ArticleMolecular biology and evolution2015
Evaluating the use of ABBA-BABA statistics to locate introgressed loci.
Article in Molecular biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 363 papers.
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363 citing papers in PubMed.
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- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
- Divergent habitat selection across many loci maintains species boundaries during introgression.bioRxiv : the preprint server for biology · 2026Article
- Unknown Biases: Understanding How Anthropogenic Hybridization Impacts Genomic Diversity and Demographic Estimates.Animals : an open access journal from MDPI · 2026Article
- Widespread introgression and a potential role for a neo-sex chromosome in booby diversification and speciation.bioRxiv : the preprint server for biology · 2026Article
- Genome-wide SNVs revealed reticulate evolutionary history of a Eurasian-African songbird radiation (Zoological research · 2026Article
- Multi-omics analysis identifies loci associated with pyrethroid resistance across sister species in the Anopheles gambiae species complex.BMC genomics · 2026Article
- ERICA-trio: an outgroup-free deep learning method for topology inference and introgression detection.Briefings in bioinformatics · 2026Article
- Mitogenomics inMicrobial genomics · 2026Article
- Introgressed Variation in TaMYB7-A1 Drives Graded Dormancy and Climate-Adaptive Pre-Harvest Sprouting Resistance in Wheat.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genomic reconstruction of upland cotton domestication uncovers staged selection, gene flow, and flowering-time adaptation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Protocol for detecting genome-wide introgressed genes and evaluating their functional legacy.STAR protocols · 2026Article
- Genome and transcriptome analyses reveal parallel altitude adaptation in Chenopodium.Genome biology · 2026Article
- Nuclear phylogenomic analysis of Allium (Amaryllidaceae) species from Kazakhstan reveals incomplete lineage sorting and gene flow.BMC plant biology · 2026Article
- A global map for introgressed structural variation and selection in humans.Science (New York, N.Y.) · 2026Article
- Introgression and Divergence in a Young Species Group.Molecular ecology · 2026Article
- Evolution of genome-wide barriers to gene flow during complex speciation in rattlesnakes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A near telomere-to-telomere genome assembly of the Amur stickleback (Zoological research · 2026Article
303 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson's D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole-genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic ƒ(d), a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. ƒ(d) is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and ƒ(d) outliers tend to cluster in regions of low absolute divergence (d(XY)), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.
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