ReviewSystematic biology2015
The inference of gene trees with species trees.
Review in Systematic biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 88 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
88 citing papers in PubMed.
- Phlag: scalable detection of genomics regions with unexplained phylogenetic heterogeneity.Bioinformatics (Oxford, England) · 2026Article
- Phylogenetic discordance arises from incomplete lineage sorting and pre-speciation introgression during erosion-mediated radiation of Asian warty newts.Zoological research · 2026Article
- The Diversity of Bacterial Symbionts in Major Agricultural Lepidopteran Pests in Australia.International journal of microbiology · 2026Article
- TMEM45 protein family - Ancient residents of the cell endomembrane.Frontiers in molecular biosciences · 2026Review
- Comparative Genomics Using GeneDiscoveR: A Toolbox for the Identification of Gene Candidates Associated with Plant Traits.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Leveraging Weighted Quartet Distributions for Enhanced Species Tree Inference from Genome-Wide Data.Genome biology and evolution · 2025Article
- PhyloTune: An efficient method to accelerate phylogenetic updates using a pretrained DNA language model.Nature communications · 2025Article
- Teasing apart the sources of phylogenetic tree discordance across three genomes in the oak family (Fagaceae).BMC plant biology · 2025Article
- A comprehensive phylogeny of mammalian PRNP gene reveals no influence of prion misfolding propensity on the evolution of this gene.PLoS pathogens · 2025Article
- Ages, sizes and (trees within) trees of taxa and of urns, from Yule to today.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Persistent, Private, and Mobile Genes: A Model for Gene Dynamics in Evolving Pangenomes.Molecular biology and evolution · 2025Article
- Poplar: a phylogenomics pipeline.Bioinformatics advances · 2025Article
- Whole-genome based phylogeny and comparative genomics of Sporidiobolales and related taxa ofIMA fungus · 2025Article
- Patterns recovered in phylogenomic analysis ofMicrobial genomics · 2024Article
- AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss.Bioinformatics (Oxford, England) · 2024Article
- wQFM-DISCO: DISCO-enabled wQFM improves phylogenomic analyses despite the presence of paralogs.Bioinformatics advances · 2024Article
- Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation.Molecular biology and evolution · 2023Article
- ncOrtho: efficient and reliable identification of miRNA orthologs.Nucleic acids research · 2023Article
- "Correcting" Gene Trees to be More Like Species Trees Frequently Increases Topological Error.Genome biology and evolution · 2023Article
- Phylogenomic Testing of Root Hypotheses.Genome biology and evolution · 2023Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issuedErratum.2016
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can coexist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree-species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree-species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.