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Open AccessArticle

The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses

1
Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
2
Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
3
Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119048 Moscow, Russia
*
Author to whom correspondence should be addressed.
Viruses 2019, 11(11), 1032; https://doi.org/10.3390/v11111032
Received: 7 October 2019 / Revised: 4 November 2019 / Accepted: 4 November 2019 / Published: 6 November 2019
(This article belongs to the Special Issue Human Picornaviruses)
Statistical phylogenetic methods are a powerful tool for inferring the evolutionary history of viruses through time and space. The selection of mathematical models and analysis parameters has a major impact on the outcome, and has been relatively well-described in the literature. The preparation of a sequence dataset is less formalized, but its impact can be even more profound. This article used simulated datasets of enterovirus sequences to evaluate the effect of sample bias on picornavirus phylogenetic studies. Possible approaches to the reduction of large datasets and their potential for introducing additional artefacts were demonstrated. The most consistent results were obtained using “smart sampling”, which reduced sequence subsets from large studies more than those from smaller ones in order to preserve the rare sequences in a dataset. The effect of sequences with technical or annotation errors in the Bayesian framework was also analyzed. Sequences with about 0.5% sequencing errors or incorrect isolation dates altered by just 5 years could be detected by various approaches, but the efficiency of identification depended upon sequence position in a phylogenetic tree. Even a single erroneous sequence could profoundly destabilize the whole analysis by increasing the variance of the inferred evolutionary parameters. View Full-Text
Keywords: Bayesian phylogenetics; sample bias; picornaviruses; enterovirus A71 Bayesian phylogenetics; sample bias; picornaviruses; enterovirus A71
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Vakulenko, Y.; Deviatkin, A.; Lukashev, A. The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses. Viruses 2019, 11, 1032.

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