Table 4.

The tests of congruency among the nuclear and mitochondrial genealogies

Tree topology or phylogenetic hypothesis	COII-ND1		DHFR-TS		TR
	-ln (L)	P	-ln (L)	P	-ln (L)	P
Strict congruency test
COII-ND1 ML topology	3592.25027		3015.04197	0.0011	2561.47821	0.0140
DHFR-TSML topology	4013.97303	<0.0001	2841.36899		2593.27602	0.0324
TRML topology	3875.89194	<0.0001	2956.60300	0.0076	2503.77611
Relaxed congruency tests
Congruent to basic nuclear topology	3742.62997	<0.0001
Congruent to basic mitochondrial topology			2938.09706	0.0079	2540.51230	0.0082
Clade A congruent to TR or DHFR-TSML topology			2847.54852	0.7799	2509.74392	0.5044
Clade B congruent to TR or DHFR-TSML topology			2850.76382	0.7263	2522.05809	0.0191
Clade C congruent to TR or DHFR-TSML topology			2918.74561	0.0169	2503.77611*	1.0000

P is the probability of getting at least the observed Δ -ln (L) value under the null hypothesis that there is no significant difference between the ML tree and the alternative topology (SH test; RELL approximation). ML values are in boldface. Analyses are only for strains with all three genes sequenced. The DHFR-TS topology compared with the TR data only includes the H2 haplotypes from clade C (results with the H1 haplotypes are similar). The first two relaxed congruency tests compare the likelihood of the ML tree for the given mitochondrial or nuclear dataset with that of a tree in which only the position of strains 12-FLORIDA, 27-CANIII, and nd(27)-EP 255 is forced to be congruent with their position in the nuclear or mitochondrial topologies, respectively. The last three rows are for relaxed congruency tests in which strict congruency is forced for one major clade at a time. 

^*Identical to the ML value, because all TR sequences from clade C are identical.