Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: Evidence from case studies in the Metazoa

Table 1 Data set characteristics

Taxon	Gene(s)	Species	Alignment length*	Partition	Saturatio Iss n	Iss.c S	P	Iss.c A	P
Chilopoda	18S	61	2576 (1822)	stems	0.062	0.715	0.000	0.398	0.000
				loops	0.806	0.710	0.426	0.390	0.001
Hexapoda	18S+28S	94	9217 (4413)	stems	0.181	0.765	0.000	0.476	0.000
				loops	0.549	0.758	0.000	0.465	0.101
Echinodermata	18S	144	2045 (1706)	stems	0.129	0.721	0.000	0.406	0.000
				loops	0.457	0.722	0.000	0.408	0.418
Heterobranchia	28S	50	3609 (2388)	stems	0.033	0.652	0.000	0.302	0.000
				loops	0.473	0.649	0.491	0.297	0.492
Tunicata	18S	88	1990 (1960)	stems	0.239	0.729	0.000	0.419	0.000
				loops	0.444	0.741	0.000	0.438	0.898
Primates	12S+16S	54	1788 (1362)	stems	0.115	0.743	0.000	0.441	0.000
				loops	0.327	0.762	0.000	0.471	0.000
Mammalia	12S+16S	126	3102 (1875)	stems	0.168	0.775	0.000	0.492	0.000
				loops	0.393	0.764	0.000	0.474	0.027
Anisoptera	12S+16S+28S	108	5968 (5239)	stems	0.043	0.756	0.000	0.460	0.000
				loops	0.059	0.733	0.000	0.425	0.000

Characteristics of the applied test data sets including the results of the test for substitution saturation in loop and stem partitions. Iss: estimated index of substitution saturation for the data set. Iss.c S and Iss.c A: critical values for the index of substitution saturation (ISS) if the true tree is symmetrical (S) or asymmetrical (A). Iss > Iss.c indicates saturation.
*original (ambiguous positions excluded)

ISSN: 2730-7182