On the Distribution of Tract Lengths During Adaptive Introgression
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On the Distribution of Tract Lengths During Adaptive Introgression. / Shchur, Vladimir; Svedberg, Jesper; Medina, Paloma; Corbett-Detig, Russell; Nielsen, Rasmus.
I: G3: Genes, Genomes, Genetics (Bethesda), Bind 10, Nr. 10, 2020, s. 3663-3673.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - On the Distribution of Tract Lengths During Adaptive Introgression
AU - Shchur, Vladimir
AU - Svedberg, Jesper
AU - Medina, Paloma
AU - Corbett-Detig, Russell
AU - Nielsen, Rasmus
PY - 2020
Y1 - 2020
N2 - Admixture is increasingly being recognized as an important factor in evolutionary genetics. The distribution of genomic admixture tracts, and the resulting effects on admixture linkage disequilibrium, can be used to date the timing of admixture between species or populations. However, the theory used for such prediction assumes selective neutrality despite the fact that many famous examples of admixture involve natural selection acting for or against admixture. In this paper, we investigate the effects of positive selection on the distribution of tract lengths. We develop a theoretical framework that relies on approximating the trajectory of the selected allele using a logistic function. By numerically calculating the expected allele trajectory, we also show that the approach can be extended to cases where the logistic approximation is poor due to the effects of genetic drift. Using simulations, we show that the model is highly accurate under most scenarios. We use the model to show that positive selection on average will tend to increase the admixture tract length. However, perhaps counter-intuitively, conditional on the allele frequency at the time of sampling, positive selection will actually produce shorter expected tract lengths. We discuss the consequences of our results in interpreting the timing of the introgression ofEPAS1from Denisovans into the ancestors of Tibetans.
AB - Admixture is increasingly being recognized as an important factor in evolutionary genetics. The distribution of genomic admixture tracts, and the resulting effects on admixture linkage disequilibrium, can be used to date the timing of admixture between species or populations. However, the theory used for such prediction assumes selective neutrality despite the fact that many famous examples of admixture involve natural selection acting for or against admixture. In this paper, we investigate the effects of positive selection on the distribution of tract lengths. We develop a theoretical framework that relies on approximating the trajectory of the selected allele using a logistic function. By numerically calculating the expected allele trajectory, we also show that the approach can be extended to cases where the logistic approximation is poor due to the effects of genetic drift. Using simulations, we show that the model is highly accurate under most scenarios. We use the model to show that positive selection on average will tend to increase the admixture tract length. However, perhaps counter-intuitively, conditional on the allele frequency at the time of sampling, positive selection will actually produce shorter expected tract lengths. We discuss the consequences of our results in interpreting the timing of the introgression ofEPAS1from Denisovans into the ancestors of Tibetans.
KW - adaptive introgression
KW - tract length
KW - adaptation
KW - EPAS1
KW - admixture
KW - selection
KW - HUMAN-POPULATIONS
KW - SELECTION MODELS
KW - LINKAGE
KW - ADMIXTURE
KW - ADAPTATION
KW - DISEQUILIBRIUM
KW - HITCHHIKING
KW - COALESCENT
KW - UNIT
U2 - 10.1534/g3.120.401616
DO - 10.1534/g3.120.401616
M3 - Journal article
C2 - 32763953
VL - 10
SP - 3663
EP - 3673
JO - G3: Genes, Genomes, Genetics (Bethesda)
JF - G3: Genes, Genomes, Genetics (Bethesda)
SN - 2160-1836
IS - 10
ER -
ID: 250539559