Table 1. Comparison of tree alternatives for hsp82.

		Criteria
Model	Tree	BP	PP	KH	SH
Nucleotide model, all positions	B	0.732 (0.004)	0.900 (0.000)	0.729 (0.004)	0.729 (0.004)
	C	0.268 (0.004)	0.100 (0.000)	0.271 (0.004)	0.271 (0.004)
Nucleotide model, codon positions 1 and 2	B	0.408 (0.005)	0.313 (0.000)	0.362 (0.005)	0.362 (0.005)
	C	0.592 (0.005)	0.687 (0.000)	0.638 (0.005)	0.638 (0.005)
Nucleotide model, codon position 3	B	0.923 (0.003)	0.998 (0.000)	0.912 (0.003)	0.994 (0.001)
	C	0.076 (0.003)	0.002 (0.000)	0.088 (0.003)	0.168 (0.004)
Codon model, estimated frequency	B	0.021 (0.001)	5 × 10-11 (0.000)	0.016 (0.001)	0.016 (0.001)
	C	0.979 (0.001)	1.000 (0.000)	0.984 (0.001)	0.984 (0.001)
Codon model, equal frequency	B	0.362 (0.005)	0.011 (0.000)	0.349 (0.005)	0.349 (0.005)
	C	0.638 (0.005)	0.989 (0.000)	0.651 (0.005)	0.651 (0.005)

Tree B has all gene copies diverging after the separation of bdelloid families as in Fig. 1B; in tree C the most divergent copies separate before the bdelloid radiation as in Fig. 1C. Scores are shown for the bootstrap (BP), posterior probability (PP), Kishino-Hasegawa (KH), and Shimodaira-Hasegawa (SH) tests, with standard error in parentheses.