Question

1. Compare and contrast the methods of Principle Components Analysis vs. admixture analysis (i.e., the ADMIXTURE computer program) in the analysis of modern and ancient human DNAs. Describe the mathematical steps used to perform each of these methods, and what we can learn from the results. Why do many authors use both methods? What assumptions or limitations (if any) are required by each of these methods?

Answer 1

• In principal component analysis , the general genetic differences between the sample are taken in to account and they are plotted using techniques like single value decomposition . It also allows data reduction and forms one or more variable from large measure of mixed variables.
• In admixture analysis , using allele frequencies the data is plotted and calculated for the amounts of sharing the common ancestry .
• In admixture analysis , Hardy weinberg can be followed using the genotypes of known samples and from this genotypic frequency of unknown can be calculated.
• But in pCA , it uses allelic frequencies but shows only orthogonal projections and deviation from the principal component.
• This method shows the structure of the population but not the information about individual in the population.
• But admixture analysis calculations gives the details of the individuals in particular smaple . Hence it is more useful compared to PCA.
• Moreover the tools used in admixture analysis are flexible compared to PCA.