ArticlePLoS genetics2024
Leveraging shared ancestral variation to detect local introgression.
Article in PLoS genetics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- A Rarefaction Approach to Identify Local Introgression in a Three Population Tree.bioRxiv : the preprint server for biology · 2026Article
- Recent advances in methods to characterize archaic introgression in modern humans.Genome research · 2026Review
- Polarising SNPs Without Outgroup.Molecular ecology resources · 2026Article
- TheScience (New York, N.Y.) · 2025Article
- Computational Genomics and Its Applications to Anthropological Questions.American journal of biological anthropology · 2024Review
- Five-leaf Generalizations of the D-statistic Reveal the Directionality of Admixture.Molecular biology and evolution · 2024Article
- Article
- Pharmacogenetic Variation in Neanderthals and Denisovans and Implications for Human Health and Response to Medications.Genome biology and evolution · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Introgression is a common evolutionary phenomenon that results in shared genetic material across non-sister taxa. Existing statistical methods such as Patterson's D statistic can detect introgression by measuring an excess of shared derived alleles between populations. The D statistic is effective to detect genome-wide patterns of introgression but can give spurious inferences of introgression when applied to local regions. We propose a new statistic, D+, that leverages both shared ancestral and derived alleles to infer local introgressed regions. Incorporating both shared derived and ancestral alleles increases the number of informative sites per region, improving our ability to identify local introgression. We use a coalescent framework to derive the expected value of this statistic as a function of different demographic parameters under an instantaneous admixture model and use coalescent simulations to compute the power and precision of D+. While the power of D and D+ is comparable, D+ has better precision than D. We apply D+ to empirical data from the 1000 Genome Project and Heliconius butterflies to infer local targets of introgression in humans and in butterflies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.