ArticlePLoS biology2022
Ghost lineages can invalidate or even reverse findings regarding gene flow.
Article in PLoS biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Article
- Efficient amplicon panels for evaluating hybridization and genetic structure in the Schistosoma haematobium species group.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2026Article
- Phylogeny-aware Simulations Suggest a Low Impact of Unsampled Lineages in the Inference of Gene Flow During Eukaryogenesis.Genome biology and evolution · 2025Article
- HGTs are not SPRs: In the Presence of Ghost Lineages, Series of Horizontal Gene Transfers do not Result in Series of Subtree Pruning and Regrafting.Molecular biology and evolution · 2025Article
- Phylogenomics resolves key relationships inEvolution letters · 2025Article
- Host-Calibrated Time Tree Caps the Age of Giant Viruses.Molecular biology and evolution · 2025Article
- Admixture in the fungal pathogen Blastomyces.Genetics · 2024Article
- Review
- Uncovering ghost introgression through genomic analysis of a distinct eastern Asian hickory species.The Plant journal : for cell and molecular biology · 2024Article
- Ancient and Recent Hybridization in the Oreochromis Cichlid Fishes.Molecular biology and evolution · 2024Article
- Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information.Systematic biology · 2024Article
- Genome Evolution and Introgression in the New Zealand mud Snails Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa.Genome biology and evolution · 2024Article
- On the impact of incomplete taxon sampling on the relative timing of gene transfer events.PLoS biology · 2024Article
- Response to "On the impact of incomplete taxon sampling on the relative timing of gene transfer events".PLoS biology · 2024Article
- Paleomicrobiology: Tracking the past microbial life from single species to entire microbial communities.Microbial biotechnology · 2024Review
- Ghost admixture in eastern gorillas.Nature ecology & evolution · 2023Article
- Ghost introgression facilitates genomic divergence of a sympatric cryptic lineage inEcology and evolution · 2023Article
- Review
- Detecting cryptic ghost lineage introgression in four-taxon genomic datasets.Applications in plant sciencesArticle
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Introgression, endosymbiosis, and gene transfer, i.e., horizontal gene flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on extant genomes. One of them is the effect of HGF on branch lengths of constructed phylogenies. This signature has been formalized in statistical tests for HGF detection and used for example to detect massive adaptive gene flows in malaria vectors or to order evolutionary events involved in eukaryogenesis. However, these studies rely on the assumption that ghost lineages (all unsampled extant and extinct taxa) have little influence. We demonstrate here with simulations and data reanalysis that when considering the more realistic condition that unsampled taxa are legion compared to sampled ones, the conclusion of these studies become unfounded or even reversed. This illustrates the necessity to recognize the existence of ghosts in evolutionary studies.
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