RT Journal Article
SR Electronic
T1 FSTruct: an <em>F</em><sub><em>ST</em></sub> -based tool for measuring ancestry variation in inference of population structure
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.09.24.461741
DO 10.1101/2021.09.24.461741
A1 Morrison, Maike L.
A1 Alcala, Nicolas
A1 Rosenberg, Noah A.
YR 2021
UL http://biorxiv.org/content/early/2021/09/25/2021.09.24.461741.abstract
AB 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 StatementThe authors have declared no competing interest.