Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa.
Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
BMC Genomics. 2019 May 14;20(1):368. doi: 10.1186/s12864-019-5735-9.
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.
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.
Consequently, we report here phylogenetic tree incongruence without strong evidence of recombination.
人乳头瘤病毒（HPV）具有遗传多样性，属于五个不同的属：α、β、γ、μ和ν。所有乳头瘤病毒都有双链 DNA 基因组，由于它们共同利用高保真度的宿主细胞 DNA 聚合酶进行复制，因此被认为进化缓慢。尽管人们已经做出了广泛的努力来对所有感染人类的 HPV 物种进行编目，但仍有可能有许多尚未被发现。在这里，我们使用以前研究中表征的十个新型γ乳头瘤病毒（γ-PV）和相关 HPV 的序列来分析这些病毒在全基因组和个别基因水平上的进化动态。
我们发现不同基因的系统发育树之间存在统计学上显著的不一致，这意味着在γ-PV 多样化的进化过程中存在基因间的变异。然而，我们只能检测到单个重组事件的令人信服的证据，仅凭这一点，就无法解释基因系统发育之间观察到的不一致。α、β、μ、ν和γ属的最后共同祖先（LCA）的分歧时间预测存在于 4970 万至 5850 万年前，在分裂成五个主要谱系之前。此时，γ-PV 的 LCA 预测存在于 4530 万至 6750 万年前：大约在灵长类动物的灵长目和狐猴目分支的时候。
因此，我们在这里报告了没有强烈重组证据的系统发育树不一致。
