Bustamante et al. (2005) looked at patterns of natural selection acting on protein-coding genes in the human genome. Of the 3377 genes analyzed, they found 304 (9.0%) showed evidence of rapid amino acid evolution. Here we focus on two loci from their study: SRMS and THEDC1.
a) Within SRMS, Bustamante et al. found 1 nonsynonymous site and 8 synonymous sites that differed between humans and chimpanzees. They also found 9 nonsynonymous sites within humans and 4 synonymous sites. Carry out a chi-square test (X2) of polymorphism and divergence (i.e. McDonald-Kreitman test) and interpret the result. For calculations of X2 use a critical value of 3.84. (6 marks)
b) Within THEDC1, Bustamante et al. found 14 nonsynonymous sites and 9 synonymous sites that differed between humans and chimpanzees. They also found 1 nonsynonymous site within humans and 6 synonymous sites. Carry out a chi-square test of polymorphism and divergence and interpret the result. (6 marks)
c) Given your findings in a) and b), which (if any) of SRMS and THEDC1 would have been included in the 304 genes mentioned above from Bustamante et al.’s study? Explain your reasoning. (2 marks)
d) Which of the two genes, if any, is more interesting from the perspective of adaptation? (2 marks)
Bustamante et al. (2005) looked at patterns of natural selection acting on protein-coding genes in the human genome. Of the 3377 genes analyzed, they found 304 (9.0%) showed evidence of rapid amino acid evolution. Here we focus on two loci from their study: SRMS and THEDC1.
a) Within SRMS, Bustamante et al. found 1 nonsynonymous site and 8 synonymous sites that differed between humans and chimpanzees. They also found 9 nonsynonymous sites within humans and 4 synonymous sites. Carry out a chi-square test (X2) of polymorphism and divergence (i.e. McDonald-Kreitman test) and interpret the result. For calculations of X2 use a critical value of 3.84. (6 marks)
b) Within THEDC1, Bustamante et al. found 14 nonsynonymous sites and 9 synonymous sites that differed between humans and chimpanzees. They also found 1 nonsynonymous site within humans and 6 synonymous sites. Carry out a chi-square test of polymorphism and divergence and interpret the result. (6 marks)
c) Given your findings in a) and b), which (if any) of SRMS and THEDC1 would have been included in the 304 genes mentioned above from Bustamante et al.’s study? Explain your reasoning. (2 marks)
d) Which of the two genes, if any, is more interesting from the perspective of adaptation? (2 marks)
