Figure 2. Case 2 in Congruence and conflict: case studies of morphotaxonomy versus rDNA gene tree phylogeny among articulate brachiopods (Brachiopoda: Rhynchonelliformea), with description of a new genus

Figure 2. Case 2: Cancellothyridoid gene tree. Best maximum-likelihood tree (GTR + invariant + gamma model) from RAxML with thorough bootstrap support (%), based on 2810 nucleotides of aligned sequences from up to four genes (12S and 16S mitochondrial, and SSU and LSU nuclear) from 30 in-group and three rhynchonellide out-group taxa. Gblocks was used to prune potentially misaligned and gap sites (18% were discarded). In-group backbone nodes with no bootstrap support value attached are considered to be unsupported (may be collapsed; boostrap <50%). Four taxa, marked (LSU), are represented by LSU sequence data alone, and in each case this sequence clusters with the cognate multiple sequences, indicating that the LSU fragment alone can accurately place the taxon.