Discordance of Species Trees with Their Most Likely Gene Trees

Because of the stochastic way in which lineages sort during speciation, gene trees may differ in topology from each other and from species trees. Surprisingly, assuming that genetic lineages follow a coalescent model of within-species evolution, we find that for any species tree topology with five or more species, there exist branch lengths for which gene tree discordance is so common that the most likely gene tree topology to evolve along the branches of a species tree differs from the species phylogeny. This counterintuitive result implies that in combining data on multiple loci, the straightforward procedure of using the most frequently observed gene tree topology as an estimate of the species tree topology can be asymptotically guaranteed to produce an incorrect estimate. We conclude with suggestions that can aid in overcoming this new obstacle to accurate genomic inference of species phylogenies.

• Publication year

  2006

• Venue

  PLoS Genetics

• Publication date

  2006-05-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1371/journal.pgen.0020068PMID 16733550PMCID 1464820
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

  2008cited by this paper
• BMC Evolutionary Biology BioMed Central Methodology article Rooted triple consensus and anomalous gene trees

  2008cited by this paper
• Discordance of species trees with their most likely gene trees: the case of five taxa.

  2008cited by this paper
• Inconsistency of phylogenetic estimates from concatenated data under coalescence.

  2007cited by this paper
• Maximum likelihood supertrees.

  2007cited by this paper
• Inferring phylogeny despite incomplete lineage sorting.

  2006cited by this paper
• GENE TREE DISTRIBUTIONS UNDER THE COALESCENT PROCESS

  2005cited by this paper
• On the Meaning and Existence of an Effective Population Size

  2005cited by this paper
• Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree.

  2005cited by this paper
• SPECIATIONAL HISTORY OF AUSTRALIAN GRASS FINCHES (POEPHILA) INFERRED FROM THIRTY GENE TREES*

  2005cited by this paper
• Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci.

  2003cited by this paper
• Genome-scale approaches to resolving incongruence in molecular phylogenies

  2003cited by this paper
• Frequent inconsistency of parsimony under a simple model of cladogenesis.

  2003cited by this paper
• The probability of topological concordance of gene trees and species trees.

  2002cited by this paper
• Properties of phylogenetic trees generated by Yule-type speciation models.

  2001influential reference
• Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today

  2001cited by this paper
• Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees.

  2001cited by this paper
• Gene trees and species trees are not the same.

  2001cited by this paper
• From Gene Trees to Species Trees

  2000cited by this paper
• DNA archives and our nearest relative: the trichotomy problem revisited.

  2000cited by this paper
• Molecular phylogeny of the hominoids: inferences from multiple independent DNA sequence data sets.

  1997cited by this paper
• Extension Operations on Sets of Leaf-Labeled Trees

  1995cited by this paper
• Probabilities of Evolutionary Trees

  1994influential reference
• Inferences of species phylogeny in relation to segregation of ancient polymorphisms.

  1991cited by this paper
• Gene genealogy in three related populations: consistency probability between gene and population trees.

  1989cited by this paper
• A Framework for the Quantitative Study of Evolutionary Trees

  1989cited by this paper
• Relationships between gene trees and species trees.

  1988cited by this paper
• Gene genealogy and variance of interpopulational nucleotide differences.

  1985cited by this paper
• Line-of-descent and genealogical processes, and their applications in population genetics models.

  1984cited by this paper
• TESTING THE CONSTANT‐RATE NEUTRAL ALLELE MODEL WITH PROTEIN SEQUENCE DATA

  1983cited by this paper
• Evolutionary relationship of DNA sequences in finite populations.

  1983cited by this paper
• Some Maximal Solutions of the Generalized Subadditive Inequality

  1982cited by this paper
• Cases in which Parsimony or Compatibility Methods will be Positively Misleading

  1978cited by this paper
• The probabilities of rooted tree-shapes generated by random bifurcation

  1971influential reference

• Maximally probable tree topologies with $r$-furcation

  2026influential citation
• Unraveling the Genetic Diversity of Lernaea Parasites Infecting Carp Through 18 S rRNA Gene Analysis

  2026cites this paper
• Phylogenomic conflict in Lycium (Solanaceae): Revealing the roles of hybridization, incomplete lineage sorting, and biogeographic history using nuclear and mitochondrial genomes

  2026cites this paper
• When high dispersal meets high diversification: the case of the White-bellied Cuckooshrike, Coracina papuensis

  2026cites this paper
• The many origins of extremophile fishes

  2025cites this paper
• QT-WEAVER: Correcting quartet distribution improves phylogenomic analyses despite gene tree estimation error

  2025cites this paper
• On the robustness to gene tree rooting (or lack thereof) of triplet-based species tree estimation methods

  2025cites this paper
• Maximising informativeness for target capture-based phylogenomics in Erica (Ericaceae)

  2025cites this paper
• Phylogenomics of Marine Angelfishes: Diagnosing Sources of Systematic Discordance for an Iconic Reef Fish Family (F: Pomacanthidae)

  2025influential citation
• Whole genome shotgun phylogenomics resolve the diving beetle tree of life

  2025cites this paper
• Phylogenomic incongruence in Castanopsis (Fagaceae) is primarily caused by gene flow rather than incomplete lineage sorting.

  2025cites this paper
• Unravelling the Web of Life: Incomplete Lineage Sorting and Hybridisation as Primary Mechanisms Over Polyploidisation in the Evolutionary Dynamics of Pear Species

  2025cites this paper
• Phylogenetic analysis suggests early divergence followed by convergent morphological evolution in the Silene sections Odontopetalae and Sordidae (Caryophyllaceae)

  2025cites this paper
• Genome sequences of extant and extinct gibbons reveal their phylogeny, demographic history, and conservation status.

  2025cites this paper
• Biology’s Einstein Moment: Specifying Lineal Frames of Reference and Rejecting Absolute Biological History

  2025cites this paper
• Population Size Differences Can Lead to Biases in Phylogenetic Inference and Introgression Detection in the Presence of Purifying Selection.

  2025cites this paper
• Dynamics of genome evolution in the era of pangenome analysis.

  2025cites this paper
• Introgressed variants obscure phylogenetic relationships but are not subject to positive selection in Australasian long-tailed parrots.

  2025cites this paper
• Recombination and phylogenetic inference

  2025cites this paper
• Positively misleading errors

  2025influential citation
• Phylogenomics reveals the slow-burning fuse of diatom evolution

  2025cites this paper
• The Genomic Landscape, Causes, and Consequences of Extensive Phylogenomic Discordance in Murine Rodents

  2025cites this paper
• A comprehensive phylogeny of mammalian PRNP gene reveals no influence of prion misfolding propensity on the evolution of this gene

  2025cites this paper
• Diversification and evolution of Hawaiian Megalagrion damselflies ( Pinapinao , Odonata: Coenagrionidae)

  2025cites this paper
• Exploring species delimitation of high-altitude flower bugs (Heteroptera: Anthocoridae) in the presence of complex reticulate evolution: the case of a biodiversity hotspot in the Qinghai–Tibet Plateau and surrounding mountains

  2025cites this paper
• Species delimitation in the Eviota sigillata species complex, a widely distributed group of cryptobenthic coral reef fishes.

  2025cites this paper
• Widespread incongruence in the phylogenomics of the ancient land plant lineage, Selaginellaceae (lycophytes).

  2025cites this paper
• Labeled histories and maximally probable labeled topologies with multifurcation

  2025influential citation
• A Maximum-Likelihood Method to Construct Phylogenetic Trees Using Low-Homoplasy Markers: New Insights into Neoaves Phylogeny

  2025cites this paper
• Robust regression rescues poor phylogenetic decisions

  2025cites this paper
• Chromosome-scale Genomes Show Rapid Diversification and Ancient Gene Flow Among Bear Species

  2025cites this paper
• Phylogenomics Resolves Deep Phylogenetic Uncertainties and Hybridization in Rapidly Radiated Horseshoe Bats (Rhinolophus)

  2025cites this paper
• Improvement to GLASS/Maximum Tree Method of Species Tree Inference Using Measurement Error Modified Single Linkage Clustering

  2025cites this paper
• Unraveling myriapod evolution: sealion, a novel quartet-based approach for evaluating phylogenetic uncertainty

  2025cites this paper
• The genomic landscape of asymmetric introgression tracks chromosomal characteristics in tinamous (Aves: Tinamidae)

  2025cites this paper
• Discordant Phylogeographic Patterns in Ecologically Similar Sympatric Sister Species: Revisiting the Null Hypothesis of Comparative Phylogeography

  2025cites this paper
• Labelled histories with multifurcation and simultaneity

  2025cites this paper
• Exploring the evolutionary history of Sinocrassula (Crassulaceae) to provide a case study for the Tree of Life in succulent plants

  2025cites this paper
• Rapid Radiations Outweigh Reticulations During the Evolution of a 750-Million-Year-Old Lineage of Cyanobacteria

  2025cites this paper
• Revisiting the molecular circumscription of Sladeniaceae sensu lato (Ericales): Insights from phylogenetic discordance.

  2025cites this paper
• Evolutionary history of Middle American Rhamdia (Siluriformes: Heptapteridae) inferred from comparative mitogenomic data: Insights on historical biogeography and cave colonization in the group

  2025cites this paper
• Genomic insights and biotechnological potential of “Mesobacillus aurantius” strain S13: A canthaxanthin pigment-producing bacterium

  2025cites this paper
• DNA Barcoding of Genus Empoasca Walsh, 1862 (Hemiptera: Cicadellidae) Based on COI Gene Sequences

  2025cites this paper
• Reconsidering cytonuclear discordance in the genomic age.

  2025cites this paper
• Anomalous networks under the multispecies coalescent: theory and prevalence

  2024cites this paper
• Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus).

  2024cites this paper
• Leveraging Weighted Quartet Distributions for Enhanced Species Tree Inference from Genome-Wide Data

  2024cites this paper
• Opening the species box: What parsimonious microscopic models of speciation have to say about macroevolution

  2024cites this paper
• Charting a future for entomological taxonomy in New Zealand

  2024cites this paper
• wQFM-TREE: highly accurate and scalable quartet-based species tree inference from gene trees

  2024cites this paper
• Whole genome data confirm pervasive gene discordance in the evolutionary history of Coenonympha (Nymphalidae) butterflies.

  2024cites this paper
• Phylogenomics resolves the puzzling phylogeny of banded newts (genus Ommatotriton).

  2024cites this paper
• Unravelling relationships and inferring the biogeographic history of a group of herbaceous bamboos from the Northeast Atlantic Forest (Piresia: Olyreae: Bambusoideae)

  2024cites this paper
• Challenges in the Vespertilionidae phylogeny: resolving Pipistrellus nathusii placement and affirming generic status for Asian pipistrelles

  2024cites this paper
• Diaporthe species on palms - integrative taxonomic approach for species boundaries delimitation in the genus Diaporthe, with the description of D. pygmaeae sp. nov.

  2024cites this paper
• Inconsistency of parsimony under the multispecies coalescent.

  2024cites this paper
• Whole genome phylogenomics helps to resolve the phylogenetic position of the Zygothrica genus group (Diptera, Drosophilidae) and the causes of previous incongruences.

  2024cites this paper
• Evolutionary relationships and fine-scale geographic structuring in the temperate percichthyid genus Gadopsis (blackfishes) to support fisheries and conservation management.

  2024cites this paper
• Synergistic innovations enabled the radiation of anglerfishes in the deep open ocean.

  2024cites this paper
• A comprehensive genome survey study unveils the genomic characteristics and phylogenetic evolution of fishes in the Uranoscopidae family

  2024cites this paper
• A Guide to Phylogenomic Inference.

  2024cites this paper
• Phylogenomic analysis of target enrichment and transcriptome data uncovers rapid radiation and extensive hybridization in the slipper orchid genus Cypripedium

  2024cites this paper
• The evolution of multi-component weapons in the superfamily of leaf-footed bugs.

  2024cites this paper
• Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae)

  2024influential citation
• Incomplete lineage sorting and hybridization underlie tree discordance in Petunia and related genera (Petunieae, Solanaceae).

  2024cites this paper
• Hybridization, polyploidization, and morphological convergence make dozens of taxa into one chaotic genetic pool: a phylogenomic case of the Ficus erecta species complex (Moraceae)

  2024cites this paper
• Genomic patterns in the dwarf kingfishers of northern Melanesia reveal a mechanistic framework explaining the paradox of the great speciators

  2024cites this paper
• A phylogeny of the evening primrose family (Onagraceae) using a target enrichment approach with 303 nuclear loci

  2023cites this paper
• Patterns of enrichment and acceleration in evolutionary rates of promoters suggest a role of regulatory regions in cetacean gigantism

  2023cites this paper
• Ultraconserved elements-based phylogenomic systematics of the snake superfamily Elapoidea, with the description of a new Afro-Asian family.

  2023cites this paper
• A Mathematical Connection Between Single-Elimination Sports Tournaments and Evolutionary Trees

  2023cites this paper
• Disentangling Historical Relationships Within Poeciliidae (Teleostei: Cyprinodontiformes) Using Ultraconserved Elements.

  2023cites this paper
• Phylogenomics improves the phylogenetic resolution and provides strong evidence of mito‐nuclear discordance in two genera of a New Zealand cicada (Hemiptera: Cicadidae) species radiation

  2023cites this paper
• Unravelling phylogenetic relationships of tribe Cereeae using target enrichment sequencing.

  2023cites this paper
• Resolving marine–freshwater transitions by diatoms through a fog of discordant gene trees

  2023cites this paper
• Phylogenomics resolves key relationships in Rumex and uncovers a dynamic history of independently evolving sex chromosomes

  2023cites this paper
• Reticulate evolution of the tertiary relict Osmanthus.

  2023cites this paper
• Geographic destiny trumps taxonomy in the Roundtail Chub, Gila robusta species complex (Teleostei, Leuciscidae)

  2023cites this paper
• Interrelationships and Biogeography of the New World pufferfish genus Sphoeroides (Tetraodontiformes: Tetraodontidae) inferred using ultra-conserved DNA elements.

  2023cites this paper
• Anomaly zones for uniformly sampled gene trees under the gene duplication and loss model

  2023cites this paper
• Evaluating possible anthropogenic impacts on gene flow and loss of genetic diversity in endangered Madla Cave Meshweaver spiders (Hahniidae, Cicurina madla)

  2023cites this paper
• The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats

  2023cites this paper
• Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers

  2023cites this paper
• A shallow-scale phylogenomics approach reveals parallel patterns of diversification among sympatric populations of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae)

  2023cites this paper
• Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids

  2023cites this paper
• TRAILS: Tree reconstruction of ancestry using incomplete lineage sorting

  2023cites this paper
• The Phylogenomic and Biogeographic History of the Gartersnakes, Watersnakes, and Allies (Natricidae: Thamnophiini).

  2023cites this paper
• Quartet Fiduccia–Mattheyses revisited for larger phylogenetic studies

  2023cites this paper
• ANOMALOUS NETWORKS UNDER THE MULTISPECIES COALESCENT: THEORY AND PREVALENCE

  2023cites this paper
• Geogenomic predictors of genetree heterogeneity in an Amazonian bird (Thamnophilus aethiops)

  2023cites this paper
• Phylogenomics illuminates the evolution of orb webs, respiratory systems and the biogeographic history of the world's smallest orb-weaving spiders (Araneae, Araneoidea, Symphytognathoids).

  2023cites this paper
• Resolving marine-freshwater transitions by diatoms through a fog of gene tree discordance.

  2023cites this paper
• Genetics and Molecular Biology

  2023cites this paper
• Geogenomic predictors of genetree heterogeneity explain phylogeographic and introgression history: a case study in an Amazonian bird (Thamnophilus aethiops).

  2023cites this paper
• Evolution of stridulatory mechanisms: vibroacoustic communication may be common in leaf-footed bugs and allies (Heteroptera: Coreoidea)

  2023cites this paper
• The evolution of multi-component weapons in the superfamily of leaf-footed bugs

  2023cites this paper
• Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model

  2023cites this paper
• Quantification of congruence among gene trees with polytomies using overall success of resolution for phylogenomic coalescent analyses

  2023cites this paper
• A New Assessment of Robust Capuchin Monkey (Sapajus) Evolutionary History Using Genome-Wide SNP Marker Data and a Bayesian Approach to Species Delimitation

  2023cites this paper
• Evolutionary relationships of mitogenomes in a recently radiated Old World avian family

  2023cites this paper