ArticleMolecular biology and evolution2012
Inconsistencies in estimating the age of HIV-1 subtypes due to heterotachy.
Article in Molecular biology and evolution, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed.
- DiagnoDating: diagnostics for dated phylogenies in microbial population genetics.Molecular biology and evolution · 2026Article
- Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model.Systematic biology · 2024Article
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- Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs.Molecular biology and evolution · 2024Article
- Inferring viral transmission time from phylogenies for known transmission pairs.bioRxiv : the preprint server for biology · 2023Article
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- Exploring the dynamic variations of viral genomes via a novel genetic network.Molecular phylogenetics and evolution · 2022Article
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- Log Transformation Improves Dating of Phylogenies.Molecular biology and evolution · 2021Article
- Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae).Systematic biology · 2021Article
- A new method for inferring timetrees from temporally sampled molecular sequences.PLoS computational biology · 2020Article
- Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes.Virus evolution · 2019Article
- Divergence dating using mixed effects clock modelling: An application to HIV-1.Virus evolution · 2019Article
- Model selection may not be a mandatory step for phylogeny reconstruction.Nature communications · 2019Article
- Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences.Scientific data · 2018Article
- Maintenance and reappearance of extremely divergent intra-host HIV-1 variants.Virus evolution · 2018Article
- Global Rate Variation in Bony Vertebrates.Genome biology and evolution · 2018Article
- A comparison of methods for estimating substitution rates from ancient DNA sequence data.BMC evolutionary biology · 2018Article
- Article
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3 authors.
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Abstract
Rate heterogeneity among lineages is a common feature of molecular evolution, and it has long impeded our ability to accurately estimate the age of evolutionary divergence events. The development of relaxed molecular clocks, which model variable substitution rates among lineages, was intended to rectify this problem. Major subtypes of pandemic HIV-1 group M are thought to exemplify closely related lineages with different substitution rates. Here, we report that inferring the time of most recent common ancestor of all these subtypes in a single phylogeny under a single (relaxed) molecular clock produces significantly different dates for many of the subtypes than does analysis of each subtype on its own. We explore various methods to ameliorate this problem. We conclude that current molecular dating methods are inadequate for dealing with this type of substitution rate variation in HIV-1. Through simulation, we show that heterotachy causes root ages to be overestimated.
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