This —
“...We believe that at present no suitable outgroup sequences to root the EBOV phylogeny exist and that a temporal rooting gives the most consistent results.
This approach indicates that the outbreak in Guinea is likely caused...”
Means they don't know jack. They are guessing and pretending otherwise.
This genetic analysis is like early WW2 traffic analysis in the Pacific _before_ the Japanese-American translators gave our code breakers the coded traffic unit addresses. AKA outgroup sequences = the unit addresses.
http://www.ncbi.nlm.nih.gov/pubmed/24860690
Conclusion
The phylogenetic analysis of the five ebolavirus species here does not substantially improve on that presented by Baize et al.1 in that even when partitioning the alignment into coding and non-coding regions we get inconsistent rooting positions for the EBOV clade. We believe that at present no suitable outgroup sequences to root the EBOV phylogeny exist and that a temporal rooting gives the most consistent results.
This approach indicates that the outbreak in Guinea is likely caused by a Zaire ebolavirus lineage that has spread from Central Africa into Guinea and West Africa in recent decades, and does not represent the emergence of a divergent and endemic virus.
As the GP sequences show, without more diverse sequences, especially those from the animal reservoir, it is difficult to narrow down the estimates of when and through what means the Central African EBOV lineage has been introduced into West Africa.