Estimating the timing of multiple admixture events using 3-locus linkage disequilibrium

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  • Mason Liang
  • Mikhail Shishkin
  • Anastasia Mikhailova
  • Vladimir Shchur
  • Nielsen, Rasmus

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.

Original languageEnglish
Article numbere1010281
JournalPLOS Genetics
Volume18
Issue number7
Number of pages17
ISSN1553-7390
DOIs
Publication statusPublished - 2022

Bibliographical note

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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.

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