ArticleProceedings of the National Academy of Sciences of the United States of America2009
Simultaneous Bayesian gene tree reconstruction and reconciliation analysis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- Review
- The path-label reconciliation (PLR) dissimilarity measure for gene trees.Algorithms for molecular biology : AMB · 2025Article
- Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.The ISME journal · 2024Review
- The Theory of Gene Family Histories.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Phylogenetic reconciliation.PLoS computational biology · 2022Article
- Rooting Species Trees Using Gene Tree-Species Tree Reconciliation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Gene tree and species tree reconciliation with endosymbiotic gene transfer.Bioinformatics (Oxford, England) · 2021Article
- Review
- GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene Family Tree Inference under Gene Duplication, Transfer, and Loss.Molecular biology and evolution · 2020Article
- Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models.Journal of mathematical biology · 2020Article
- Evolution through segmental duplications and losses: a Super-Reconciliation approach.Algorithms for molecular biology : AMB · 2020Article
- Diversity of opisthokont septin proteins reveals structural constraints and conserved motifs.BMC evolutionary biology · 2019Article
- RecPhyloXML: a format for reconciled gene trees.Bioinformatics (Oxford, England) · 2018Article
- Consistency and convergence rate of phylogenetic inference via regularization.Annals of statistics · 2018Article
- TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees.BMC genomics · 2018Article
- Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family.BMC bioinformatics · 2017Article
- DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies.Genome biology and evolution · 2017Article
- Xenolog classification.Bioinformatics (Oxford, England) · 2017Article
- VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces.BMC bioinformatics · 2017Article
- Probabilistic inference of lateral gene transfer events.BMC bioinformatics · 2016Article
8 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
We present GSR, a probabilistic model integrating gene duplication, sequence evolution, and a relaxed molecular clock for substitution rates, that enables genomewide analysis of gene families. The gene duplication and loss process is a major cause for incongruence between gene and species tree, and deterministic methods have been developed to explain such differences through tree reconciliations. Although probabilistic methods for phylogenetic inference have been around for decades, probabilistic reconciliation methods are far less established. Based on our model, we have implemented a Bayesian analysis tool, PrIME-GSR, for gene tree inference that takes a known species tree into account. Our implementation is sound and we demonstrate its utility for genomewide gene-family analysis by applying it to recently presented yeast data. We validate PrIME-GSR by comparing with previous analyses of these data that take advantage of gene order information. In a case study we apply our method to the ADH gene family and are able to draw biologically relevant conclusions concerning gene duplications creating key yeast phenotypes. On a higher level this shows the biological relevance of our method. The obtained results demonstrate the value of a relaxed molecular clock. Our good performance will extend to species where gene order conservation is insufficient.
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