The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses
Abstract
:1. Introduction
2. Materials and Methods
2.1. Distribution of Picornavirus Collection Dates
2.2. Distribution of Genome Fragments Deposited in GenBank along the Genome
2.3. Preparation of the EV-A71 Reference Alignment
2.4. Generating Random Sequence Sets from the Reference Alignment
- Random sampling of data subsets corresponding to distinct studies (“random groups”). All sequences in the reference alignment were partitioned into groups based on the first five characters of the accession number. A random group was then chosen, and all sequences from this group were added to the alignment. This step was repeated until the number of sequences reached the defined value. This algorithm reproduced the situation with enterovirus sampling 15 years ago, when only a few studies were done, or the currently available sample for less common types and species.
- Random sampling of sequences (“random single”). The selected number of sequences was randomly picked from the initial data set.
- Identity filtration of sequences. Sequences that differed from any other entry in the dataset by less than the selected percentage of the nucleotide sequence were omitted. The comparison of sequences by the script started from the first sequence in the dataset; therefore, the initial alignment was shuffled prior to each repetition of sampling.
- “Smart picking”. All sequences in the initial alignment were partitioned into groups based on the first five characters of the accession number. Sequences from the subsets with a size that did not exceed the user-defined threshold were all included in the final dataset; for bigger subsets, one sequence or a defined fraction of randomly chosen sequences was added to the reduced dataset. This sampling algorithm allowed the inclusion of unique sequences from small studies and reduced the number of sequences from massive epidemiological investigations. For each Genbank number range, at least two sequences were included, or 1% from the larger studies. These conditions were necessary to sufficiently reduce the large EV-A71 dataset; less stringent parameters may be recommended for taxa with fewer studies presented in GenBank.
2.5. Bayesian Phylogenetic Analysis
2.6. Effect of Sequencing Errors and Errors in Annotation on Evolutionary Estimates
3. Results and Discussion
3.1. Selection of a Genome Region and Recombination Analysis
3.2. Selection of a Taxon
3.3. Effect of Dataset Size and Sample Bias on Evolutionary Estimates
3.4. Approaches to Reducing the Dataset
- Random sampling of sequences. In this case, the sequences from large studies (sometimes originating from narrow samples, such as outbreaks) would be over-represented, while rare (but very informative) sequences may be lost. This results in a significant variation of the key evolutionary estimates (Figure 4a) and the Bayesian estimation of past population dynamics using Bayesian Skygrid analysis (Figure 5a).
- Identity filtration—discarding sequences that are almost identical to each other. This can be done using Jalview [51], CD-HIT [52], UCLUST [53], the skipredundant tool in EMBOSS software [54], or in-house scripts. This approach ensures that the reduced dataset is as informative in terms of genetic diversity as the original one because all rare sequences are preserved. Identity filtration can be considered in most phylogenetic studies because it is simple and results in a much more limited variation of evolutionary estimates than random picking (Figure 4b). However, an overly stringent reduction can lead to increased deviations of evolutionary estimates (Figure 4c). In the case of statistical phylogenetic studies, identity filtration can introduce bias by itself. Most prominently, it can result in artefacts in the Bayesian Skygrid analysis, because artificial removal of similar sequences universally discards the most recent tree nodes and thus simulates explosive population growth at a time that corresponds to the cut-off threshold (Figure 5b,c, circled).
- “Smart picking” first identifies the sequences that most likely belong to distinct studies based on the first five characters (two letters and three digits) of the GenBank accession number. All small studies are then included, while datasets from larger studies are reduced by random sampling proportionally to their size. In this way, rare sequences are less likely to be lost, and no bias should be introduced. Indeed, the variation of evolutionary estimates in this case was low (Figure 4d), and no artefacts were apparent in the Skygrid analysis (Figure 5d). This algorithm was implemented using in-house scripts (available at https://github.com/v-julia/sample_bias). This method requires more manual tuning than the identity filtration to obtain the desired dataset size, and overly complicated datasets, such as EV-A71, may be difficult to reduce. However, smart sampling is also less prone to introducing additional bias in population dynamics analysis (Figure 5d in comparison to Figure 5b,c, circled), and produces reproducible population size estimates (Figure 5d).
3.5. Managing Ambiguous Sequence Characters
- Discard sequences with too many ambiguous characters, which may be a sign of poor sequence quality rather than natural heterogeneity (0.1%–0.2%, or one position in the full VP1, should have minimal effect on the analysis, see below);
- In the remaining sequences, identify a region (e.g., 100 nt) with an ambiguous character and blast it against the dataset;
- Identify the frequency of different nucleotides at this position in the most closely related sequences;
- Replace the ambiguous character with the most common nucleotide among the most closely related sequences.
3.6. Effect of Sequencing Errors on Evolutionary Estimates
3.7. Effect of Annotation Errors on Evolutionary Estimates
4. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Virus | Rate, ×10−3 s/s/y | Reference |
---|---|---|
Hepatitis A virus | 1.0 | [3] |
1.21–2.0 | [4] | |
0.6 | [5] | |
Duck Hepatitis A Virus | 0.6–1.9 | [6] |
FMDV | serotype O–6.0 serotype A–11.9 serotype Asia-1–3.1 | [7] |
serotype Asia1–5.9 | [8] | |
serotype SAT1–3.00 serotype SAT2–4.0 | [9] | |
Parechovirus | 2.8 | [10] |
Non-polio enteroviruses | 6.0–11.0 | [11] |
3.40–11.9 | [12] | |
Enterovirus A71 | 3.6–5.3 | [13] |
4.2–4.6 | [14] | |
Poliovirus | 10.0 | [15] |
Teschovirus A | 1.62 | [12] |
2.46 | [16] | |
Cardiovirus A | 1.61 | [12] |
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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. https://doi.org/10.3390/v11111032
Vakulenko Y, Deviatkin A, Lukashev A. The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses. Viruses. 2019; 11(11):1032. https://doi.org/10.3390/v11111032
Chicago/Turabian StyleVakulenko, Yulia, Andrei Deviatkin, and Alexander Lukashev. 2019. "The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses" Viruses 11, no. 11: 1032. https://doi.org/10.3390/v11111032
APA StyleVakulenko, Y., Deviatkin, A., & Lukashev, A. (2019). The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses. Viruses, 11(11), 1032. https://doi.org/10.3390/v11111032