Question 14-3: What are the key intrinsic and technology-related limitations to

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Question 14-3: What are the key intrinsic and technology-related limitations to admixture inference and dating? Question 14-4: Discuss the benefits and limitations of admixture mapping. Question 14-5: Using the HapMap browser (http://hapmap ncbi.nlm.nih.gov/ choose Phase 1, 2, and 3 data merged) and the formula for determining admixture rate M (Section 14.3) estimte the proportion of European admixture in African Americars and Mexicans(MEX)onthebasis ofaleefrequencyden of the following two SNPs, rs1426654 and rs2227282. Forp sources consider data from the CEU, YRI, an For parental Question 14-6: Below are mtDNA and Y-chromosome haplogroup (hg) data fo Greenland, Madagascar and the Cook Islands. Use r populations from three places:

Explanation / Answer

Question 14.3 The consequences of admixture and gene flow may be difficult to distinguish because in modern populations we detect not only the proportions of admixture established when the populations first met, but the summation of cumulative gene flow from the time when they first met to the present day. Moreover, the imprint of past admixture in modern populations has also been modified by the drift, selection, and mutation processes that shape all living organisms.

While admixture at the population level can be detected in a single genetic locus, multiple loci will be required to infer admixed ancestry in a single individual.

This raises the additional complication that some alleles may have their ancestry in one parental population while other alleles have their ancestry in another. This is an inevitable consequence of sexual reproduction and diploidy.

Question 14-4. Admixture mapping is a powerful method of gene mapping for diseases or traits that show differential risk by ancestry. Admixture mapping is sensitive to ill-defined phenotypes, confounders, unknown inheritance patterns, and potential interactions between genetic and environmental risk factors.

Admixture mapping originally worked best for recent admixture, approximately <20 generations. Currently, the availability of improved methods and larger data sets allow for investigation of admixture dating back to <100 generations. Thus, resolution of admixture mapping is better than that of linkage analysis but not as good as association analysis.

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