Journal Club - The physiology and habitat of the last universal common ancestor

Post date: Nov 8, 2016 9:54:39 PM

Our journal club paper this week was "The physiology and habitat of the last universal common ancestor," from William Martin's lab. They looked for genes that are present in multiple archaeal and bacterial lineages, and are monophyletically distributed between them. This returned 355 genes, which they inferred were present in the last common ancestor of bacteria and archaea. Based on this list, they convincingly argue that the last universal common ancestor lived in a hydrothermal setting gaining energy from geochemistry, consistent with previous studies.

A lot of genes are notably absent from their list, such as amino acid biosynthesis genes. This didn't seem surprising to us, as we expected a large false negative rate, due to loss of gene families since the last universal common ancestor, or due to horizontal gene transfer. We weren't as sure what to expect regarding false positives - gene families that were not in the last universal common ancestor but appear to be, perhaps due to uncalled horizontal transfer events. Indeed, the authors note that of the 355 genes, six use oxygen as a substrate or protect against oxygen damage, even though at the time of the last universal common ancestor we don't think oxygen was present in the environment at notable levels.