Using Indel Information to Improve Phylogeny Estimation for Emerging Pathogens
Author Information
Author(s): Benjamin D Redelings, Marc A Suchard
Primary Institution: North Carolina State University
Hypothesis
Can incorporating indel information improve the resolution of phylogenies for rapidly evolving pathogens?
Conclusion
Indel information can enhance the phylogenetic resolution of recently diverged pathogens, and alignment uncertainty should be considered in analyses.
Supporting Evidence
- Indel information was shown to increase phylogenetic resolution in examples from within-host viral sequences.
- Alignment uncertainty significantly affects phylogenetic inference.
- Codon-based models can unrealistically force indels to align with codon boundaries.
Takeaway
This study shows that using gaps in genetic sequences can help scientists better understand how quickly viruses change and relate to each other.
Methodology
The study uses a Bayesian framework with Markov chain Monte Carlo to jointly estimate alignment and phylogeny, incorporating indel information.
Potential Biases
Potential biases arise from alignment ambiguity and the treatment of duplications as random insertions.
Limitations
The model assumes spatially homogeneous indel rates and does not account for within-sequence homology or indel hotspots.
Digital Object Identifier (DOI)
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