Deconstructing the tree of life

Abstract

It has long been accepted that life evolved following a tree-like pattern, and the tree representing the evolutionary history of all life forms is generally known as the ‘tree of life’ [ 1 McInerney J.O. et al. The prokaryotic tree of life: past, present . . and future?. Trends Ecol. Evol. 2008; 23: 276-281 Abstract Full Text Full Text PDF PubMed Scopus (70) Google Scholar ]. The use of trees in biology can be backtraced to pre-darwinian times [ 2 Lamarck J.B. Philosophie Zoologique. Dentu, 1809 Google Scholar ], and most of the current analytical tools used in evolutionary biology are, to some extent, tree dependent (e.g. [ 3 Loytynoja A. Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science. 2008; 320: 1632-1635 Crossref PubMed Scopus (588) Google Scholar ]). Yet, evidence is accumulating that trees are often inadequate to model organismal evolution (e.g. [ 1 McInerney J.O. et al. The prokaryotic tree of life: past, present . . and future?. Trends Ecol. Evol. 2008; 23: 276-281 Abstract Full Text Full Text PDF PubMed Scopus (70) Google Scholar ]). Network-like patterns resulting from horizontal gene transfers (HGT) have long been known to affect microbial evolution [ 1 McInerney J.O. et al. The prokaryotic tree of life: past, present . . and future?. Trends Ecol. Evol. 2008; 23: 276-281 Abstract Full Text Full Text PDF PubMed Scopus (70) Google Scholar ]. More surprisingly, it is now becoming clear that, despite the fact that the metazoan germline cells are sequestered within the gonads, and thus protected from possible contacts with foreign DNA, HGT also had a role in animal evolution [ 4 Gladyshev E.A. et al. Massive horizontal gene transfer in bdelloid rotifers. Science. 2008; 320: 1210-1213 Crossref PubMed Scopus (323) Google Scholar ].