Table 2. Phylogenetic results from filtered datasets.

	3 types (site-rates, %GC, %missing)					2 types (site-rates, %missing)
TURTLE	50%	40%	30%	20%	10%	50%	40%	30%	20%	10%
Archosaur	7e-5	2e-5	1e-4	1e-4	0.031	X	X	X	0.313	0.173
Crocodilian	X	X	X	X	X	0.006	0.119	0.32	X	X
Lepidosaur	6e-79	5e-33	8e-98	2e-54	6e-6	1e-68	1e-7	2e-59	1e-46	1e-48
Basal Sauropsid	4e-5	3e-117	4e-5	2e-8	2e-4	8e-65	2e-50	2e-70	1e-56	1e-44
Basal Amniote	6e-5	7e-10	1e-6	1e-84	0.001	5e-26	1e-4	5e-7	1e-6	12e-5
	3 types (site-rates, %GC, %missing)					2 types (site-rates, %missing)
LISSAMPHIBIA	50%	40%	30%	20%	10%	50%	40%	30%	20%	10%
Batrachia	7e-36	7e-34	3e-6	2e-65	4e-52	0.004	0.003	0.019	0.015	0.003
Procera	7e-11	5e-61	5e-5	2e-66	93–94	0.029	0.405	0.375	0.131	3e-4
Paraphyletic
Frog-Salamander	3e-76	2e-7	1e-6	6e-67	5e-6	2e-7	0.004	1e-4	0.002	0.001
Paraphyletic
Caecilian-Salamander	X	X	X	X	X	7e-11	0.036	X	X	X
Other	–	–	–	–	–	X	X	–	–	–

Varying amounts of suspect sites were removed and tested. A) Position of turtles in the amniote phylogeny using three descriptive statistics (site-rates, %GC, and %missing), B) position of turtles in the amniote phylogeny using two descriptive statistics (excluding %GC), C) interrelationships of Lissamphibian groups using three descriptive statistics (site-rates, %GC, and %missing), D) interrelationships of Lissamphibian groups using two descriptive statistics (excluding %GC). The percentage in each column represents the percentage of sites removed from the dataset. Values in cells represent p-values, “X” denotes the best tree, and trees statistically indistinguishable from the best tree are in bold font (Approximately Unbiased topology test p-value >5%).