ArticleBioinformatics (Oxford, England)2023
Phylogenomic branch length estimation using quartets.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
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- Evidence of introgression amid phylogenetic conflict in Brachyotum, a plant radiation from the Tropical Andes.American journal of botany · 2026Article
- Integrative utilization of genomic resources for improved phylogenetic resolution in Sonerileae (Melastomataceae).American journal of botany · 2026Article
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- A Practical Guide for Harnessing Phylogenomics in Biocontrol: Accounting for Topological Uncertainty and Phylogenetic Distance in the Centrifugal Phylogenetic Method and Beyond.Evolutionary applications · 2026Article
- Phylogenomics reveals the evolution of floral traits associated with pollinators and pollinator-prey conflict within the carnivorous Pinguicula subgenus Temnoceras.American journal of botany · 2026Article
- Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss.Genome biology and evolution · 2025Article
- Genome-wide phylogeny reshapes our understanding of the evolution of deep-sea dragonfishes, bristlemouths, viperfishes, and allies (Stomiiformes).BMC ecology and evolution · 2025Article
- A combination of stabilizing selection and random walk are associated with phylogenetic signal in hard pines.Annals of botany · 2025Article
- Shifts in bee diet breadths are associated with gene gains and losses and positive selection across olfactory receptors.G3 (Bethesda, Md.) · 2025Article
- Extensive genome evolution distinguishes maize within a stable tribe of grasses.bioRxiv : the preprint server for biology · 2025Article
- Poplar: a phylogenomics pipeline.Bioinformatics advances · 2025Article
- Admixture in the fungal pathogen Blastomyces.Genetics · 2024Article
- Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock.Genome biology and evolution · 2024Review
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Authors and funding
4 authors.
Funding
Abstract
motivationBranch lengths and topology of a species tree are essential in most downstream analyses, including estimation of diversification dates, characterization of selection, understanding adaptation, and comparative genomics. Modern phylogenomic analyses often use methods that account for the heterogeneity of evolutionary histories across the genome due to processes such as incomplete lineage sorting. However, these methods typically do not generate branch lengths in units that are usable by downstream applications, forcing phylogenomic analyses to resort to alternative shortcuts such as estimating branch lengths by concatenating gene alignments into a supermatrix. Yet, concatenation and other available approaches for estimating branch lengths fail to address heterogeneity across the genome.
resultsIn this article, we derive expected values of gene tree branch lengths in substitution units under an extension of the multispecies coalescent (MSC) model that allows substitutions with varying rates across the species tree. We present CASTLES, a new technique for estimating branch lengths on the species tree from estimated gene trees that uses these expected values, and our study shows that CASTLES improves on the most accurate prior methods with respect to both speed and accuracy. AVAILABILITY AND IMPLEMENTATION: CASTLES is available at https://github.com/ytabatabaee/CASTLES.
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