Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants

Table 1 Number of orthogroups and early eukaryotic duplications identified in analysis I

	NJ-BS^a		ML-BS		ML-aLRT^b
	≥ 50%	≥ 70%	≥ 50%	≥ 70%	≥ 50%	≥ 70%
Type I orthogroup with duplication	205 (136)	119 (88)	199 (135)	104 (82)	282 (188)	234 (166)
Type I orthogroup total	522	435	511	445	599	560
Type II orthogroup with duplication	100 (63)	61 (43)	72 (46)	37 (29)	81 (60)	85 (66)
Type II orthogroup total	235^c	260	229^c	234	176^c	196
Total orthogroup with duplication	305 (199)	180 (131)	271 (181)	141 (111)	363 (248)	319 (232)
Orthogroup total	757	695	740	679	775	756
Percentage	40.3% (26.3%)	25.9% (18.8%)	36.6% (24.5%)	20.8% (16.3%)	46.8% (32.0%)	42.2% (30.7%)

Type I orthogroup refers to orthogroups with a prokaryotic outgroup; type II orthogroup refers to orthogroups without a prokaryotic outgroup. Entries in bold and in parentheses indicate that the duplications were inferred based on stringent criteria that required that at least one species was present in both paralogous clades. ^aBS, bootstrap test. ^baLRT, approximate likelihood-ratio test. ^cThese numbers of type II orthogroups at a support level of ≥ 70% are greater than that at a support level of ≥ 50% since some type II orthogroups with ≥ 70% support were from type I orthogroups with ≥ 50% support whose prokaryotic outgroup had support less than 70%.

ISSN: 1474-760X