ArticleSystematic biology2016
A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction.
Article in Systematic biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Phylo2Vec: A Vector Representation for Binary Trees.Systematic biology · 2025Article
- Variational Supertrees for Bayesian Phylogenetics.Bulletin of mathematical biology · 2024Article
- Comparing Phylogeographies to Reveal Incompatible Geographical Histories within Genomes.Molecular biology and evolution · 2024Article
- wQFM-DISCO: DISCO-enabled wQFM improves phylogenomic analyses despite the presence of paralogs.Bioinformatics advances · 2024Article
- Estimating transcriptome complexities across eukaryotes.BMC genomics · 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
- Gene Tree Discord, Simplex Plots, and Statistical Tests under the Coalescent.Systematic biology · 2022Article
- DISCO: Species Tree Inference using Multicopy Gene Family Tree Decomposition.Systematic biology · 2022Article
- Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation.Algorithms for molecular biology : AMB · 2021Article
- ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy.Molecular biology and evolution · 2020Article
- Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing.Scientific reports · 2020Article
- FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models.Bioinformatics (Oxford, England) · 2020Article
- Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing.NAR genomics and bioinformatics · 2020Article
- PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees.BMC evolutionary biology · 2019Article
- PhyloToL: A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes.Molecular biology and evolution · 2019Article
- Microbial sequence typing in the genomic era.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2018Review
- FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization.Bioinformatics (Oxford, England) · 2017Article
- Article
- Multilocus inference of species trees and DNA barcoding.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2016Review
- SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees.Systematic biology · 2016Article
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3 authors.
Funding
Abstract
Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models.
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