454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher

Table 2 Synonymous and nonsynonymous rates

Sites	dN	dS	Z	P
	Cluster I putative psudogenes
All	0.033(0.007)	0.029(0.008)	0.37	0.71
ABS	0.029(0.011)	0.047(0.029)	-0.64	0.52
non-ABS	0.035(0.009)	0.024(0.010)	0.91	0.36
	Cluster II putative expressed alleles
All	0.210(0.032)	0.119(0.032)	1.97	0.051
ABS	0.455(0.081)	0.128(0.054)	3.30	0.001*
non-ABS	0.139(0.033)	0.117(0.035)	0.55	0.58
	Group II.A - putative pseudogenes
All	0.021(0.009)	0.007(0.008)	1.29	0.20
ABS	0.019(0.013)	0.000(0.000)	1.65	0.10
non-ABS	0.022(0.010)	0.009(0.008)	0.95	0.34

The average rates of nonsynonymous substitutions per nonsynonymous site (dN) and synonymous substitutions per synonymous sites (dS) computed according to the Nei-Gojobori method, with standard errors obtained through 1000 bootstrap replicates in parentheses, and the results of the Z test of neutrality. * denotes significant P.

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