Table 5. Results of the approximately unbiased (AU), Shimodaira-Hasegawa (SH) and weighted Shimodaira-Hasegawa (wSH) tests for the cytochrome b set and topologies assuming different relationships between three Yellow-headed Amazona lineages: C – Central American, S – South American, NS – Northern South American including A. barbadensis (Ab) and its relative A. ochrocephala ochrocephala.

Selected sites	P-values from AU/SH/wSH tests for topology:
	(C,Ab)	(C,NS)	(S,NS)	(S,C)
all	0.771/0.816/0.852	0.572/0.713/0.652	0.211/0.272/0.484	0.220/0.262/0.462
with rates <2	0.450/0.636/0.531	0.867/0.897/0.943	0.116/0.236/0.417	0.104/0.234/0.402
with rates <1	0.887/0.894/0.938	0.200/0.621/0.392	0.033/0.091/0.197	0.034/0.082/0.175
with rates <0.5	0.096/0.519/0.061	0.937/0.996/0.998	0.031/0.178/0.300	0.031/0.103/0.005
with rates <0.1	0.002/0.187/0.006	0.998/1.000/1.000	4E-92/4e-05/7e-06	1E-65/0/0

The tests were performed for all sites and sites with decreasing substitution different site rate. P-values of the best tree are underlined whereas those less than 0.05 are in bold.