Rapid evolution of BRCA1 and BRCA2in humans and other primates

Table 1 PAML Analysis of BRCA1 and BRCA2

M1a-M2a	ω₀^a	codon freq.^b	2ΔlnL^c	df^c	p-value^c	M1a-M2a	ω₀^a	codon freq.^b	2ΔlnL^c	df^c	p-value^c
BRCA1	0.4	f61	10.0	2	0.0066	BRCA2	0.4	f61	21.3	2	<0.0001
	0.4	f3x4	6.1	2	0.0466		0.4	f3x4	16.1	2	0.0003
	1.6	f61	10.0	2	0.0066		1.6	f61	21.3	2	<0.0001
	1.6	f3x4	6.1	2	0.0466		1.6	f3x4	16.1	2	0.0003
M7-M8	ω ₀ ^a	codon freq. ^b	2ΔlnL ^c	df ^c	p-value^c	M7-M8	ω ₀ ^a	codon freq. ^b	2ΔlnL ^c	df ^c	p-value^c
*BRCA1*	0.4	f61	10.6	2	0.0049	*BRCA2*	0.4	f61	23.3	2	<0.0001
	0.4	f3x4	6.2	2	0.0447		0.4	f3x4	18.6	2	<0.0001
	1.6	f61	10.6	2	0.0049		1.6	f61	23.3	2	<0.0001
	1.6	f3x4	6.2	2	0.0447		1.6	f3x4	18.6	2	<0.0001
M8a-M8	ω ₀ ^a	codon freq. ^b	2ΔlnL ^c	df ^c	p-value^c	M8a-M8	ω ₀ ^a	codon freq.^b	2ΔlnL ^c	df ^c	p-value^c
*BRCA1*	0.4	f61	10.1	1	0.0015	*BRCA2*	0.4	f61	19.9	1	<0.0001
	0.4	f3x4	6.2	1	0.013		0.4	f3x4	15.1	1	0.0001
	1.6	f61	10.1	1	0.0015		1.6	f61	19.9	1	<0.0001
	1.6	f3x4	6.2	1	0.013		1.6	f3x4	15.1	1	0.0001

^aInitial seed value for ω (dN/dS).
^bModel of codon frequency.
^cTwice the difference in the natural logs of the likelihoods (2 × ΔlnL) of the two models being compared (a model that allows positive selection (M2a or M8) is compared to a null model (M1a, M7, M8a)). This value is used in a likelihood ratio test along with the degrees of freedom (df). The p-value indicates the confidence with which the null model can be rejected.

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