ArticleSystematic biology2011
Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees.
Article in Systematic biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- ZW sex chromosome structure in Amborella trichopoda.Nature plants · 2024Article
- Chromosome-level genome provides insight into the evolution and conservation of the threatened goral (Naemorhedus goral).BMC genomics · 2024Article
- A Study of GUS Expression inPlants (Basel, Switzerland) · 2023Article
- Phylogenomic Analyses of 2,786 Genes in 158 Lineages Support a Root of the Eukaryotic Tree of Life between Opisthokonts and All Other Lineages.Genome biology and evolution · 2022Article
- Evolution and diversity of the angiosperm anther: trends in function and development.Plant reproduction · 2021Review
- Article
- Exact median-tree inference for unrooted reconciliation costs.BMC evolutionary biology · 2020Article
- FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models.Bioinformatics (Oxford, England) · 2020Article
- Article
- Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses.Scientific reports · 2017Article
- Fast and accurate branch lengths estimation for phylogenomic trees.BMC bioinformatics · 2016Article
- Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.Genome biology and evolution · 2015Article
- A composite genome approach to identify phylogenetically informative data from next-generation sequencing.BMC bioinformatics · 2015Article
- Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes.AoB PLANTS · 2015Article
- Improved gene tree error correction in the presence of horizontal gene transfer.Bioinformatics (Oxford, England) · 2015Article
- The inference of gene trees with species trees.Systematic biology · 2015Review
- The Complete Chloroplast Genome of Guadua angustifolia and Comparative Analyses of Neotropical-Paleotropical Bamboos.PloS one · 2015Article
- Phylotranscriptomic analysis of the origin and early diversification of land plants.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Transcriptomic analysis of a psammophyte food crop, sand rice (Agriophyllum squarrosum) and identification of candidate genes essential for sand dune adaptation.BMC genomics · 2014Article
- Are the duplication cost and Robinson-Foulds distance equivalent?Journal of computational biology : a journal of computational molecular cell biology · 2014Article
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6 authors.
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Abstract
Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.
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