You collect genomic data from a population of Northern red-legged frog (Rana aur

Question

You collect genomic data from a population of Northern red-legged frog (Rana aurora) from coastal California, Oregon, and Washington. The motivation of your study is to determine whether the type of selection targets specific genomic regions. You separate gene regions into three categories: introns, exons and, 5’ untranslated regions (5’UTRs). To determine whether selection is acting upon these regions, you separate each genomic region as evolving via Positive selection or Neutral selection. The following table summarizes your observed results:   

a) What is the total number of genomic regions under positive selection regardless of region?

b) What is the total number of genomic regions under neutral selection regardless of region?

c) What is the total number of introns regardless of type of selection?

d) What is the total number of exons regardless of type of selection?

e) What is the total number of 5’UTRs regardless of type of selection?

Fill in the expected results table below. Report your answers using two decimal places:

f) What is the value for cell A?

g) What is the value for cell B?

h) What is the value for cell C?

i) What is the value for cell D?

j) What is the value for cell E?

k) What is the value for cell F?

L) Provide your null and alternative hypothesis.

m) What is the sum of your X2 values or 2 calculated?

n) What are your degrees of freedom (DF) given the data?

o) What is the critical 2 value given the dataset and assuming an =0.05

p) Would you accept or reject the null hypothesis?

Explanation / Answer

a) 166

b) 103

c) 159

d) 62

e) 48

f) E(A)=(159*166)/269 = 98.12

g) E(B) = (62*166)/269 = 38.26

h) E(C) = 29.62

i) 60.88

j) 23.74

k) 18.38

l) H0: genomic regions and selections are independent

   H1 ; genomic regions and selections are not independent

m) The chi-square value = 24.23

n) df = 2 since (3-1)(2-1) = 2

o) The critical value of chi-square = 5.99

p) Here chi-square value(24.23) > chisquare critical (5.99), we reject H0

i.e. genomic regions and selections are not independent

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