ArticleBMC bioinformatics2011
Maximum likelihood models and algorithms for gene tree evolution with duplications and losses.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 43 citations in OpenAlex.
- Orthology and near-cographs in the context of phylogenetic networks.Algorithms for molecular biology : AMB · 2025Article
- The complete mitochondrial genome ofMitochondrial DNA. Part B, Resources · 2023Article
- WGDTree: a phylogenetic software tool to examine conditional probabilities of retention following whole genome duplication events.BMC bioinformatics · 2022Article
- Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models.Journal of mathematical biology · 2020Article
- Isometric gene tree reconciliation revisited.Algorithms for molecular biology : AMB · 2017Article
- Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants.BMC evolutionary biology · 2015Article
- Event inference in multidomain families with phylogenetic reconciliation.BMC bioinformatics · 2015Article
- The inference of gene trees with species trees.Systematic biology · 2015Review
- Diet shapes the evolution of the vertebrate bitter taste receptor gene repertoire.Molecular biology and evolution · 2014Article
- Refining discordant gene trees.BMC bioinformatics · 2014Article
- DrML: probabilistic modeling of gene duplications.Journal of computational biology : a journal of computational molecular cell biology · 2014Article
- Reconciliation of gene and species trees.BioMed research international · 2014Article
- Computational approaches to species phylogeny inference and gene tree reconciliation.Trends in ecology & evolution · 2013Review
- How old is my gene?Trends in genetics : TIG · 2013Review
- Genome-scale coestimation of species and gene trees.Genome research · 2013Article
- iGTP: a software package for large-scale gene tree parsimony analysis.BMC bioinformatics · 2010Article
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Authors and funding
3 authors at 3 institutions in 2 countries.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe abundance of new genomic data provides the opportunity to map the location of gene duplication and loss events on a species phylogeny. The first methods for mapping gene duplications and losses were based on a parsimony criterion, finding the mapping that minimizes the number of duplication and loss events. Probabilistic modeling of gene duplication and loss is relatively new and has largely focused on birth-death processes.
resultsWe introduce a new maximum likelihood model that estimates the speciation and gene duplication and loss events in a gene tree within a species tree with branch lengths. We also provide an, in practice, efficient algorithm that computes optimal evolutionary scenarios for this model. We implemented the algorithm in the program DrML and verified its performance with empirical and simulated data.
conclusionsIn test data sets, DrML finds optimal gene duplication and loss scenarios within minutes, even when the gene trees contain sequences from several hundred species. In many cases, these optimal scenarios differ from the lca-mapping that results from a parsimony gene tree reconciliation. Thus, DrML provides a new, practical statistical framework on which to study gene duplication.
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