Evolution of microbes and viruses: a paradigm shift in evolutionary biology?

A natural, key question to ask then is: are the topologies of the trees for individual genes substantially congruent? In other words, is it possible to identify a statistically significant central trend in the vast “forest” of gene trees? Statistical analysis of thousands of phylogenetic trees for diverse genes of prokaryotes (in fact, all genes with sufficient degree of conservation to obtain a reliable tree topology) has shown that a highly significant central trend is indeed detectable in the phylogenetic forest (Puigbo et al., 2009 , 2012 ; Koonin et al., 2011 ).

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Rather, they have shown that the bona fide unit of tree-like evolution is an individual gene not a genome, and a “tree of life” can only be conceived as a statistical trend in the “forest” of gene trees (Koonin and Wolf, 2009b ).

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