ArticleJournal of computational biology : a journal of computational molecular cell biology2013
Recovering the treelike trend of evolution despite extensive lateral genetic transfer: a probabilistic analysis.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- CAMUS: scalable phylogenetic network estimation.Bioinformatics (Oxford, England) · 2026Article
- Impact of Data Error on Phylogenetic Network Inference from Gene Trees Under the Multispecies Network Coalescent.Methods in molecular biology (Clifton, N.J.) · 2026Article
- CASTER: Direct species tree inference from whole-genome alignments.Science (New York, N.Y.) · 2025Article
- Neutral phylogenetic models and their role in tree-based biodiversity measures.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Median quartet tree search algorithms using optimal subtree prune and regraft.Algorithms for molecular biology : AMB · 2024Article
- Recent progress on methods for estimating and updating large phylogenies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs.Systematic biology · 2022Article
- A New Phylogenomic Approach For Quantifying Horizontal Gene Transfer Trends in Prokaryotes.Scientific reports · 2020Article
- Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.Nature communications · 2019Article
- Reconstruction of real and simulated phylogenies based on quartet plurality inference.BMC genomics · 2018Article
- The Performance of Two Supertree Schemes Compared Using Synthetic and Real Data Quartet Input.Journal of molecular evolution · 2018Article
- A phylogenomic study quantifies competing mechanisms for pseudogenization in prokaryotes-The Mycobacterium leprae case.PloS one · 2018Article
- Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction.BMC genomics · 2016Article
- Which Phylogenetic Networks are Merely Trees with Additional Arcs?Systematic biology · 2015Article
- Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer.BMC genomics · 2015Article
- Reconciliation of gene and species trees.BioMed research international · 2014Article
- Recovering the treelike trend of evolution despite extensive lateral genetic transfer: a probabilistic analysis.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
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2 authors.
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Abstract
Lateral gene transfer (LGT) is a common mechanism of nonvertical evolution, during which genetic material is transferred between two more or less distantly related organisms. It is particularly common in bacteria where it contributes to adaptive evolution with important medical implications. In evolutionary studies, LGT has been shown to create widespread discordance between gene trees as genomes become mosaics of gene histories. In particular, the Tree of Life has been questioned as an appropriate representation of bacterial evolutionary history. Nevertheless a common hypothesis is that prokaryotic evolution is primarily treelike, but that the underlying trend is obscured by LGT. Extensive empirical work has sought to extract a common treelike signal from conflicting gene trees. Here we give a probabilistic perspective on the problem of recovering the treelike trend despite LGT. Under a model of randomly distributed LGT, we show that the species phylogeny can be reconstructed even in the presence of surprisingly many (almost linear number of) LGT events per gene tree. Our results, which are optimal up to logarithmic factors, are based on the analysis of a robust, computationally efficient reconstruction method and provides insight into the design of such methods. Finally, we show that our results have implications for the discovery of highways of gene sharing.
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