Table 1.

The data sets used in this study, DS1-11 (eukaryote) and VL1-6 (bacterial/archaeal)

Data	N	Cols	Type of data	Study	Est error
DS1	27	1949	rRNA; 18s	Hedges et al. (1990)	0.0048
DS2	29	2520	rDNA; 18s	Garey et al. (2012)	0.0002
DS3	36	1812	mtDNA; COII (1678); cytb (679-1812)	Yang and Yoder (2003)	0.0002
DS4	41	1137	rDNA; 18s	Henk et al. (2003)	0.0006
DS5	50	378	Nuclear protein coding; wingless	Lakner et al. (2008)	0.0005
DS6	50	1133	rDNA; 18s	Zhang and Blackwell (2001)	0.0023
DS7	59	1824	mtDNA; COII; and cytb	Yoder and Yang (2004)	0.0011
DS8	64	1008	rDNA; 28s	Rossman et al. (2001)	0.0009
DS9	67	955	Plastid ribosomal protein; s16 (rps16)	Ingram and Doyle (2004)	0.0164
DS10	67	1098	rDNA; 18s	Suh and Blackwell (1999)	0.0164
DS11	71	1082	rDNA; internal transcribed spacer	Kroken and Taylor (2000)	0.0008
VL1	40	271	UDP-2,3-diacylglucosamine hydrolase	Beiko et al. (2006)	0.0019
VL2	44	472	coproporphyrinogen III oxidase	Beiko et al. (2006)	0.0007
VL3	50	442	GARTFase	Beiko et al. (2006)	0.005
VL4	52	129	hypothetical protein	Beiko et al. (2006)	0.0484
VL5	53	349	fructose-1,6-bisphosphatase	Beiko et al. (2006)	0.007
VL6	63	294	pyridoxine 5′-phosphate synthase	Beiko et al. (2006)	0.0542

Notes: N = number of species; Cols = number of nucleotides; Est error = Estimated maximum standard error of split frequencies in golden runs (in %); rDNA = ribosomal DNA; rRNA = ribosomal RNA; mtDNA = mitochondial DNA; COII = cytochrome oxidase subunit II GARTFase = phosphoribosylglycinamide formyltransferase 2.