title: The phylogenetic forest and the quest for the elusive tree of life.
abstract: Extensive horizontal gene transfer (HGT) among prokaryotes seems to undermine the tree of life (TOL) concept. However, the possibility remains that the TOL can be salvaged as a statistical central trend in the phylogenetic "forest of life" (FOL). A comprehensive comparative analysis of 6901 phylogenetic trees for prokaryotic genes revealed a signal of vertical inheritance that was particularly strong among the 102 nearly universal trees (NUTs), despite the high topological inconsistency among the trees in the FOL, most likely, caused by HGT. The topologies of the NUTs are similar to the topologies of numerous other trees in the FOL; although the NUTs cannot represent the FOL completely, they reflect a significant central trend. Thus, the original TOL concept becomes obsolete but the idea of a "weak" TOL as the dominant trend in the FOL merits further investigation. The totality of gene trees comprising the FOL appears to be a natural representation of the history of life given the inherent tree-like character of the replication process.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. koonin@ncbi.nlm.nih.gov
authors.forename: E V
authors.initials: EV
authors.lastname: Koonin
authors.forename: Y I
authors.initials: YI
authors.lastname: Wolf
authors.forename: P
authors.initials: P
authors.lastname: Puigbò
mesh_terms: D005075:Biological Evolution; D022761:Gene Transfer, Horizontal; D056186:Metagenomics; D008957:Models, Genetic; D010802:Phylogeny; D011387:Prokaryotic Cells
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