It is generally believed that the exponentially accumulating genetic molecular data will bring us closer to resolving one of the most fundamental issues in biology – decipher the history of life on Earth. So far, however, this abundance of data only seems to blur our understanding of the problem. This is largely due to horizontal gene transfer (HGT), the passage of genetic material between organisms not through lineal descent, which, to a large extent, is mediated by viruses (bacteriophages), plasmids, and transposons.  Evolution in light of HGT tangles the traditional universal Tree of Life, turning it into a network of relationships. HGT is rampant and particularly common in bacterial evolution where it has been recognized to play an important role in microbial adaptation and selection.

Despite the above, the belief in a single, underlying species tree still attracts efforts to overcome this confounding histories. In particular there is ample evidence that a strong tree-like signal can be extracted, even in the presence of extensive HGT. As a result, the bacterial phylogeny is usually inferred from genes that are thought to be immune to HGT, typically ribosomal RNA genes. Nevertheless, even these genes are subjected to HGT, obfuscating the central trend of evolutionary relationships. Moreover, as these genes are highly conserved, the amount of evolutionary signal they provide falls short for reliable classification within a genus or even a family. Alternatively, it was shown that gene order conservation among related genomes, denoted as synteny, or rather the loss thereof is more informative and is very strongly correlated with gene sequencing similarity.

In light of the above, we embarked a project to harness loss of synteny for the goal of greater understanding of prokaryotic evolution via three seemingly discordant applications: (1) the construction of the species tree depicting the central trend of microbial evolution, (2) identification of HGT between closely related organisms, and (3) intercepting exceptional genome architecture. The project was awarded an ISF grant with several publications addressing the goals stated above have been published or submitted.