheif (P value)
Core phylogeny	rbs	0.197 (0.685)	0.097 (0.555)	−0.043 (0.364)	0.037 (0.374)
	topA	0 (1)	0.618 (0.006)	0.034 (0.224)	0.143 (0.282)
	spoT	1 (0.146)	0.595 (0.018)	0.440 (0.007)	0.466 (0.007)
	pykF	0.392† (0.007)	0.02 (0.667)	0.031 (0.27)	0.057 (0.299)
	Growth rate	0.43 (0.024)
Accessory phylogeny	rbs	0 (1)	0.508 (0.437)	−0.073 (0.446)	0.01 (0.526)
	topA	1 (0.371)	1.028 (0.048)	0.034 (0.258)	0.143 (0.316)
	spoT	1 × 10−6 (1)	0.783 (0.143)	0.533 (0.003)	0.558 (0.002)
	pykF	0 (1)	0.348 (0.649)	0.027 (0.282)	0.066 (0.275)
	Growth rate	0 (1)
Biolog phylogeny	rbs	0 (1)	0.678 (0.257)	−0.053 (0.408)	0.002 (0.477)
	topA	1 (0.281)	0.868 (0.205)	0.127 (0.15)	0.247 (0.184)
	spoT	1 × 10−6 (1)	0.933 (0.120)	0.151 (0.090)	0.286 (0.066)
	pykF	0 (1)	0.565 (0.339)	−0.043 (0.451)	−0.022 (0.506)
	Growth rate	0 (1)

Pagel’s lambda tests were against a null of 0, corresponding to a lack of phylogenetic signal. Other tests compare actual data to permuted datasets.

^*P values indicate results of tests comparing observations to the null hypothesis of no phylogenetic signal. Values in bold indicate significant tests.

^†The value remains significant after dropping the very divergent recipient strain E1118 (belonging to clade IV; Fig. 1).