Table 1.
Summary of previously published analyses of unexpected taxonomic character distributions.
| Reference | Character | Results | Conclusion |
|---|---|---|---|
| Pearson et al. (2003) | Sterol synthesis | Basal branching | HGT |
| Chen et al. (2007) | Sterol synthesis | Basal branching | HGT |
| Desmond and Gribaldo (2009) | Sterol synthesis | Basal and internal branching | HGT or VGT |
| Frickey and Kannenberg (2009) | Sterol synthesis | Intermediate | HGT or VGT |
| Jenkins et al. (2002) | Tubulin | Basal branching | VGT |
| Pilhofer et al. (2011) | Tubulin | Basal branching | VGT |
| Chistoserdova et al. (2004) | Methanogenesis | Intermediate | VGT |
| Bauer et al. (2004) | Methanogenesis | Intermediate | HGT or VGT |
| Vorholt et al. (2005) | Methylotrophy | Intermediate | VGT |
| Kalyuzhnaya et al. (2005) | Methylotrophy | Basal branching | HGT |
| Op den Camp et al. (2009) | Methanotrophy | Intermediate | VGT |
| Dunfield et al. (2007) | Methanotrophy | Internal branching | VGT |
| Khadem et al. (2011) | Rubisco | Intermediate | VGT |
For each publication (citation provided in the “Reference” column), the table indicates the character analyzed, a summary of the phylogenetic relationships (“Results”), and conclusions reached in the reference concerning the evolutionary origins of the unexpected character distributions (“Conclusions”). In the “Results” column, according to the trees presented in the publication: “Basal Branching” indicates that the most recent lineage (i.e., branch) common to the ancestry of sequences from both PVC and other organisms is near the root of the tree; “Internal Branching” indicates that one or more PVC genes are more closely related to a specific subset of eukaryotes than they are to others (i.e., the PVC genes emerged from “within” the eukaryotes); “Intermediate” indicates that the unrooted phylogenies contain three clusters (i.e., clans) of sequences (PVC, non-PVC bacteria, and others). In the “Conclusions” column: “HGT” indicates that the most likely scenario for the evolution of the gene family was inferred to involve some instance of HGT; “VGT” (vertical gene transfer) indicates that the most likely scenario for the evolution of the gene family was inferred NOT to involve HGT; “HGT or VGT” indicates that the authors considered the evidence to provide similar levels of support for the HGT and VGT alternatives.