The Darwinian tree of life in light of horizontal gene transfer (is still sound)

Horizontal gene transfer (HGT) is the process whereby nucleic acids are transmitted from the genome of one species to another, without inheritance by descent (i.e. parent to child). Some people believe that there is no prokaryotic tree of life, proposing there to be a ‘thicket’ of shared genetic material instead. It is therefore extremely important to understand HGT, due to its divergence from assumptions made in phylogenetic analyses, such as a direct ancestry of homologous proteins.
Previous studies have focused on trying to predict precisely which genes have been horizontally transferred where, based on multiple sequence alignments and searches for a ‘footprint’, or biochemical signal peculiar to the parent genome. This is a very difficult approach, and the signal is quickly lost with evolutionary time. We propose avoiding this prediction of horizontal transfer events, by taking a more global view instead.
We searched for proteins comprised of sets of structural-domains (domain architectures, as identified in the SUPERFAMILY database) that showed disparity in their deletion rates across the tree of life. This did not provide concrete identification of individual HGT events, but created an enriched set of possible contenders, acting as an indicator towards HGT across all organisms.

Our research suggests an upper bound of 30% for the percentage of domain architectures in bacteria involved in HGT, suggesting that bacteria do indeed possess an underlying Darwinian tree.

No relevant conflicts of interest declared.