Skip to main content
Figure 13 | BMC Evolutionary Biology

Figure 13

From: Genome trees constructed using five different approaches suggest new major bacterial clades

Figure 13

A census of the topologies of maximum-likelihood trees for individual protein families. Thermotoga and Aquifex. In each panel, the left top icon shows the grouping tested and the remaining icons show the most common alternative topologies for the given species/group. Dotted lines indicate optional presence of (possibly several) members of the indicated group (e.g. "proteo" with several dotted lines leading to it means that any number and combination of proteobacterial proteins could be present on the given branch). For each icon, the number of COG trees with the given topology (upper number) and the size of the subset supported by at least 70% bootstrap values (lower number) are indicated. Uncertain topologies (lacking clearly defined taxonomic units on the other side of the subtree or those without bootstrap support) are indicated by multiple dotted lines without indication of the neighbor. Abbreviations: TA – Thema and/or Aquae; DMS – any combination of Deira, Myctu and SynPC. Note that, in some cases, which involve taxonomic clades rather than single organisms (e.g. spirochetes), failure of the corresponding species to form a clade in the given tree may lead to asymmetrical counts of topologies. For example, if a particular tree has a (Deira,(Trepa, Borbu)) branch, this tree will be included in both the Deira-spiro and spiro-Deira tallies. If, however, the subtree ((Deira, Trepa),(Aquae, Borbu)) is present, then the Deira-spiro and Aquae-spiro tallies gain one count each, but the spiro-Deira and spiro-Aquae tallies do not; instead, a case of spirochete polyphyly is registered.

Back to article page