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This section focuses first on how we estimate distances, depending upon the level of interest, and then highlights some approaches for visualizing and gaining inferences from the distance matrix itself.
If we compute genetic distances (with PLINK), we get a matrix of 4532 by 4532 animals, with more than 10 million pairwise combinations. So a "rather" long list to scroll through, let alone make sense of it. Fortunately, we can apply some clever statistical methods to simplify it for us.
Genetic distances give the extent of gene differences between populations (and hence genetic relationships among them) measured by some numerical quantity and usually refer to the gene differences as measured by a function of gene frequencies.
The Geographic Distance Matrix Generator is a platform-independent Java application that implements the same powerful suite of spherical functions as the Perpendicular Distance Calculator to compute all pair wise distances from a simple list of geographic coordinates.
24 maj 2017 · In this simulation study, we analyze the behavior of different genetic distances in Island (null hypothesis) and stepping stone models displaying varying neighborhood sizes.
12 paź 2018 · To demonstrate how to use multiple-matrix animal models, we provide a simulated dataset of a population of merpeople (mermaids and mermen). This imaginary population contains ten semelparous generations, of between 150 and 250 individuals per generation (total population size 1806).
21 kwi 2021 · We develop gene-set distance analysis (GSDA) by generalizing distance correlations to evaluate the association of a gene set with categorical and censored event-time variables. We also develop a backward elimination procedure to identify a subset of genes that empirically drive significant associations.
