ArticleBMC evolutionary biology2007
Inferring angiosperm phylogeny from EST data with widespread gene duplication.
Article in BMC evolutionary biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Genome-wide signatures of plastid-nuclear coevolution point to repeated perturbations of plastid proteostasis systems across angiosperms.The Plant cell · 2021Article
- FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models.Bioinformatics (Oxford, England) · 2020Article
- Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants.Scientific reports · 2020Article
- Locus-aware decomposition of gene trees with respect to polytomous species trees.Algorithms for molecular biology : AMB · 2018Article
- Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics.Molecular biology and evolution · 2014Article
- Are the duplication cost and Robinson-Foulds distance equivalent?Journal of computational biology : a journal of computational molecular cell biology · 2014Article
- Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars.Frontiers in plant science · 2014Article
- DrML: probabilistic modeling of gene duplications.Journal of computational biology : a journal of computational molecular cell biology · 2014Article
- Refining discordant gene trees.BMC bioinformatics · 2014Article
- Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance.Algorithms for molecular biology : AMB · 2013Article
- Targeted enrichment: maximizing orthologous gene comparisons across deep evolutionary time.PloS one · 2013Article
- Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life.Systematic biology · 2012Article
- Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence.BMC bioinformatics · 2012Article
- Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem.BMC bioinformatics · 2012Article
- A consistent phylogenetic backbone for the fungi.Molecular biology and evolution · 2012Article
- Article
- A functional phylogenomic view of the seed plants.PLoS genetics · 2011Article
- Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees.Systematic biology · 2011Article
- Maximum likelihood models and algorithms for gene tree evolution with duplications and losses.BMC bioinformatics · 2011Article
- An ILP solution for the gene duplication problem.BMC bioinformatics · 2011Article
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2 authors.
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Abstract
backgroundMost studies inferring species phylogenies use sequences from single copy genes or sets of orthologs culled from gene families. For taxa such as plants, with very high levels of gene duplication in their nuclear genomes, this has limited the exploitation of nuclear sequences for phylogenetic studies, such as those available in large EST libraries. One rarely used method of inference, gene tree parsimony, can infer species trees from gene families undergoing duplication and loss, but its performance has not been evaluated at a phylogenomic scale for EST data in plants.
resultsA gene tree parsimony analysis based on EST data was undertaken for six angiosperm model species and Pinus, an outgroup. Although a large fraction of the tentative consensus sequences obtained from the TIGR database of ESTs was assembled into homologous clusters too small to be phylogenetically informative, some 557 clusters contained promising levels of information. Based on maximum likelihood estimates of the gene trees obtained from these clusters, gene tree parsimony correctly inferred the accepted species tree with strong statistical support. A slight variant of this species tree was obtained when maximum parsimony was used to infer the individual gene trees instead.
conclusionDespite the complexity of the EST data and the relatively small fraction eventually used in inferring a species tree, the gene tree parsimony method performed well in the face of very high apparent rates of duplication.
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