ArticleProceedings of the National Academy of Sciences of the United States of America2012
Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. 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 181 papers, 1 of them a synthesis that pooled it.
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Who cites it
181 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary.Frontiers in genetics · 2019Pooled it
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- Phylogenomic subsampling and upsampling for efficient evolutionary analyses of big data.bioRxiv : the preprint server for biology · 2026Article
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- Phylogeny of waterfowl (Anseriformes) constructed using genome sequences provides insights into topological incongruences.Molecular biology and evolution · 2026Article
- Phylogenomics of Marine Angelfishes: Diagnosing Sources of Systematic Discordance for an Iconic Reef Fish Family (F: Pomacanthidae).Systematic biology · 2025Article
- Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss.Genome biology and evolution · 2025Article
- Timing and Pattern of Early Diversification in Drosophilidae (Diptera).Molecular biology and evolution · 2025Article
- Leveraging Weighted Quartet Distributions for Enhanced Species Tree Inference from Genome-Wide Data.Genome biology and evolution · 2025Article
- Ancient reticulation, incomplete lineage sorting and the evolution of the pyrenoid at the dawn of hornwort diversification.Annals of botany · 2025Article
- Accurate, scalable, and fully automated inference of species trees from raw genome assemblies using ROADIES.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Reconciling Gene Tree Discordance and Biogeography in European Crows.Molecular ecology · 2025Article
- Comparative genomics and phylogenetic analysis of mitochondrial genomes of Neocinnamomum.BMC plant biology · 2025Article
- Resolving phylogenetic conflicts in Pandanales: the dual roles of gene flow and whole-genome duplication.Frontiers in plant science · 2025Article
121 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
The reconstruction of the Tree of Life has relied almost entirely on concatenation methods, which do not accommodate gene tree heterogeneity, a property that simulations and theory have identified as a likely cause of incongruent phylogenies. However, this incongruence has not yet been demonstrated in empirical studies. Several key relationships among eutherian mammals remain controversial and conflicting among previous studies, including the root of eutherian tree and the relationships within Euarchontoglires and Laurasiatheria. Both bayesian and maximum-likelihood analysis of genome-wide data of 447 nuclear genes from 37 species show that concatenation methods indeed yield strong incongruence in the phylogeny of eutherian mammals, as revealed by subsampling analyses of loci and taxa, which produced strongly conflicting topologies. In contrast, the coalescent methods, which accommodate gene tree heterogeneity, yield a phylogeny that is robust to variable gene and taxon sampling and is congruent with geographic data. The data also demonstrate that incomplete lineage sorting, a major source of gene tree heterogeneity, is relevant to deep-level phylogenies, such as those among eutherian mammals. Our results firmly place the eutherian root between Atlantogenata and Boreoeutheria and support ungulate polyphyly and a sister-group relationship between Scandentia and Primates. This study demonstrates that the incongruence introduced by concatenation methods is a major cause of long-standing uncertainty in the phylogeny of eutherian mammals, and the same may apply to other clades. Our analyses suggest that such incongruence can be resolved using phylogenomic data and coalescent methods that deal explicitly with gene tree heterogeneity.
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