Lateral transfer: a survey and new developments

Exponentially accumulating genetic molecular data were supposed to bring us closer to resolving one of the most fundamental issues in biology—the reconstruction of the tree of life. This tree should encompass the evolutionary history of all living creatures on earth and trace back a few billions of years to the most ancient microbial ancestor. Ironically, this abundance of data only blurs our traditional beliefs and seems to make this goal harder to achieve than initially thought. This is largely due to lateral gene transfer, the passage of genetic material between organisms not through lineal descent. Evolution in light of lateral transfer tangles the tra-ditional universal tree of life, turning it into a network of relationships. Lateral transfer is a significant factor in microbial evolution and is the mechanism of antibiotic resistance spread in bacteria species. In this paper we survey current methods designed to cope with lateral transfer in conjunction with vertical inheritance. We distinguish between phylogenetic-based methods and sequence-based methods and illuminate the advantages and disadvantages of each. Finally, we sketch a new statisti-cally rigorous approach aimed at identifying lateral transfer between two genomes