Table 1. Summary of phylogenetic results from different datasets.

		NUCL				N12				DEGEN1				AA
TURTLE	Individual	All taxa	16 taxa	All taxa	16 taxa	All taxa	16 taxa	All taxa	16 taxa	All taxa	16 taxa	All taxa	16 taxa	All taxa	16 taxa	All taxa	16 taxa	Slow
	Genes	75 genes	75 genes	31 genes	31 genes	75 genes	75 genes	31 genes	31 genes	75 genes	75 genes	31 genes	31 genes	75 genes	75 genes	31 genes	31 genes	Genes
Basal Amniote	0%	0.003	2e-40	3e-7	1e-59	0.001	1e-5	8e-5	0.005	0.001	0.005	0.274	0.237	0.001	6e-6	0.477	0.32	5e-6
Basal Sauropsid	13%	3e-4	1e-4	0.001	0.056	0.009	0.188	0.32	0.383	0.07	0.351	0.424	0.454	0.117	0.137	0.398	0.586	5e-4
Turtle-Lepidosaur	10%	2e-5	1e-4	2e-4	0.016	0.144	0.339	0.412	X	X	X	X	X	X	X	X	X	1e-6
Turtle-Archosaur	19%	0.143	0.177	0.327	0.471	X	X	X	0.505	0.601	0.151	0.526	0.041	0.345	0.295	0.283	0.027	0.477
Turtle-Crocodilian	29%	X	X	X	X	0.428	0.489	0.448	0.31	0.094	0.062	0.152	0.007	0.094	0.038	0.167	0.006	X
Other	29%	–	–	–	–	–	–	–	–	–	–	–	–	–	–	–	–	–
		NUCL				N12				DEGEN1				AA
LISSAMPHIBIA	Individual	All taxa	16 taxa	All taxa	16 taxa	All taxa	16 taxa	All taxa	16 taxa	All taxa	16 taxa	All taxa	16 taxa	All taxa	16 taxa	All taxa	16 taxa	Slow
	Genes	75 genes	75 genes	26 genes	26 genes	75 genes	75 genes	26 genes	26 genes	75 genes	75 genes	26 genes	26 genes	75 genes	75 genes	26 genes	26 genes	Genes
Batrachia	18%	0.009	0.008	0.204	0.402	X	X	X	X	X	0.643	X	X	0.539	X	X	0.644	0.234
Procera	12%	0.002	0.003	0.037	0.069	0.311	0.339	0.29	0.183	0.394	X	0.419	0.215	0.334	0.343	0.169	0.094	0.087
Paraphyletic
Frog-Salamander	9%	0.001	0.001	0.004	0.153	0.512	0.587	0.273	0.403	0.386	0.087	0.269	0.074	X	0.337	0.361	0.235	0.188
Paraphyletic
Caecilian-Salamander	12%	0.103	0.209	0.184	0.093	0.185	0.198	0.061	0.013	0.166	0.093	0.074	0.012	0.23	0.224	0.042	0.018	0.873
Other	48%	X	X	X	X	–	–	–	–	–	–	–	–	–	–	–	X	X

Summary of results from phylogenetic analyses for turtle placement within the amniote phylogeny, and relationships of Lissamphibia (extant amphibians). Individual gene and concatenated analyses were performed. For individual gene analyses, percentages denote the proportion of genes supporting the hypothesis. For the concatenated analyses, the cell with “X” for each column denote the most likely topology based on RAxML likelihood scores, while the numbers in cells represent p-values based on approximately unbiased topology tests (Shimodaira 2002). Cells in bold font denote statistically indistinguishable topologies (p-value>0.05) from the most likely topology. Sixteen total concatenated analyses were performed (4 data transformations × 4 datasets). Data were transformed in an attempt to reduce the rate of evolution: NUCL = complete nucleotide dataset, N12 = 1^st and 2^nd codon positions only (Edwards et al. 1991, Blouin et al. 1998), DEGEN1 = codon degeneracy (Regier et al. 2010), AA = amino acids (Meyer 1994). Three different datasets were compiled in attempts to minimize the amount of missing data: 16 taxa (reduced taxon set to include the taxa with the most complete data for each major vertebrate group), 31 genes (for turtle question, genes with representatives from all the major groups in question), 26 genes (for lissamphibian question, genes with representatives from all the major groups in question). The last column summarizes the results from phylogenetic analyses when removing the 19 most quickly evolving genes (25% of total genes).