Table 1

Number of orthogroups and early eukaryotic duplications identified in analysis I

NJ-BSa

ML-BS

ML-aLRTb




≥ 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

235c

260

229c

234

176c

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%.

Zhou et al. Genome Biology 2010 11:R38   doi:10.1186/gb-2010-11-4-r38

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