ArticleBMC genomics2022
Assessing the relative performance of fast molecular dating methods for phylogenomic data.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Revisiting Algorithms, Tools, and Applications for Sequence and Phylogenetic Analyses in the NGS-Based Omics Era.Biochemical genetics · 2026Review
- Reduced evolutionary constraint accompanies ongoing radiation in deep-sea anglerfishes.Nature ecology & evolution · 2025Article
- Host-Calibrated Time Tree Caps the Age of Giant Viruses.Molecular biology and evolution · 2025Article
- Challenges in Assembling the Dated Tree of Life.Genome biology and evolution · 2024Article
- Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock.Genome biology and evolution · 2024Review
- Phylogenomics of the psychoactive mushroom genusProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Speciation across the Earth driven by global cooling in terrestrial orchids.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Data-driven guidelines for phylogenomic analyses using SNP data.Applications in plant sciencesArticle
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3 authors.
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Abstract
Advances in genome sequencing techniques produced a significant growth of phylogenomic datasets. This massive amount of data represents a computational challenge for molecular dating with Bayesian approaches. Rapid molecular dating methods have been proposed over the last few decades to overcome these issues. However, a comparative evaluation of their relative performance on empirical data sets is lacking. We analyzed 23 empirical phylogenomic datasets to investigate the performance of two commonly employed fast dating methodologies: penalized likelihood (PL), implemented in treePL, and the relative rate framework (RRF), implemented in RelTime. They were compared to Bayesian analyses using the closest possible substitution models and calibration settings. We found that RRF was computationally faster and generally provided node age estimates statistically equivalent to Bayesian divergence times. PL time estimates consistently exhibited low levels of uncertainty. Overall, to approximate Bayesian approaches, RelTime is an efficient method with significantly lower computational demand, being more than 100 times faster than treePL. Thus, to alleviate the computational burden of Bayesian divergence time inference in the era of massive genomic data, molecular dating can be facilitated using the RRF, allowing evolutionary hypotheses to be tested more quickly and efficiently.
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