ArticlePLoS biology2020
Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression.
Article in PLoS biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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63 citing papers in PubMed.
- Population Size Differences Can Lead to Biases in Phylogenetic Inference and Introgression Detection in the Presence of Purifying Selection.Systematic biology · 2026Article
- IQ-TREE 3: phylogenomic inference software using complex evolutionary models.Molecular biology and evolution · 2026Article
- SLC52A1 is a neofunctionalized primate urate transporter enabling intestinal urate secretion.The Journal of biological chemistry · 2026Article
- Deep learning reveals genomic regions introgressed between two recurrently hybridizing lynx species.Molecular biology and evolution · 2026Article
- Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments Using AIC.Systematic biology · 2026Article
- Dental topography and diet in marsupials and comparisons with primates.Journal of mammalian evolution · 2026Article
- Introgression across Narrow Contact Zones Shapes the Genomic Landscape of Phylogenetic Variation in an African Bird Clade.Systematic biology · 2025Article
- Evaluating UCE Data Adequacy and Integrating Uncertainty in a Comprehensive Phylogeny of Ants.Systematic biology · 2025Article
- When are Quarnets Sufficient to Reconstruct Semi-directed Phylogenetic Networks?Bulletin of mathematical biology · 2025Article
- Phylogenetic networks empower biodiversity research.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Ancient reticulation, incomplete lineage sorting and the evolution of the pyrenoid at the dawn of hornwort diversification.Annals of botany · 2025Article
- Squirrel: Reconstructing Semi-directed Phylogenetic Level-1 Networks from Four-Leaved Networks or Sequence Alignments.Molecular biology and evolution · 2025Article
- Phylogenomics resolves key relationships inEvolution letters · 2025Article
- CASTER: Direct species tree inference from whole-genome alignments.Science (New York, N.Y.) · 2025Article
- The Genomic Landscape, Causes, and Consequences of Extensive Phylogenomic Discordance in Murine Rodents.Genome biology and evolution · 2025Article
- getphylo: rapid and automatic generation of multi-locus phylogenetic trees.BMC bioinformatics · 2025Article
- Genome-scale evolution in local populations of wild chimpanzees.Scientific reports · 2025Article
- Orphan genes are not a distinct biological entity.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- TINNiK: inference of the tree of blobs of a species network under the coalescent model.Algorithms for molecular biology : AMB · 2024Article
- The Meaning and Measure of Concordance Factors in Phylogenomics.Molecular biology and evolution · 2024Review
3 more citing papers are in PubMed but not listed here.
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Authors and funding
14 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here, we present new reference genome assemblies for 3 Old World monkey (OWM) species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place.
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