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FSTruct: an FST -based tool for measuring ancestry variation in inference of population structure

View ORCID ProfileMaike L. Morrison, View ORCID ProfileNicolas Alcala, Noah A. Rosenberg
doi: https://doi.org/10.1101/2021.09.24.461741
Maike L. Morrison
*Department of Biology, Stanford University, Stanford, CA 94305 USA
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  • For correspondence: maikem@stanford.edu
Nicolas Alcala
‡International Agency for Research on Cancer (IARC/WHO), Genomic Epidemiology Branch, Lyon, France
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Noah A. Rosenberg
*Department of Biology, Stanford University, Stanford, CA 94305 USA
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Abstract

In model-based inference of population structure from individual-level genetic data, individuals are assigned membership coefficients in a series of statistical clusters generated by clustering algorithms. Distinct patterns of variability in membership coefficients can be produced for different groups of individuals, for example, representing different predefined populations, sampling sites, or time periods. Such variability can be difficult to capture in a single numerical value; membership coefficient vectors are multivariate and potentially incommensurable across groups, as the number of clusters over which individuals are distributed can vary among groups of interest. Further, two groups might share few clusters in common, so that membership coefficient vectors are concentrated on different clusters. We introduce a method for measuring the variability of membership coefficients of individuals in a predefined group, making use of an analogy between variability across individuals in membership coefficient vectors and variation across populations in allele frequency vectors. We show that in a model in which membership coefficient vectors in a population follow a Dirichlet distribution, the measure increases linearly with a parameter describing the variance of a specified component of the membership vector. We apply the approach, which makes use of a normalized FST statistic, to data on inferred population structure in three example scenarios. We also introduce a bootstrap test for equivalence of two or more groups in their level of membership coefficient variability. Our methods are implemented in the R package FSTruct.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/MaikeMorrison/FSTruct

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted September 25, 2021.
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FSTruct: an FST -based tool for measuring ancestry variation in inference of population structure
Maike L. Morrison, Nicolas Alcala, Noah A. Rosenberg
bioRxiv 2021.09.24.461741; doi: https://doi.org/10.1101/2021.09.24.461741
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FSTruct: an FST -based tool for measuring ancestry variation in inference of population structure
Maike L. Morrison, Nicolas Alcala, Noah A. Rosenberg
bioRxiv 2021.09.24.461741; doi: https://doi.org/10.1101/2021.09.24.461741

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