The ancient history of the structure of ribonuclease P and the early origins of Archaea

BMC Bioinformatics

Table 2 Statistics of trees of RPR molecules (*)

Matrix	No. of trees	Tree length	CI	RI	RC	g₁	Archaea	Bacteria	Eukarya
Archaea
Structure (30/129)	8	1,003	0.49/0.46	0.70	0.34	-0.75	—	—	—
Sequence (30/887)	5	1,523	0.81/0.71	0.84	0.68	-0.54	—	—	—
Combined (30/1,016)	2	3,451	0.63/0.53	0.67	0.42	-0.62	—	—	—
Bacteria
Structure (81/129)	162	2,453	0.30/0.30	0.75	0.23	-0.55	—	—	—
Sequence (81/1,040)	7	5,107	0.38/0.31	0.61	0.23	-0.51	—	—	—
Combined (81/1,169)	4	8,799	0.39/0.34	0.65	0.26	-0.52	—	—	—
Eukarya
Structure (22/129)	1	1,090	0.55/0.54	0.80	0.44	-0.60	—	—	—
Sequence (22/404)	32	1,531	0.60/0.59	0.77	0.47	-0.58	—	—	—
Combined (22/533)	8	3,042	0.63/0.61	0.78	0.49	-0.58	—	—	—
All superkingdoms
Structure (133/129)	>10,000	4,260	0.25/0.25	0.81	0.20	-0.24	+/+	-/-	+/+
Sequence (133/692)	>10,000	8,564	0.22/0.21	0.64	0.15	-0.30	+/+	-/-	-/-
Combined (133/821)	6	14,359	0.25/0.24	0.72	0.18	-0.26	+/+	-/-	+/+
Structural characters
Stabilizing (133/26)	>10,000	1,476	0.23	0.81	0.19	-0.20	-	-	-
De-stabilizing (133/77)	>10,000	2,210	0.29/0.28	0.84	0.24	-0.25	+	-	+
Folding domains
S domain (133/42)	>10,000	1,478	0.32	0.85	0.267	-0.21	-	-	-
C domain (133/87)	>10,000	2,342	0.25/0.25	0.83	0.210	-0.24	+	-	+

(*) - Trees were derived from data matrices partitioned according to superkingdom, or structural characters of RPR folding domains, and from complete data matrices of sequence, structure, or combined sequence and structure. The number of taxa/characters analyzed is shown in parentheses. Symbols "+" and "-" are used to indicate the existence of monophyletic or non-monophyletic groupings of RPRs, respectively (data of the trees derived from MP and NJ analyses are given in tandem). CI, consistency index (with and without uninformative characters are given in tandem); RI, retention index; RC, rescaled consistency index; symbol "-" indicates non-applicable data.

ISSN: 1471-2105