ArticleMolecular biology and evolution2016
Clustering Genes of Common Evolutionary History.
Article in Molecular biology and evolution, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Genomic Analysis of Megalocytivirus Genomes Reveals Widespread Recombination.Genome biology and evolution · 2026Article
- Comparative phylotranscriptomics reveals glycolytic adaptation associated with prolonged larval development in the coastal slipper lobsterAnimal cells and systems · 2026Article
- Genomic analysis ofbioRxiv : the preprint server for biology · 2025Article
- Analyzing microbial evolution through gene and genome phylogenies.Biostatistics (Oxford, England) · 2024Article
- Geodesics to characterize the phylogenetic landscape.PloS one · 2023Article
- Robust Analysis of Phylogenetic Tree Space.Systematic biology · 2022Article
- Developing a bioinformatics pipeline for comparative protein classification analysis.BMC genomic data · 2022Article
- An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets.Genome biology and evolution · 2021Article
- UNSUPERVISED CLUSTERING OF AIRWAY TREE STRUCTURES ON HIGH-RESOLUTION CT: THE MESA LUNG STUDY.Proceedings. IEEE International Symposium on Biomedical Imaging · 2021Article
- A Semi-Automated SNP-Based Approach for Contaminant Identification in Biparental Polyploid Populations of Tropical Forage Grasses.Frontiers in plant science · 2021Article
- A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries.PLoS computational biology · 2020Article
- Article
- Choice of species affects phylogenetic stability of deep nodes: an empirical example in Terrabacteria.Bioinformatics (Oxford, England) · 2019Article
- Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae).BMC evolutionary biology · 2019Article
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- Gain-of-function experiments with bacteriophage lambda uncover residues under diversifying selection in nature.Evolution; international journal of organic evolution · 2018Article
- SWPhylo - A Novel Tool for Phylogenomic Inferences by Comparison of Oligonucleotide Patterns and Integration of Genome-Based and Gene-Based Phylogenetic Trees.Evolutionary bioinformatics online · 2018Article
- Principal component analysis and the locus of the Fréchet mean in the space of phylogenetic trees.Biometrika · 2017Article
- Comparative Genomics of Apomictic Root-Knot Nematodes: Hybridization, Ploidy, and Dynamic Genome Change.Genome biology and evolution · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent-due to events such as incomplete lineage sorting or horizontal gene transfer-it can be misleading to infer a single tree. To address this, many previous contributions have taken a mechanistic approach, by modeling specific processes. Alternatively, one can cluster loci without assuming how these incongruencies might arise. Such "process-agnostic" approaches typically infer a tree for each locus and cluster these. There are, however, many possible combinations of tree distance and clustering methods; their comparative performance in the context of tree incongruence is largely unknown. Furthermore, because standard model selection criteria such as AIC cannot be applied to problems with a variable number of topologies, the issue of inferring the optimal number of clusters is poorly understood. Here, we perform a large-scale simulation study of phylogenetic distances and clustering methods to infer loci of common evolutionary history. We observe that the best-performing combinations are distances accounting for branch lengths followed by spectral clustering or Ward's method. We also introduce two statistical tests to infer the optimal number of clusters and show that they strongly outperform the silhouette criterion, a general-purpose heuristic. We illustrate the usefulness of the approach by 1) identifying errors in a previous phylogenetic analysis of yeast species and 2) identifying topological incongruence among newly sequenced loci of the globeflower fly genus Chiastocheta We release treeCl, a new program to cluster genes of common evolutionary history (http://git.io/treeCl).
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