Thesis

Population Genetics Using CODIS and Y-Chromosome Loci for a South India Population

Population Genetics is the study of populations using information found from genomic data which can consist of single nucleotide polymorphisms and microsatellites such as short tandem repeat. These repeats are genetically inheritable with one length of repeating DNA STRs inherited from each parental chromosome. STRs are being used in population studies to generate allele frequencies for many different nationalities. The theory is that specific alleles will be consistent within a population or nationality. This is a potential source of information about both population histories and evolutionary processes. For this population study, 220 bloodstain samples were taken from individuals living in two different communities in Southern India. DNA from these bloodstains was extracted using the chelex method. The extracted DNA was quantified using the Quantifiler® kit. Based on the information from the Quantifiler® kit, dilutions were made for each DNA extraction and amplified by PCR using the AmpFLSTR® Identifiler® and Yfiler® kits and run on a 3130 xl Genetic Analyzer. The data was genotyped using GeneMapper® ID software and the alleles were statistically analyzed to determine the genotype and allele frequencies. The results showed that the null hypothesis that the population was in Hardy-Weinberg Equilibrium cannot be rejected. There was not enough deviation between the expected and observed heterozygosity to claim that the population is evolving outside of the Hardy-Weinberg proportions. The Chi-Square test also supported this observation since it was found to be less than the critical value for this test. The inbreeding coefficient, FIS, show some inbreeding within the population but it was not high enough to say that the population was inbred. The gene diversity and genetic distance indicated that within the population there is a close genetic relationship. However, the gene diversity for the Y-chromosome showed that the population was more diverse when compared to the gene diversity of three United States’ populations consisting of African-Americans, Caucasians and Hispanics. An AMOVA test done using the Yfiler alleles showed that the South Indian population was genetically similar to the Tamil Nadu Lyengar population found in southern India.

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