Dr. Ajith Harish (Uppsala University)
in: 'Frontiers in Ecology and Evolution': "The Tree of Life: What genomes tell (and what genes cannot!)"
by Dr. Ajith Harish (Uppsala University)
Evolution as viewed through genome trees brings into question the founding operational assumptions of the traditional gene tree approach. The fundamental assumptions of the gene tree approach that are singularly important to evolutionary interpretations of the tree of life (ToL) are: a. that protein-coding sequences are molecular fossils; b. that gene trees are equivalent to species trees; c. that the ToL is assumed to be rooted in a simple akaryote cell implying that akaryotes are primitive, and d. that the notion that all or most incongruities between sequence alignment-based gene trees are due to horizontal transfer (HT), which includes the endosymbiotic models postulated for the origins of eukaryotes. What has been unusual about these particular assumptions is that though each was taken on board explicitly, they are defended in the face of factual challenge by a stolid disregard for the conflicting observations. The factual challenges to the mainstream gene tree-inspired evolutionary view are numerous and most convincingly summarized as: Genome trees tell a very different story. Phylogeny inferred from protein structural-domains does not support any one of the principle evolutionary interpretations of gene trees: a. 3D protein domain structures are the molecular fossils of evolution, while coding sequences are transients; b. Species trees are very different from gene trees; c. The ToL is rooted in a surprisingly complex universal common ancestor (UCA) that is distinct from any specific modern descendant and d. HT including endosymbiosis is a negligible player in genome evolution from UCA to the present.