Estimating the timing of multiple admixture events using 3-locus linkage disequilibrium
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Estimating the timing of multiple admixture events using 3-locus linkage disequilibrium. / Liang, Mason; Shishkin, Mikhail; Mikhailova, Anastasia; Shchur, Vladimir; Nielsen, Rasmus.
In: PLOS Genetics, Vol. 18, No. 7, e1010281, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Estimating the timing of multiple admixture events using 3-locus linkage disequilibrium
AU - Liang, Mason
AU - Shishkin, Mikhail
AU - Mikhailova, Anastasia
AU - Shchur, Vladimir
AU - Nielsen, Rasmus
N1 - Publisher Copyright: Copyright: © 2022 Liang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2022
Y1 - 2022
N2 - Estimating admixture histories is crucial for understanding the genetic diversity we see in present-day populations. Allele frequency or phylogeny-based methods are excellent for inferring the existence of admixture or its proportions. However, to estimate admixture times, spatial information from admixed chromosomes of local ancestry or the decay of admixture linkage disequilibrium (ALD) is used. One popular method, implemented in the programs ALDER and ROLLOFF, uses two-locus ALD to infer the time of a single admixture event, but is only able to estimate the time of the most recent admixture event based on this summary statistic. To address this limitation, we derive analytical expressions for the expected ALD in a three-locus system and provide a new statistical method based on these results that is able to resolve more complicated admixture histories. Using simulations, we evaluate the performance of this method on a range of different admixture histories. As an example, we apply the method to the Colombian and Mexican samples from the 1000 Genomes project. The implementation of our method is available at https://github.com/Genomics-HSE/LaNeta.
AB - Estimating admixture histories is crucial for understanding the genetic diversity we see in present-day populations. Allele frequency or phylogeny-based methods are excellent for inferring the existence of admixture or its proportions. However, to estimate admixture times, spatial information from admixed chromosomes of local ancestry or the decay of admixture linkage disequilibrium (ALD) is used. One popular method, implemented in the programs ALDER and ROLLOFF, uses two-locus ALD to infer the time of a single admixture event, but is only able to estimate the time of the most recent admixture event based on this summary statistic. To address this limitation, we derive analytical expressions for the expected ALD in a three-locus system and provide a new statistical method based on these results that is able to resolve more complicated admixture histories. Using simulations, we evaluate the performance of this method on a range of different admixture histories. As an example, we apply the method to the Colombian and Mexican samples from the 1000 Genomes project. The implementation of our method is available at https://github.com/Genomics-HSE/LaNeta.
U2 - 10.1371/journal.pgen.1010281
DO - 10.1371/journal.pgen.1010281
M3 - Journal article
C2 - 35839249
AN - SCOPUS:85135390365
VL - 18
JO - P L o S Genetics
JF - P L o S Genetics
SN - 1553-7390
IS - 7
M1 - e1010281
ER -
ID: 324598628