Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.
Bottom Line: Topological differences are observed not only at deep speciation events, but also within younger clades, such as Hominidae, Rodentia, Laurasiatheria, or rosids.The evolutionary relationships of 27 archaea and bacteria are highly inconsistent.The largest concordant species tree includes 77 of the QfO reference organisms at the most.
Affiliation: Swiss-Prot, Swiss Institute of Bioinformatics, Geneva, Switzerland firstname.lastname@example.org.Show MeSH
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Mentions: To assess the level of discordance between the different species trees and the individual gene trees, we compared each species tree node with 458,108 gene phylogenies built for proteins encoded in 65 QfO reference species (Huerta-Cepas, Capella-Gutierrez, et al. 2014). This analysis was performed on ToLc-147 as well as on each species tree. By analyzing results according to the assigned consistency levels, we show that gene tree topologies coincide more often with consistent nodes (consistency levels L90 and L70) in species trees than with conflicting ones (consistency levels L10, L30, and L50) (fig. 4). This trend is also observed in the individual box plots for each project (supplementary file S3, Supplementary Material online). Interestingly, species trees which differ from the consensus tree (hereafter named “alternative species topologies” and assigned category “AT” for practical reasons) occur as the most dispersed group. The range of its gene tree support values corresponds to that determined for incongruent nodes. In fact, category AT includes many prokaryotic speciation nodes which are still polytomous in ToLc-147 because of incongruent topologies in the species trees, thus explaining the comparatively tall box plot. Even when assuming ToLc-147 to present the true tree, gene trees congruent with alternative species topologies can be correct, for instance, when containing xenologs or pseudo-orthologs. ToLc-147 with annotated gene tree support is presented in supplementary file S4, Supplementary Material online.Fig. 4.—
Affiliation: Swiss-Prot, Swiss Institute of Bioinformatics, Geneva, Switzerland email@example.com.