Increased evolutionary rate in the 2014 West African Ebola outbreak is due to transient polymorphism and not positive selection

Gire et al. (Science 345:1369-1372, 2014) analyzed 81 complete genomes sampled from the 2014 Zaire ebolavirus (EBOV) outbreak and reported \"rapid accumulation of [...] genetic variation\" and a substitution rate that was \"roughly twice as high within the 2014 outbreak as between outbreaks.\" These findings have received widespread attention, and many have perceived Gire et al. (2014)s results as implying rapid adaptation of EBOV to humans during the current outbreak. Here, we argue that, on the contrary, sequence divergence in EBOV is rather limited, and that the currently available data contain no robust signal of particularly rapid evolution or adaptation to humans. The doubled substitution rate can be attributed entirely to the application of a molecular-clock model to a population of sequences with minimal divergence and segregating polymorphisms. Our results highlight how subtle technical aspects of sophisticated evolutionary analysis methods may result in highly-publicized, misconstrued statements about an ongoing public health crisis.