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VolcanoFinder: genomic scans for adaptive introgression

Genomic scans for adaptive introgression
Authors: Setter, Derek; Mousset, Sylvain; Cheng, Xiaoheng; Nielsen, Rasmus; DeGiorgio, Michael; Hermisson, Joachim;

VolcanoFinder: genomic scans for adaptive introgression

Abstract

Abstract Recent research shows that introgression between closely-related species is an important source of adaptive alleles for a wide range of taxa. Typically, detection of adaptive introgression from genomic data relies on comparative analyses that require sequence data from both the recipient and the donor species. However, in many cases, the donor is unknown or the data is not currently available. Here, we introduce a genome-scan method— VolcanoFinder —to detect recent events of adaptive introgression using polymorphism data from the recipient species only. VolcanoFinder detects adaptive introgression sweeps from the pattern of excess intermediate-frequency polymorphism they produce in the flanking region of the genome, a pattern which appears as a volcano-shape in pairwise genetic diversity. Using coalescent theory, we derive analytical predictions for these patterns. Based on these results, we develop a composite-likelihood test to detect signatures of adaptive introgression relative to the genomic background. Simulation results show that VolcanoFinder has high statistical power to detect these signatures, even for older sweeps and for soft sweeps initiated by multiple migrant haplotypes. Finally, we implement VolcanoFinder to detect archaic introgression in European and sub-Saharan African human populations, and uncovered interesting candidates in both populations, such as TSHR in Europeans and TCHH-RPTN in Africans. We discuss their biological implications and provide guidelines for identifying and circumventing artifactual signals during empirical applications of VolcanoFinder . Author summary The process by which beneficial alleles are introduced into a species from a closely-related species is termed adaptive introgression. We present an analytically-tractable model for the effects of adaptive introgression on non-adaptive genetic variation in the genomic region surrounding the beneficial allele. The result we describe is a characteristic volcano-shaped pattern of increased variability that arises around the positively-selected site, and we introduce an open-source method VolcanoFinder to detect this signal in genomic data. Importantly, VolcanoFinder is a population-genetic likelihood-based approach, rather than a comparative-genomic approach, and can therefore probe genomic variation data from a single population for footprints of adaptive introgression, even from a priori unknown and possibly extinct donor species.

Countries
Austria, United States, Austria, United Kingdom
Keywords

106014 Genomics, POSITIVE SELECTION, Introgression, Population/methods, Thyrotropin, QH426-470, MOLECULAR POPULATION-GENETICS, Intermediate Filament Proteins, Models, Receptors, S100 Proteins/genetics, European Continental Ancestry Group/genetics, Neanderthals, AFRICAN-AMERICANS, Genome, Human/genetics, S100 Proteins, SOFT SWEEPS, Receptors, Thyrotropin, Genomics, Blacks, Europe, TSH RECEPTOR, SDG 3 – Gesundheit und Wohlergehen, Volcanoes, APOLIPOPROTEIN L, THYROID-STIMULATING HORMONE, Genetic footprinting, NEANDERTHAL, Human, Research Article, 570, Evolution, Population, 106013 Genetics, Black People, Genetic Introgression, White People, Antigens/genetics, Evolution, Molecular, Genetic, SDG 3 - Good Health and Well-being, 106014 Genomik, Genetics, Humans, Computer Simulation, Polymorphism, Antigens, Selection, Genetic, 106013 Genetik, Selection, Africa South of the Sahara, Alleles, Thyrotropin/genetics, Polymorphism, Genetic, Models, Genetic, Whites, Genome, Human, STRUCTURED POPULATIONS, Human Genome, African Continental Ancestry Group/genetics, Molecular, Genome analysis, NICOTINE DEPENDENCE, Genetics, Population, Haplotypes, Intermediate Filament Proteins/genetics, Software, Developmental Biology

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    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
75
Top 1%
Top 10%
Top 1%
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gold