Horizontal Gene Transfer and the History of Life

Abstract

Microbes acquire DNA from a variety of sources. The last decades, which have seen the development of genome sequencing, have revealed that horizontal gene transfer has been a major evolutionary force that has constantly reshaped genomes throughout evolution. However, because the history of life must ultimately be deduced from gene phylogenies, the lack of methods to account for horizontal gene transfer has thrown into confusion the very concept of the tree of life. As a result, many questions remain open, but emerging methodological developments promise to use information conveyed by horizontal gene transfer that remains unexploited today.

Figure 1.

The processes of discord. Three biological processes can generate gene trees that differ from the species tree. (A) The combined action of gene duplication and loss, (B) horizontal gene transfer, and (C) deep coalescence, where polymorphic alleles can remain present in a population for a time than spans two speciations (black squares show the alleles that coexist for this period). In each of these examples, the genes from species C and D are closest relatives, although species C is more closely related to species B (adapted from Maddison 1997).

Figure 2.

Gene tree/species tree reconciliation and the timing of events. Models of reconciliation invoking horizontal gene transfer (T, in addition to duplications, D, and losses, L) implicitly or explicitly imply a partial order of evolutionary events in a tree. Here, the scenario of reconciliation of the gene tree and the species contains a transfer that implies that the speciation at time t₁ occurred before the speciation at t₂. The reconciliation of a large number of gene trees (typically, from all the homologous genes represented in the genomes under study) with a species tree can yield a fully resolved time order of evolutionary events (Szöllősi et al. 2012).