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

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dc.contributor.authorMurahwa, Alltalents T
dc.contributor.authorNindo, Fredrick
dc.contributor.authorOnywera, Harris
dc.contributor.authorMeiring, Tracy L
dc.contributor.authorMartin, Darren P
dc.contributor.authorWilliamson, Anna-Lise
dc.date.accessioned2019-06-11T08:38:09Z
dc.date.available2019-06-11T08:38:09Z
dc.date.issued2019-05-14
dc.date.updated2019-05-19T03:46:24Z
dc.description.abstractAbstract 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.identifier.apacitationMurahwa, A. T., Nindo, F., Onywera, H., Meiring, T. L., Martin, D. P., & Williamson, A. (2019). Evolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analyses. http://hdl.handle.net/11427/30203en_ZA
dc.identifier.chicagocitationMurahwa, Alltalents T, Fredrick Nindo, Harris Onywera, Tracy L Meiring, Darren P Martin, and Anna-Lise Williamson "Evolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analyses." (2019) http://hdl.handle.net/11427/30203en_ZA
dc.identifier.citationMurahwa, 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.ris TY - AU - Murahwa, Alltalents T AU - Nindo, Fredrick AU - Onywera, Harris AU - Meiring, Tracy L AU - Martin, Darren P AU - Williamson, Anna-Lise AB - 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. DA - 2019-05-14 DB - OpenUCT DP - University of Cape Town KW - Human papillomavirus KW - Gamma-PVs KW - Most recent common ancestor KW - Phylogenetic incongruence KW - Recombination KW - Molecular divergence LK - https://open.uct.ac.za PY - 2019 T1 - Evolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analyses TI - Evolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analyses UR - http://hdl.handle.net/11427/30203 ER - en_ZA
dc.identifier.urihttps://doi.org/10.1186/s12864-019-5735-9
dc.identifier.urihttp://hdl.handle.net/11427/30203
dc.identifier.vancouvercitationMurahwa AT, Nindo F, Onywera H, Meiring TL, Martin DP, Williamson A. Evolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analyses. 2019; http://hdl.handle.net/11427/30203.en_ZA
dc.language.rfc3066en
dc.rights.holderThe Author(s).
dc.subjectHuman papillomavirus
dc.subjectGamma-PVs
dc.subjectMost recent common ancestor
dc.subjectPhylogenetic incongruence
dc.subjectRecombination
dc.subjectMolecular divergence
dc.titleEvolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analyses
dc.typeJournal Article
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