TABLE 3.

Log likelihood values for the maximum likelihood tree for each reference locus and for this tree as a fit to the data from the other loci^a

Isolate group and reference locus	−In L	αb	Ts/Tv	99th percentile of −ln L for random trees	−ln L value for other loci
					adk	atpG	frdB	fucK	mdh	pgi	recA
Encapsulated
adk	944.2	0.006	2.83	1,002.0		1,021.8	1,020.6	1,024.3	1,053.1	1,021.7	987.9
atpG	762.8	0.069	2.63	828.8	837.4		828.2	827.6	835.2	779.5	826.4
frdB	913.6	0.243	2.82	979.6	1,011.5	985.6		992.4	978.4	983.8	985.6
fucK	589.3	783.7	4.34	624.3	624.4	589.3	628.1		624.4	589.3	589.3
mdh	945.3	0.006	2.91	965.0	963.6	963.8	965.1	965.6		960.3	965.1
pgi	1,152.7	0.074	1.93	1,200.7	1,248.9	1,202.8	1,209.2	1,247.1	1,219.4		1,242.9
recA	790.5	0.003	2.19	856.7	801.2	823.2	849.6	823.2	840.6	823.2
Noncapsulated
adk	810.7	0.006	9.21	824.3		832.7	849.2	840.0	848.3	849.3	814.9
atpG	791.9	0.069	3.44	835.4	849.9		868.3	874.9	867.5	869.8	850.1
frdB	914.6	0.004	2.58	947.8	971.5	984.6		971.5	988.8	1,000.0	982.0
fucK	599.2	0.111	4.38	619.7	638.8	655.7	653.0		654.5	652.1	646.6
mdh	893.3	0.051	4.3	947.7	984.3	967.0	990.5	990.5		980.9	975.1
pgi	1,058.8	0.052	4.56	1,112.0	1,191.5	1,176	1,195.2	1,195.2	1,187.2		1,184.5
recA	745.1	0.002	1.21	785.8	755.6	820.6	822.8	783.2	820.9	842.3

^aThose values that are closer to the -ln L value of the reference locus than the 99th percentile of values for the 200 random tree topologies are shown in boldface type and denote significant congruence between the loci.

^bα, a parameter describing the rate variation among sites. (see Materials and Methods).