Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature

Maddamsetti, Rohan; Johnson, Daniel T.; Spielman, Stephanie J.; Petrie, Katherine L.; Marks, Debora S.; Meyer, Justin R.

A major question in evolutionary biology is what traits cause diversification. It is thought that key innovations allow species to unlock new ecological opportunities, which in turn drives enhanced diversification rates (Mayr 1970) . This should be recorded in phylogenies as a sudden increase in tree bushiness within monophyletic groups. Analyses that test correlations between subtree diversification rates and trait states have recently been found to be prone to false positives (Rabosky and Goldberg 2015) . Given this finding, we took an alternative approach to test whether variation identified in our study leads to cladogenesis. Rather than focusing on bushiness, we evaluated whether indels tended to occur on longer branches. We reasoned that if the indels cause host shifts, then the lineages they occur in will uncover new ecological opportunities. This will have two important consequences, (1) the hostshift may cause elevated rates of molecular evolution as the virus adapts to its new niche, and (2) lineages with different hosts will no longer compete with each other and will be more likely to coexist for deep evolutionary time. Each process would be recorded in the phylogeny as a correlation between innovative traits and the length of the branch they occur on. Indeed, there is overwhelming evidence that lineages that evolved indels at residues associated with an experimental host-shift take longer to coalesce than other lineages. This demonstrates that changes associated with receptor usage are associated with ecological diversification.