Populations living at high altitudes have to overcome many physiological challenges such as hypoxia (reduced oxygen
Homework #8 BICD 100 Fall 2022 4. Populations living at high altitudes have to overcome many physiological challenges such as hypoxia (reduced oxygen). Researchers conducted a GWAS to try and identify the genetic mechanisms of high-altitude adaptation, sampling over 3,008 individuals from a high-altitude Tibetan population, and 7,287 people living at lower altitudes that were of Eastern Asian ancestry (Figure 1). Additional studies were conducted and are described below (Table 1). Analyze the data and answer the questions below. 10 -log .(P -value) Figure 1. Manhattan plot of GWAS comparing high-altitude Tibetans to low-altitude population. The horizonal line indicates a significance threshold. Table 1. A haplotype near the SNP cluster on chromosome 2 was identified. The haplotype consists of a SNP in the EPSA1 promoter, and an insertion/deletion allele upstream of the promoter. Haplotype A is the C allele fo the SNP and an insertion 742 basepairs upstream of the start of transcription site for EPSA1. The B haplotype has a G allele of the SNP, and lacks the insertion. EPSA1 codes for a transcription factor. Below is a summary of experiments and data collected regarding these haplotypes. Birth weight has been previously shown to be correlated to infant survival (higher birthweights correlated with greater survival). Measurement Haplotype A Haplotype B Haplotype frequency in high altitude 0.591 0.346 population Haplotype frequency in low altitude 0.013 0.847 population @2022 MCDONNELL, UC SAN DIEGO, DO NOT COPY OR DISTRIBUTE WITHOUT PERMISSION 5
Homework #8 BICD 100 Fall 2022 Expression level of EPSA1 in cell culture* 2.5* * 1.1 Mean birth weight (10 individuals) 3500 grams* * 3000 grams *Human cell cultures that contained cells that either had haplotype A or haplotype B (otherwise considered the same at all other loci). Expression (mRNA) levels of EPSA1 were then measured. Levels are normalized to a control culture expressing another variant of the haplotype. **p<0.01 from statistical test comparing results from haplotype A to haplotype B. A. Indicate if each claim can be supported by the data above, and provide an explanation. Be sure to refer to and explain how the data supports or does not support the claim. If not supported, indicate what data would be needed in order to support. Claim Does data Explain (should be correct and complete with support? respect to the data provided above) 1: Genetic variations of Yes multiple loci are correlated with high altitude No adaptation. Partially 2: Haplotype A causes Yes increased expression of EPSA1. No Partially 3: Reduced expression of Yes EPSA1 causes reduced hypoxia tolerance in the No low altitude population. Partially 4: Genetic variations on Yes chromosome 2 are correlated to increased No fitness (survival). @ 2022 MCDONNELL, UC SAN DIEGO, DO NOT COPY OR DISTRIBUTE WITHOUT PERMISSION 6
Homework #8 BICD 100 Fall 2022 Partially B. Brainstorm: Although haplotype A and B are found in a variety of human populations, the frequencies of them vary among populations. Why might the difference in frequency of haplotype A and B in the two populations be considered an adaptation (note that a genetic adaptation is defined in a change in allele frequency as a result of selective pressure)? Explain in 2-3 sentences. C. Brainstorm: Other high-altitude populations from different parts of the world were found to have different haplotypes (consisting of different loci). Why might there be different haplotypes between high-altitude populations from geographically different areas, despite both living at high altitude? Explain in 1-2 sentences. @2022 MCDONNELL, UC SAN DIEGO, DO NOT COPY OR DISTRIBUTE WITHOUT PERMISSION 7
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