Phylogenetic trees of individual genes of prokaryotes (archaea and bacteria) generally have different topologies, largely owing to extensive horizontal gene transfer (HGT), suggesting that the Tree of Life (TOL) should be replaced by a net of life as the paradigm of prokaryote evolution. nearly universal trees (NUTs). Although diverse routes of net-like evolution collectively dominate the FOL, the pattern of tree-like evolution that reflects the consistent topologies of the NUTs is the most prominent coherent trend. We show that the contributions of tree-like and net-like evolutionary processes substantially differ across bacterial and archaeal lineages and between functional classes of genes. Evolutionary simulations indicate that the central tree-like signal cannot be realistically explained by a self-reinforcing pattern of biased HGT. as an adequate depiction of the entire history of life forms on earth (Darwin 1859). The three-domain tree of ribosomal RNA (rRNA) that was subsequently buttressed by trees of other universal genes, such as ribosomal proteins and core RNA polymerase subunits, is perceived as a veritable triumph of tree thinking in biology (Woese 1987; Woese et al. 1990; Pace 1997; Ciccarelli et al. 2006; Pace 2006). However, phylogenomics, that is, genome-wide analysis of gene phylogenies (Delsuc et al. 2005), reveals a more complex picture of evolution. Indeed, at least among prokaryotes (archaea and bacteria), phylogenetic trees of individual genes generally possess different topologies; this diversity of tree topologies cannot be explained away by artifacts of phylogenetic reconstruction and is largely attributed to extensive horizontal gene transfer (HGT) in the prokaryotic world (Doolittle 1999b; Koonin et al. 2001; Koonin and Wolf 2008). These developments suggest that the TOL might need to be replaced by a R 278474 net of life as the paradigm of evolution, at least, for prokaryotes (Hilario and Gogarten 1993; Gogarten et al. 2002; Boucher et al. 2003; Bapteste et al. 2005, 2009; Gogarten and R 278474 Townsend 2005; Doolittle and Bapteste 2007; Bapteste and Boucher 2008; Dagan et al. 2008; Koonin and Wolf 2008; Doolittle 2009). Although there is no question that HGT happens among prokaryotes frequently, the conundrum between your TOL and the web of life can be definately not being solved (O’Malley and Boucher 2005; Bapteste et al. 2009). The sights of evolutionary biologists change from the protection R 278474 of the original TOL, when HGT can be dismissed as a comparatively small nuisance (Kurland et al. 2003; Ge et al. 2005; Kunin et al. 2005); to proposals that preferential HGT between microorganisms that are typically considered related and put R 278474 into the same taxon could considerably donate to the noticed topologies of phylogenetic trees and shrubs in prokaryotes, maybe, to a larger extent compared to the tree-like inheritance, and moreover, the efforts of both types of evolutionary procedures can extremely challenging to disentangle (Gogarten et al. 2002; Andam et al. 2010); and completely towards the iconoclastic proven fact that any constant tree-like sign in the advancement of prokaryotes could possibly be an illusion due to non-random patterns of HGT (Olendzenski et al. 2002). The intermediate look at, that regardless of the main part of Rabbit polyclonal to POLDIP2 HGT in the advancement of prokaryotes, TOL could be salvageable like a statistical central tendency, continues to be proposed aswell (Wolf et al. 2002). Lately, we reported a comparative evaluation of 7 around,000 phylogenetic trees and shrubs for prokaryote genes that jointly constitute the Forest of Existence (FOL) and demonstrated how the FOL will gravitate to a single-tree topology. This statistically significant tendency was particularly prominent among nearly universal trees (NUTs), that is, trees for highly conserved genes that are represented in all or almost all prokaryote genomes (Puigbo et al. 2009). Here, we describe a quantitative measure of the tree and net signals in evolution that is derived from an analysis of all quartets of species in all trees of the FOL. We find that, although diverse routes of net-like evolution jointly dominate the FOL, the pattern of tree-like evolution that recapitulates the consensus topology of the NUTs is the single most prominent coherent trend. Evolutionary simulations suggest that the central tree-like signal.