4. Consider the following multiple sequence alignment (spaces included for ease

Question

4. Consider the following multiple sequence alignment (spaces included for ease of reading) for the proto-insulin gene Human: ATGGCCCTGT GGATGCGCCT CCTGCCCCTG CTGGCGCTGC TGGCCCTCTG Sheep: ATGGCCATGT GGACACGCCT GGTGCCCCTG CTGGCCCTGC TGGCACTCTG Chick: ATGGCTCTAT GGACACGCCT TCTGCCTCTA CTGGCCCTGC TAGCCCTCTG a) (4pt) You are considering the Jukes-Cantor model of sequence evolution, which is a single parameter model of evolution (typically described simply as a) Given only the comparison between Human and Sheep as training data, what is vour best estimate of a? b) (3pt) Would the mutation rate be greater or less than the observed substitution rate for mammals? Why? c) (3pt) From the standpoint of constructing a phylogenetic tree, how many positions (columns) in this alignment are informative?

Explanation / Answer

In the Jukes and Cantor model, the rate of nucleotide substitution is the same for all pairs of the four nucleotides A T G C. The multiple hit correction equation for this model produces a maximum likelihood estimate of the number of nucleotide substitutions between 2 sequences. it needs an equality of substitution rates among the sites would be denoted by alpha.

The estimate of alpha between human and sheep would be C nucleotide.

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