The evolutionary history of all life forms is usually represented as a vertical tree-like process. In prokaryotes, however, the vertical signal is partly obscured by the massive influence of horizontal gene transfer (HGT). The HGT creates widespread discordance between evolutionary histories of different genes as genomes become mosaics of gene histories. Thus, the Tree of Life (TOL) has been questioned as an appropriate representation of the evolution of prokaryotes. Nevertheless a common hypothesis is that prokaryotic evolution is primarily tree-like, and a routine effort is made to place new isolates in their appropriate location in the TOL. Moreover, it appears desirable to exploit non–tree-like evolutionary processes for the task of microbial classification. In this talk, we present a novel approach that builds on the straightforward observation that gene order conservation (‘synteny’) decreases in time as a result of gene mobility. This is particularly true in prokaryotes, mainly due to HGT. Using a ‘synteny index’ (SI) that measures the average synteny between a pair of genomes, we developed several tools, particularly for phylogenetic reconstruction and HGT detection. These tools are mainly effective between closely related taxa where the traditional phylogenetic signal is weak and uninformative. From the technical viewpoint, they are easy to use and implement, and computationally lightweight, an important feature compare to competitive approaches.
These tools form an essential part of the microbiologist toolbox and can aid in understanding the evolution and the emergence of new virulent and drug-resistant strains that is often time-sensitive.
