Figure 3

Neighbor Joining, seven-gene, gaps-as-missing, and single-outgroup trees. A: Neighbor Joining topology for both 3 Mbp and 12 Mbp alignments; B: Most parsimonious tree from TNT based on seven gene loci, with boopstrap resampling frequencies below the branches; C: Most parsimonious tree from TNT when gaps in 3 Mbp alignment are treated as missing; D: Most parsimonious tree from TNT when C. psychrerythraea is the only outgroup taxon. Taxa with variable placement are highlighted to show topology differences in A, C, and D.