Generalised Bayesian distance-based phylogenetics for the genomics era Article Swipe
Matthew J. Penn
,
Neil Scheidwasser
,
Mark P. Khurana
,
Christl A. Donnelly
,
David A. Duchêne
,
Samir Bhatt
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.48550/arxiv.2502.04067
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.48550/arxiv.2502.04067
As whole genomes become widely available, maximum likelihood and Bayesian phylogenetic methods are demonstrating their limits in meeting the escalating computational demands. Conversely, distance-based phylogenetic methods are efficient, but are rarely favoured due to their inferior performance. Here, we extend distance-based phylogenetics using an entropy-based likelihood of the evolution among pairs of taxa, allowing for fast Bayesian inference in genome-scale datasets. We provide evidence of a close link between the inference criteria used in distance methods and Felsenstein's likelihood, such that the methods are expected to have comparable performance in practice. Using the entropic likelihood, we perform Bayesian inference on three phylogenetic benchmark datasets and find that estimates closely correspond with previous inferences. We also apply this rapid inference approach to a 60-million-site alignment from 363 avian taxa, covering most avian families. The method has outstanding performance and reveals substantial uncertainty in the avian diversification events immediately after the K-Pg transition event. The entropic likelihood allows for efficient Bayesian phylogenetic inference, accommodating the analysis demands of the genomic era.
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- Type
- preprint
- Language
- en
- Landing Page
- http://arxiv.org/abs/2502.04067
- https://arxiv.org/pdf/2502.04067
- OA Status
- green
- Related Works
- 10
- OpenAlex ID
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https://openalex.org/W4407245217Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.48550/arxiv.2502.04067Digital Object Identifier
- Title
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Generalised Bayesian distance-based phylogenetics for the genomics eraWork title
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preprintOpenAlex work type
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enPrimary language
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2025Year of publication
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2025-02-06Full publication date if available
- Authors
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Matthew J. Penn, Neil Scheidwasser, Mark P. Khurana, Christl A. Donnelly, David A. Duchêne, Samir BhattList of authors in order
- Landing page
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https://arxiv.org/abs/2502.04067Publisher landing page
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https://arxiv.org/pdf/2502.04067Direct link to full text PDF
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YesWhether a free full text is available
- OA status
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greenOpen access status per OpenAlex
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https://arxiv.org/pdf/2502.04067Direct OA link when available
- Concepts
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Phylogenetics, Genomics, Bayesian probability, Evolutionary biology, Computational biology, Biology, Data science, Computer science, Artificial intelligence, Genome, Genetics, GeneTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.60-million-site | 122 |
| abstract_inverted_index.diversification | 144 |
| cited_by_percentile_year | |
| countries_distinct_count | 0 |
| institutions_distinct_count | 6 |
| citation_normalized_percentile |