ArticleSystematic biology2014
Supertrees Based on the Subtree Prune-and-Regraft Distance.
Article in Systematic biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Navigating the mysterious space of evolutionary histories.Proceedings of the National Academy of Sciences of the United States of America · 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
- Assessing the impact of phylogenetic reconstruction error on genetic reassortment inference in segmented viruses.PloS one · 2026Article
- Biological causes and impacts of rugged tree landscapes in phylodynamic inference.bioRxiv : the preprint server for biology · 2025Article
- HGTs are not SPRs: In the Presence of Ghost Lineages, Series of Horizontal Gene Transfers do not Result in Series of Subtree Pruning and Regrafting.Molecular biology and evolution · 2025Article
- Comparison of phylogenetic trees defined on different but mutually overlapping sets of taxa: A review.Ecology and evolution · 2024Review
- Phylogenomic Testing of Root Hypotheses.Genome biology and evolution · 2023Article
- Computing nearest neighbour interchange distances between ranked phylogenetic trees.Journal of mathematical biology · 2021Article
- Linear-time algorithms for phylogenetic tree completion under Robinson-Foulds distance.Algorithms for molecular biology : AMB · 2020Article
- PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees.BMC evolutionary biology · 2019Article
- Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- A quantitative taxonomy of human hand grasps.Journal of neuroengineering and rehabilitation · 2019Article
- The Performance of Two Supertree Schemes Compared Using Synthetic and Real Data Quartet Input.Journal of molecular evolution · 2018Article
- On Unrooted and Root-Uncertain Variants of Several Well-Known Phylogenetic Network Problems.Algorithmica · 2018Article
- BCD Beam Search: considering suboptimal partial solutions in Bad Clade Deletion supertrees.PeerJ · 2018Article
- Bad Clade Deletion Supertrees: A Fast and Accurate Supertree Algorithm.Molecular biology and evolution · 2017Article
- Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
- Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi.G3 (Bethesda, Md.) · 2017Article
- Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.Systematic biology · 2017Article
- Multilocus inference of species trees and DNA barcoding.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2016Review
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Supertree methods reconcile a set of phylogenetic trees into a single structure that is often interpreted as a branching history of species. A key challenge is combining conflicting evolutionary histories that are due to artifacts of phylogenetic reconstruction and phenomena such as lateral gene transfer (LGT). Many supertree approaches use optimality criteria that do not reflect underlying processes, have known biases, and may be unduly influenced by LGT. We present the first method to construct supertrees by using the subtree prune-and-regraft (SPR) distance as an optimality criterion. Although calculating the rooted SPR distance between a pair of trees is NP-hard, our new maximum agreement forest-based methods can reconcile trees with hundreds of taxa and>50 transfers in fractions of a second, which enables repeated calculations during the course of an iterative search. Our approach can accommodate trees in which uncertain relationships have been collapsed to multifurcating nodes. Using a series of benchmark datasets simulated under plausible rates of LGT, we show that SPR supertrees are more similar to correct species histories than supertrees based on parsimony or Robinson-Foulds distance criteria. We successfully constructed an SPR supertree from a phylogenomic dataset of 40,631 gene trees that covered 244 genomes representing several major bacterial phyla. Our SPR-based approach also allowed direct inference of highways of gene transfer between bacterial classes and genera. A Small number of these highways connect genera in different phyla and can highlight specific genes implicated in long-distance LGT. [Lateral gene transfer; matrix representation with parsimony; phylogenomics; prokaryotic phylogeny; Robinson-Foulds; subtree prune-and-regraft; supertrees.].
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