ArticleBioinformatics (Oxford, England)2012
Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 176 papers.
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176 citing papers in PubMed.
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- Coping with Ineffective Overlap in Multilocus Phylogenetics.Systematic biology · 2026Article
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- A machine learning framework for interpreting phylogenetic tree patterns in interkingdom horizontal gene transfer.Frontiers in bioinformatics · 2026Article
- Evaluating Pretrained Protein Language Model Embeddings as Proxies for Functional Similarity.Journal of molecular evolution · 2025Article
- Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.Journal of molecular evolution · 2025Review
- Sketch, capture and layout phylogenies.PLoS computational biology · 2025Article
- Chlorophyllide a Oxygenase (CAO) Gene Duplication Across the Viridiplantae.Journal of molecular evolution · 2025Article
- Convergent evolution ofProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Evolutionary and functional differentiation of the glutamate receptor-like family in tea (Camellia sinensis) plants and other plants.Functional & integrative genomics · 2025Article
- Mechanisms, detection, and impact of horizontal gene transfer in plant functional evolution.The Plant cell · 2025Review
- The path-label reconciliation (PLR) dissimilarity measure for gene trees.Algorithms for molecular biology : AMB · 2025Article
- Feature Architecture-Aware Ortholog Search With fDOG Reveals the Distribution of Plant Cell Wall-Degrading Enzymes Across Life.Molecular biology and evolution · 2025Article
116 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationGene duplication (D), transfer (T), loss (L) and incomplete lineage sorting (I) are crucial to the evolution of gene families and the emergence of novel functions. The history of these events can be inferred via comparison of gene and species trees, a process called reconciliation, yet current reconciliation algorithms model only a subset of these evolutionary processes.
resultsWe present an algorithm to reconcile a binary gene tree with a nonbinary species tree under a DTLI parsimony criterion. This is the first reconciliation algorithm to capture all four evolutionary processes driving tree incongruence and the first to reconcile non-binary species trees with a transfer model. Our algorithm infers all optimal solutions and reports complete, temporally feasible event histories, giving the gene and species lineages in which each event occurred. It is fixed-parameter tractable, with polytime complexity when the maximum species outdegree is fixed. Application of our algorithms to prokaryotic and eukaryotic data show that use of an incomplete event model has substantial impact on the events inferred and resulting biological conclusions. AVAILABILITY: Our algorithms have been implemented in Notung, a freely available phylogenetic reconciliation software package, available at http://www.cs.cmu.edu/~durand/Notung. CONTACT: mstolzer@andrew.cmu.edu.
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