Bacteriophage, horizontal gene transfer and the origin of DNA genomes

The Horizontal Gene Transfer (HGT) debate is about the role played by this mode of gene inheritance in evolution of Life. HGT in prokaryotes may be one reason why species trees built on the basis of different sets of molecular characters are different - the conundrum dubbed “the tree of one percent” after the observation that the consensus ribosomal RNA-based phylogeny of prokaryotes is in fact supported by only a percent of all trees built on the basis of other, protein-coding sequences. I will present the empirical data on gene content and protein sequence evolution in bacteriophages with double-strand DNA genomes. I show that the distributions of genomes and of protein families by the number of HGT events they have experienced have one fat tail and one long tail, i.e., even though the absolute number of inferred HGT events in phage world is high, the frequency of such events in the majority of genomes and protein families is low. These trends suggest that in the evolution of Life, horizontal gene transfer may be “common” under some definitions, but this does not amount to complete erasure of vertical inheritance signal, and that the existing framework of phylogenetic inference needs to be modified, not abandoned, in order to reconstruct both vertical and horizontal gene transfer events in evolution. I will also present the probabilistic reconstruction of gene content in the putative last universal common ancestor (LUCA) from which bacteria and archaea have evolved