ArticleSystematic biology2022
Robust Analysis of Phylogenetic Tree Space.
Article in Systematic biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- kamino: fast proteome-wide variant calling for amino acid phylogenomics.Molecular biology and evolution · 2026Article
- Convergent evolution of ST2 and ST164 mediates dissemination of the blaAnnals of clinical microbiology and antimicrobials · 2026Article
- SciPhy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data.Nature communications · 2026Article
- PALINCODE: Recording cell lineage with ternary palindromic CRISPR bits.bioRxiv : the preprint server for biology · 2026Article
- Dispersal, adaptation and persistence of H5N1 in the sub-Antarctic and Antarctica.bioRxiv : the preprint server for biology · 2026Article
- But the Clock, Tick-Tock: An Empirical Case Study Highlights the Preeminence of Relaxed Clock Models in Total-Evidence Dating.Systematic biology · 2026Article
- Biological causes and impacts of rugged tree landscapes in phylodynamic inference.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- T-shaped alignments integrating HIV-1 near full-length genome and partial pol sequences can improve phylogenetic inference of transmission clusters.PLoS computational biology · 2025Article
- Ancient Hybridisation Fuelled Diversification in Acropora Corals.Molecular ecology · 2025Article
- Spaces of ranked tree-child networks.Journal of mathematical biology · 2025Article
- Combining fossil taxa with and without morphological data improves dated phylogenetic analyses.Biology letters · 2025Article
- Infinite Mixture Models for Improved Modeling of Across-Site Evolutionary Variation.Molecular biology and evolution · 2025Article
- Mitonuclear Coevolution in Bumblebees (Bombus): Genomic Signatures and Its Role in Climatic Niche Adaptation.Genome biology and evolution · 2025Article
- Reference-Free Variant Calling with Local Graph Construction with ska lo (SKA).Molecular biology and evolution · 2025Article
- Solu: a cloud platform for real-time genomic pathogen surveillance.BMC bioinformatics · 2025Article
- Comparative investigation of immune-related biomarkers related to alopecia areata subtypes.Archives of medical science : AMS · 2025Article
- Toward a phylogenomic classification of magnoliids.American journal of botany · 2025Article
- Improving microbial phylogeny with citizen science within a mass-market video game.Nature biotechnology · 2025Article
- Molecular epidemiology of HIV-1 in Hungary: an evolving contact zone of colliding virus subtypes.Frontiers in microbiology · 2025Article
- Constellation-based classification of avian reovirus in turkeys reveals shared virus origins among different meat-type farms.Frontiers in veterinary science · 2025Article
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Phylogenetic analyses often produce large numbers of trees. Mapping trees' distribution in "tree space" can illuminate the behavior and performance of search strategies, reveal distinct clusters of optimal trees, and expose differences between different data sources or phylogenetic methods-but the high-dimensional spaces defined by metric distances are necessarily distorted when represented in fewer dimensions. Here, I explore the consequences of this transformation in phylogenetic search results from 128 morphological data sets, using stratigraphic congruence-a complementary aspect of tree similarity-to evaluate the utility of low-dimensional mappings. I find that phylogenetic similarities between cladograms are most accurately depicted in tree spaces derived from information-theoretic tree distances or the quartet distance. Robinson-Foulds tree spaces exhibit prominent distortions and often fail to group trees according to phylogenetic similarity, whereas the strong influence of tree shape on the Kendall-Colijn distance makes its tree space unsuitable for many purposes. Distances mapped into two or even three dimensions often display little correspondence with true distances, which can lead to profound misrepresentation of clustering structure. Without explicit testing, one cannot be confident that a tree space mapping faithfully represents the true distribution of trees, nor that visually evident structure is valid. My recommendations for tree space validation and visualization are implemented in a new graphical user interface in the "TreeDist" R package. [Multidimensional scaling; phylogenetic software; tree distance metrics; treespace projections.].
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