Phylogenetic utility of the nuclear rDNA ITS region in subfamily Ixoroideae (Rubiaceae):: comparisons with cpDNA rbcL sequence data

ITS of the nrDNA were sequenced for 21 taxa in Ixoroideae and outgroups (Rubiaceae) and compared with sequences of the cp-gene rbcL. Separate and combined analyses were performed. ITS-variation was extensive and, because of alignment ambiguities, some sites were excluded from the analyses. Several topologies from the rbcL analysis that conflicted with earlier classifications are corroborated by the ITS data: 1) Posoqueria should be excluded from Gardenieae. 2) The disputed genus Bertiera, previously in Gardenieae, is basal in an extended Coffeeae, including Tricalysia. 3) Ixora should be excluded from Pavetteae. 4) Vangueria, (Antirheoideae), belongs to Ixoroideae. This affiliation of Antirheoideae tribes with Ixoroideae is also shown by new ITS and rbcL data for Alberta. Incongruities found between the two data sets may be caused by density of taxon sampling, different evolutionary rates, phylogenetic sorting, homoplasy caused by functional constraints, or sampling of non-orthologous ITS types.