ArticleMolecular biology and evolution2019
Recombination-Aware Phylogenomics Reveals the Structured Genomic Landscape of Hybridizing Cat Species.
Article in Molecular biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers, 1 of them a synthesis that pooled it.
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Who cites it
72 citing papers in PubMed, 1 synthesis or guideline pooled it, 167 citations in OpenAlex.
- Evolutionary Models for the Diversification of Placental Mammals Across the KPg Boundary.Frontiers in genetics · 2019Pooled it
- Phylogenomic blind spots: the limits of UCE and BUSCO loci in the presence of gene flow.Molecular biology and evolution · 2026Article
- Imputation in the Wild: Genome-Wide Robustness and Fine-Scale Limitations of Low-Coverage Genomes in Endangered Species.Molecular ecology resources · 2026Article
- Comparative Genomics Reveals the Ancestral Recombination Landscape of Placental Mammals.bioRxiv : the preprint server for biology · 2026Article
- Genome Scans Reveal Species-Specific Selection in the Genus Lynx.Genome biology and evolution · 2026Article
- Deep learning reveals genomic regions introgressed between two recurrently hybridizing lynx species.Molecular biology and evolution · 2026Article
- Phylogenetic Resolution and Conflict in the Species-Rich Flowering Plant Family Leguminosae.Systematic biology · 2026Article
- Estimating Waiting Distances between Genealogy Changes under a Multi-Species Extension of the Sequentially Markov Coalescent.Systematic biology · 2026Article
- Article
- Strong evidence of mitochondrial polyphyly of the Leopardus tigrinus (Mammalia, Felidae) species complex revealed by expanded analyses of Andean populations.Genetics and molecular biology · 2026Article
- Continent-wide view of genomic diversity and divergence in the wolves of Asia.Communications biology · 2025Article
- Introgression across Narrow Contact Zones Shapes the Genomic Landscape of Phylogenetic Variation in an African Bird Clade.Systematic biology · 2025Article
- Fine-scale recombination rates inferred using the canFam4 assembly are strongly correlated with previous maps of dog recombination.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Genomic Insights Into the Origin, Decline and Recovery of the Once Critically Endangered Iberian Lynx.Molecular ecology · 2025Review
- Neo-sex Chromosomes Track the Mitochondrial Phylogeny and Exhibit an Extensive Added Stratum of Recombination Suppression in Honeyeaters (Aves: Meliphagidae).Genome biology and evolution · 2025Article
- Thrushes in Love: Extensive Gene Flow, With Differential Resistance and Selection, Obscures and Reveals the Evolutionary History of a Songbird Clade.Molecular ecology · 2025Article
- How many mammal species are there now? Updates and trends in taxonomic, nomenclatural, and geographic knowledge.Journal of mammalogy · 2025Article
- The Nariño Cat, the Tigrinas and Their Problematic Systematics and Phylogeography: The Real Story.Animals : an open access journal from MDPI · 2025Article
- Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.Communications biology · 2025Article
- Parameterizing Pantherinae: De Novo Mutation Rate Estimates from Panthera and Neofelis Pedigrees.Genome biology and evolution · 2025Article
12 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current phylogenomic approaches implicitly assume that the predominant phylogenetic signal within a genome reflects the true evolutionary history of organisms, without assessing the confounding effects of postspeciation gene flow that can produce a mosaic of phylogenetic signals that interact with recombinational variation. Here, we tested the validity of this assumption with a phylogenomic analysis of 27 species of the cat family, assessing local effects of recombination rate on species tree inference and divergence time estimation across their genomes. We found that the prevailing phylogenetic signal within the autosomes is not always representative of the most probable speciation history, due to ancient hybridization throughout felid evolution. Instead, phylogenetic signal was concentrated within regions of low recombination, and notably enriched within large X chromosome recombination cold spots that exhibited recurrent patterns of strong genetic differentiation and selective sweeps across mammalian orders. By contrast, regions of high recombination were enriched for signatures of ancient gene flow, and these sequences inflated crown-lineage divergence times by ∼40%. We conclude that existing phylogenomic approaches to infer the Tree of Life may be highly misleading without considering the genomic architecture of phylogenetic signal relative to recombination rate and its interplay with historical hybridization.
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