ArticleSystematic biology2022
Ghost Lineages Highly Influence the Interpretation of Introgression Tests.
Article in Systematic biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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Who cites it
56 citing papers in PubMed.
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- Phylogenomic evidence provides insights into the phylogeny and speciation patterns in the subgenus Caloscordum (Allium, Amaryllidaceae).Cladistics : the international journal of the Willi Hennig Society · 2026Article
- Phylogenetically Diverse Introgression Drives Subtle Population Structure in Pacific Rockfishes.Molecular ecology · 2026Article
- ERICA-trio: an outgroup-free deep learning method for topology inference and introgression detection.Briefings in bioinformatics · 2026Article
- Expansion From Lowland Pleistocene Refugia Followed by Cryptic Introgression in an African Elevational Generalist Bird.Molecular ecology · 2026Article
- Evidence of introgression amid phylogenetic conflict in Brachyotum, a plant radiation from the Tropical Andes.American journal of botany · 2026Article
- Genomics Insights into the Demographic History and Introgression of Tibetan Pigs.Animals : an open access journal from MDPI · 2026Article
- Latitudinal Clines in Gene Flow and Demographic Stability Reveal Drivers of Microendemism in a Radiation of Alpine Grasshoppers.Molecular ecology · 2026Article
- Species Diversification in the Sky Islands of Southwestern China Revealed by Genomic, Introgression, and Demographic Analyses of Asian Shrew Moles.Systematic biology · 2026Article
- 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
- The missing data problem in population genomics and statistical methods to address them.G3 (Bethesda, Md.) · 2026Article
- Integrative morphological, palynological, and phylogenomic evidence supports the recognition ofFrontiers in plant science · 2026Article
- Rampant Reticulation in a Rapid Radiation of Tropical Trees-Insights from Inga (Fabaceae).Systematic biology · 2025Article
- Phylogenomics of Marine Angelfishes: Diagnosing Sources of Systematic Discordance for an Iconic Reef Fish Family (F: Pomacanthidae).Systematic biology · 2025Article
- Do syngameons exist in tropical trees? Challenges to determine their existence and estimate their frequency.Biology letters · 2025Review
- Detecting Introgression in Shallow Phylogenies: How Minor Molecular Clock Deviations Lead to Major Inference Errors.Molecular biology and evolution · 2025Article
- Phylogenetically diverse introgression drives subtle population structure in Pacific rockfishes.bioRxiv : the preprint server for biology · 2025Article
- Homoploid hybrid speciation and recurrent hybridization along the northwestern Iberian mountain chains.Annals of botany · 2025Article
- Phylogenetic networks empower biodiversity research.Proceedings of the National Academy of Sciences of the United States of America · 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
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3 authors.
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Abstract
Most species are extinct, those that are not are often unknown. Sequenced and sampled species are often a minority of known ones. Past evolutionary events involving horizontal gene flow, such as horizontal gene transfer, hybridization, introgression, and admixture, are therefore likely to involve "ghosts," that is extinct, unknown, or unsampled lineages. The existence of these ghost lineages is widely acknowledged, but their possible impact on the detection of gene flow and on the identification of the species involved is largely overlooked. It is generally considered as a possible source of error that, with reasonable approximation, can be ignored. We explore the possible influence of absent species on an evolutionary study by quantifying the effect of ghost lineages on introgression as detected by the popular D-statistic method. We show from simulated data that under certain frequently encountered conditions, the donors and recipients of horizontal gene flow can be wrongly identified if ghost lineages are not taken into account. In particular, having a distant outgroup, which is usually recommended, leads to an increase in the error probability and to false interpretations in most cases. We conclude that introgression from ghost lineages should be systematically considered as an alternative possible, even probable, scenario. [ABBA-BABA; D-statistic; gene flow; ghost lineage; introgression; simulation.].
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