Clock Rooting Further Demonstrates that Guinea 2014 EBOV is a Member of the Zaïre Lineage

Abstract

While initial phylogenetic analyses concluded to Guinea 2014 EBOV falling outside the Zaïre lineage (ZEBOV), a recent re-analysis of the same dataset by Dudas and Rambaut (2014) suggested that Guinea 2014 EBOV actually is ZEBOV. Under the same hypothesis as used by these authors (the molecular clock hypothesis), we reinforce their conclusion by providing a statistical assessment of the location of the root of the Zaïre lineage. Our analysis unambiguously supports Guinea 2014 EBOV as a member of the Zaïre lineage. In addition, we also show that some uncertainty exists so as to the location of the root of the genus Ebolavirus. We release the software we used for these re-analyses. RootAnnotator allows for the easy determination of branch root posterior probability from any posterior sample of clocked trees and is freely available at http://sourceforge.net/projects/rootannotator/.

Maximum clade credibility tree of concatenated coding sequences belonging to the Zaïre clade.

MCC tree and branch root posterior probabilities (RPP) derived from the analysis run under a constant population size model (the two other models ended up with generating very similar results) and an uncorrelated relaxed clock (lognormal). In the top left corner the complete list of branches that appeared at least once in the posterior tree sample and the according RPP. Note that two possible root locations (6 and 7) do not appear in the tree as the MCC tree did not comprise the corresponding branches. All internal branches linking coloured clades/groups received very good support (posterior probability: 1.00). The only exception was the branch defining the clade comprising Guinea 2014 EBOV and DRC 2007/2008 EBOV, which was only moderately supported (posterior probability comprised between 0.56 and 0.68).

Maximum clade credibility tree of concatenated coding sequences representing the 5 species of the genus Ebolavirus.

MCC tree and branch root posterior probabilities (RPP) derived from the analysis run under a Yule process (a Birth-Death process ended up with generating very similar results) and an uncorrelated relaxed clock (lognormal). The clock was not calibrated and the scale axis therefore is in substitution per site. RPP are reported in the list appearing at the left of the tree. All internal branches received very good support (posterior probability: 1.00).