Statistical tests of neutrality based on SNP and Alu repeat data
Doctor of Philosophy
The general topic of this thesis is new neutrality tests for population genetics. Two independent SNP data sets of candidate cancer genes are explored for signatures of selection using selection tests based on the allele frequency spectrum, linkage disequilibrium, and extended core haplotypes. We show that most selection tests identify the same signature of selection within similar populations for the two data sets. Additionally, we modeled the proliferation and mutation of Alu sequences under neutrality based on Pakes' branching process with infinite alleles mutations using a time-discrete branching process with linear fractional offspring distribution. A comparison of the Alu sequence data with our model shows that the distribution of Alu sequences in subfamilies AluYa5 and AluYb8 does not follow the expected distribution derived from the branching process. This observation suggests that Alu sequences do not evolve neutrally and might be under selection. Calculations for deriving the proliferation and mutation of Alu sequences under neutrality based on Pakes' branching process with infinite alleles mutations using a continuous-time branching process with quadratic offspring distribution are shown as well.
Biology; Biostatistics; Statistics; Physics