Assign an individual of unknown provenance to population based on PCA

This script assigns an individual of unknown provenance to one or more target populations based on its proximity to each population defined by a confidence ellipse in ordinated space of two dimensions.

The following process is followed:

The space defined by the loci is ordinated to yield a series of orthogonal axes (independent), and the top two dimensions are considered. Populations for which the unknown lies outside the specified confidence limits are no longer removed from the dataset.

Usage

gl.assign.pca(x, unknown, plevel = 0.999, plot.out = TRUE, verbose = NULL)

Arguments

x: Name of the input genlight object [required].
unknown: Identity label of the focal individual whose provenance is unknown [required].
plevel: Probability level for bounding ellipses in the PCoA plot [default 0.999].
plot.out: If TRUE, plot the 2D PCA showing the position of the unknown [default TRUE]
verbose: Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Value

A genlight object containing only those populations that are putative source populations for the unknown individual.

Details

There are three considerations to assignment. First, consider only those populations for which the unknown has no private alleles. Private alleles are an indication that the unknown does not belong to a target population (provided that the sample size is adequate, say >=10). This can be evaluated with gl.assign.pa().

A next step is to consider the PCoA plot for populations where no private alleles have been detected and the position of the unknown in relation to the confidence ellipses as is plotted by this script. Note, this plot is considering only the top two dimensions of the ordination, and so an unknown lying outside the confidence ellipse can be unambiguously interpreted as it lying outside the confidence envelope. However, if the unknown lies inside the confidence ellipse in two dimensions, then it may still lie outside the confidence envelope in deeper dimensions. This second step is good for eliminating populations from consideration, but does not provide confidence in assignment.

The third step is to consider the assignment probabilities, using the script gl.assign.mahalanobis(). This approach calculates the squared Generalised Linear Distance (Mahalanobis distance) of the unknown from the centroid for each population, and calculates the probability associated with its quantile under the zero truncated normal distribution. This index takes into account position of the unknown in relation to the confidence envelope in all selected dimensions of the ordination.

Each of these approaches provides evidence, none are 100 need to be interpreted cautiously. They are best applied sequentially.

In deciding the assignment, the script considers an individual to be an outlier with respect to a particular population at alpha = 0.001 as default.

Author

Custodian: Arthur Georges -- Post to https://groups.google.com/d/forum/dartr

Examples

if (FALSE) {
#Test run with a focal individual from the Macleay River (EmmacMaclGeor) 
test <- gl.assign.pa(testset.gl, unknown='UC_00146', nmin=10, threshold=1,
verbose=3) 
test_2 <- gl.assign.pca(test, unknown='UC_00146', plevel=0.95, verbose=3)
}