Evolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analyses

 

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dc.contributor.author Murahwa, Alltalents T
dc.contributor.author Nindo, Fredrick
dc.contributor.author Onywera, Harris
dc.contributor.author Meiring, Tracy L
dc.contributor.author Martin, Darren P
dc.contributor.author Williamson, Anna-Lise
dc.date.accessioned 2019-06-11T08:38:09Z
dc.date.available 2019-06-11T08:38:09Z
dc.date.issued 2019-05-14
dc.identifier.citation Murahwa, A. T., Nindo, F., Onywera, H., Meiring, T. L., Martin, D. P., & Williamson, A. L. (2019). Evolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analyses. BMC genomics, 20(1), 368.
dc.identifier.uri https://doi.org/10.1186/s12864-019-5735-9
dc.identifier.uri http://hdl.handle.net/11427/30203
dc.description.abstract Abstract Background Human papillomaviruses (HPVs) are genetically diverse, belonging to five distinct genera: Alpha, Beta, Gamma, Mu and Nu. All papillomaviruses have double stranded DNA genomes that are thought to evolve slowly because they co-opt high-fidelity host cellular DNA polymerases for their replication. Despite extensive efforts to catalogue all the HPV species that infect humans, it is likely that many still remain undiscovered. Here we use the sequences of ten novel Gammapapillomaviruses (Gamma-PVs) characterized in previous studies and related HPVs to analyse the evolutionary dynamics of these viruses at the whole genome and individual gene scales. Results We found statistically significant incongruences between the phylogenetic trees of different genes which imply gene-to-gene variation in the evolutionary processes underlying the diversification of Gamma-PVs. We were, however, only able to detect convincing evidence of a single recombination event which, on its own, cannot explain the observed incongruences between gene phylogenies. The divergence times of the last common ancestor (LCA) of the Alpha, Beta, Mu, Nu and Gamma genera was predicted to have existed between 49.7–58.5 million years ago, before splitting into the five main lineages. The LCA of the Gamma-PVs at this time was predicted to have existed between 45.3 and 67.5 million years ago: approximately at the time when the simian and tarsier lineages of the primates diverged. Conclusion Consequently, we report here phylogenetic tree incongruence without strong evidence of recombination.
dc.subject Human papillomavirus
dc.subject Gamma-PVs
dc.subject Most recent common ancestor
dc.subject Phylogenetic incongruence
dc.subject Recombination
dc.subject Molecular divergence
dc.title Evolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analyses
dc.date.updated 2019-05-19T03:46:24Z
dc.language.rfc3066 en
dc.rights.holder The Author(s).


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