With the increased availability in genomic sequence information, it has become routine practice to construct genome-based phylogenies for depicting evolutionary relationships. This holds true particularly for bacteria, where their relatively small genomes allow the use of the full complement of shared genes for phylogenetic inference. However, with the rising flood of genomic data, incongruence between markers across the genome becomes highly prevalent, leading to questions regarding the robustness of these approaches.
Recently, a team of researchers at FABI (which included Dr Marike Palmer, Prof Fanus Venter, Dr Alistair McTaggart, Prof Martin Coetzee, Stephanie van Wyk, Juanita Avontuur, Chrizelle Beukes, Dr Gerda Fourie, Dr Quentin Santana, Dr Magriet van der Nest and Prof Emma Steenkamp) investigated the reliability and suitability of these approaches by employing a first-of-its-kind large-scale manual comparison among individual gene trees (10.7717/peerj.6698).
This study provides evidence that, despite apparent phylogenetic incongruence between different markers, all genes contribute signal toward the evolutionary hypothesis of the overall species tree. The signal for recovering individual nodes of the tree seems to be scattered throughout multiple genes spread across the genome. It thus appears as if phylogenetic signal recovered from all the genes are working together synergistically to overcome phylogenetic error.