ML analysis and BI of NucMt data set with 10 OTUs and only nucleotides (-ln L = 29,951.42). OTUs with just the genus names (e.g., Lumbricus) indicate that the sequences from different species of that genus were concatenated. NucMt consisted of 16,351 characters with 11,454 unambiguously aligned and non-saturated (in addition to Nuc: COX1 – 489; 16S rRNA – 463; 18S rRNA – 406; CYTB – 365; COX3 – 258; COX2 – 219; NAD6 – 118; ATP8 – 32). BS values shown at upper position right to node; PP's in the middle; 1-p of AU test at lower position. ML settings: Base frequencies: A = 0.2536, C = 0.2243, G = 0.2498, T = 0.2723; Rate matrix: AC = 2.3662, AG = 4.2648; AT = 2.0966, CG = 2.5643, CT = 6.7166, GT = 1.0000; α = 0.4824; Proportion of invariant sites = 0.3555. Models in BI: 28S rRNA, 12S rRNA: GTR+I+Γ ; 18S rRNA: K80+I+Γ ; EF1α = F81+I+Γ ; 16S rRNA, CYTB: GTR+Γ ; ATP8, COX1-3, NAD6 = F81+Γ. Clitellata, Echiura, Siboglinidae, Sipuncula highlighted with gray and bars indicate polychaete groups: orange = outgroup; A, blue = Aciculata; C, green = Canalipalpata; S, red = Scolecida.
Struck et al. BMC Evolutionary Biology 2007 7:57 doi:10.1186/1471-2148-7-57