First
set (27 Sept):
1) Calculate whether the genotypes in [NS 01-01] show Hardy-Weinberg proportions [Use the Chi-Square Test in Box 1.3; critical values]
2) Calculate how long it would take a population with an initial f(AA) = 0.5 and f(aa) = 0.5 to reach Hardy-Weinberg proportions
3) Show that Navajo & Australian populations in the MN blood-type example exhibit Hardy-Weinberg proportions
4) Repeat the derivation of the Hardy-Weinberg proportions, using the notation f(a) = q, and f(A) = (1-q)
5) Repeat the derivation of the General Selection Model in terms of
p = p' - p
6) Repeat the derivation of the incomplete dominance selection model in terms of "p" at equilibrium
Chapter 1: 1.1, 1.2, 1.3, 1.4, 1.5, 1.6; Consider this figure & answer question 1.9*
For the HOMEWORK assignment at [http://www.mun.ca/biology/scarr/NS_03-02smc.html] :
1) Calculate whether the genotypes in [NS 01-01] show Hardy-Weinberg proportions [Use the Chi-Square Test in Box 1.3; critical values]
2) Calculate how long it would take a population with an initial f(AA) = 0.5 and f(aa) = 0.5 to reach Hardy-Weinberg proportions
3) Show that Navajo & Australian populations in the MN blood-type example exhibit Hardy-Weinberg proportions
4) Repeat the derivation of the Hardy-Weinberg proportions, using the notation f(a) = q, and f(A) = (1-q)
5) Repeat the derivation of the General Selection Model in terms of
p = p' - p6) Repeat the derivation of the incomplete dominance selection model in terms of "p" at equilibrium
Chapter 1: 1.1, 1.2, 1.3, 1.4, 1.5, 1.6; Consider this figure & answer question 1.9*
For the HOMEWORK assignment at [http://www.mun.ca/biology/scarr/NS_03-02smc.html] :
(1)
For each individual in the present (top-most) generation,
identify its Most Recent Common Ancestor coalescent with
each of the other nine individuals.
Do these MRCA coalescents included more than one individual
(2) For each of the individuals in the bottom-most generation, identify the generation in which each lineage goes extinct.
(3) Redraw the descendants of the MRCA in lineages that lead to the present: how many separate lineages are present in each generation?
Second set (14 November)
Chapter 3: 3.1, 3.3, 3.5, 3.6, 3.7, 3.8
Chapter 4: 4.1, 4.2, 4.3
Chapter 5: 5.1, 5.2, 5.3, 5.5*
Chapter 6: 6.6
Chapter 7: 7.1, 7.2, 7.3, 7.4, 7.5, 7.7, 7.9, 7.11*, 7.12,
Third set (30 November)
7) From Exercise 4.1 & 4.2 in your text:
a. In Populations 1 & 2, the genotype frequencies below are observed: Calculate FST for the two populations
b. Data from Population 3 are added: FST for the three populations: are the three populations more highly structured than the first two?
c. What is the average frequency of allele (a) in the three populations combined? 4.2
8) From Exercise 7.4 in your text: Cystic Fibrosis (CF) is a recessive disorder that is lethal in homozygotes. The occurrence of CF at birth in North Americans of European descent is 0.0004
a. What is the frequency f(cf) = q of the CF allele?
b. If the CF allele is maintained by mutation-selection equilibrium, what is the mutation rate to maintain the allele at the observed frequency?
c. If the CF allele is maintained by heterozygote advantage, and the fitness of the CF homozygote = 0.0, what are the relative fitness values of the non-CF homozygote and the heterozygote?
9) (a) Identify [circle] & count the phylogenetically Informative sites in the following data that favor each of the three hypotheses: Species A is most closely related to B, or to C, or to D.
(b) Assuming that Species A is the outgroup to the others, which two species are most closely related to each other? Explain your answer.
[ 111 111 111 122 222 222 223 333 333 333 444 444 444 455 555 555 556 666 666 666 777 777 777 788 888 888 889 ]
[ 123 456 789 012 345 678 901 234 567 890 123 456 789 012 345 678 901 234 567 890 123 456 789 012 345 678 901 234 567 890 ]
#Species_A ATG ATC AAC ATC CGA AAA ACT CAT CCA TTA GTT AAA ATT ATC AAC AAC TCA TTC ATT GAC CTT CCA ACA CCA TCA AAC ATT TCA ACA TGA
#Species_B ... .C. ... ..T ... ... T.A ..C ..C C.T A.C ... ... ..T ..T C.. ... ... ..C ..T ..A ..C G.C ... ..T ... ..C ... G.. ...
#Species_C ... .C. ... ..T ... ... T.. ..C ..G C.C A.. ... ... G.. ... G.A ... ... ..C ..T ..C ..C ..C ... ..C ... ..C ... G.. ...
#Species_D ... .C. ... ..T ... ... ... ..C ... C.. A.A ... G.. ... ... ... ... ... ..C ... ..A ... ... ... ..C ... ..C ... ... ...
[ 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 ]
[ 999 999 999 000 000 000 011 111 111 112 222 222 222 333 333 333 344 444 444 445 555 555 555 666 666 666 677 777 777 778 ]
[ 123 456 789 012 345 678 901 234 567 890 123 456 789 012 345 678 901 234 567 890 123 456 789 012 345 678 901 234 567 890 ]
#Species_A TGG AAC TTT GGG TCC CTG TTA GGA GTG TGT CTG ATC TTG CAA ATC TTA ACA GGC TTA TTT CTA GCC ATA CAC TAT ACA TCA GAT ACA GCT
#Species_B ..A ... ..C ..C ... ..T C.. ... ..C ..C ..A .C. ..A ... ... C.C ..C ... C.C ... T.G ... ... ... ..C ... ... ..C ... ATA
#Species_C ..A ... ..C ..A ..G ..A ... ... A.C ..C ..A ... ..A ..G ..T C.G ... ... C.. ... ... ... ... ... ..C ... ... ..C ... A.A
#Species_D ..A ... ... ..C ..T ..C C.C ... A.T ..C T.A ..T C.A ... ... C.G ... ... C.T ..C ... ..T ... ..T ... ... ..T ... ..C ..C
10) The graph below shows the change in the frequency of an allele subject to natural selection [use your Excel worksheets].
(a) Based in the shape of the curve, is the mode of selection
i) Highly advantageous dominant
ii) Slightly advantageous dominant
iii) Highly advantageous recessive
iv) Slightly advantageous recessive
(b) Identify the characteristics of the curve that indicate this.
11)
The table below shows the occurrence of three SNP variants
at a diploid locus.Do these MRCA coalescents included more than one individual
(2) For each of the individuals in the bottom-most generation, identify the generation in which each lineage goes extinct.
(3) Redraw the descendants of the MRCA in lineages that lead to the present: how many separate lineages are present in each generation?
Second set (14 November)
Chapter 3: 3.1, 3.3, 3.5, 3.6, 3.7, 3.8
Chapter 4: 4.1, 4.2, 4.3
Chapter 5: 5.1, 5.2, 5.3, 5.5*
Chapter 6: 6.6
Chapter 7: 7.1, 7.2, 7.3, 7.4, 7.5, 7.7, 7.9, 7.11*, 7.12,
Third set (30 November)
7) From Exercise 4.1 & 4.2 in your text:
a. In Populations 1 & 2, the genotype frequencies below are observed: Calculate FST for the two populations
b. Data from Population 3 are added: FST for the three populations: are the three populations more highly structured than the first two?
c. What is the average frequency of allele (a) in the three populations combined? 4.2
|
|
AA |
Aa |
aa |
|
Population 1 |
40 |
40 |
40 |
|
Population 2 |
30 |
30 |
60 |
|
Population 3 |
40 |
50 |
30 |
8) From Exercise 7.4 in your text: Cystic Fibrosis (CF) is a recessive disorder that is lethal in homozygotes. The occurrence of CF at birth in North Americans of European descent is 0.0004
a. What is the frequency f(cf) = q of the CF allele?
b. If the CF allele is maintained by mutation-selection equilibrium, what is the mutation rate to maintain the allele at the observed frequency?
c. If the CF allele is maintained by heterozygote advantage, and the fitness of the CF homozygote = 0.0, what are the relative fitness values of the non-CF homozygote and the heterozygote?
9) (a) Identify [circle] & count the phylogenetically Informative sites in the following data that favor each of the three hypotheses: Species A is most closely related to B, or to C, or to D.
(b) Assuming that Species A is the outgroup to the others, which two species are most closely related to each other? Explain your answer.
[ 111 111 111 122 222 222 223 333 333 333 444 444 444 455 555 555 556 666 666 666 777 777 777 788 888 888 889 ]
[ 123 456 789 012 345 678 901 234 567 890 123 456 789 012 345 678 901 234 567 890 123 456 789 012 345 678 901 234 567 890 ]
#Species_A ATG ATC AAC ATC CGA AAA ACT CAT CCA TTA GTT AAA ATT ATC AAC AAC TCA TTC ATT GAC CTT CCA ACA CCA TCA AAC ATT TCA ACA TGA
#Species_B ... .C. ... ..T ... ... T.A ..C ..C C.T A.C ... ... ..T ..T C.. ... ... ..C ..T ..A ..C G.C ... ..T ... ..C ... G.. ...
#Species_C ... .C. ... ..T ... ... T.. ..C ..G C.C A.. ... ... G.. ... G.A ... ... ..C ..T ..C ..C ..C ... ..C ... ..C ... G.. ...
#Species_D ... .C. ... ..T ... ... ... ..C ... C.. A.A ... G.. ... ... ... ... ... ..C ... ..A ... ... ... ..C ... ..C ... ... ...
[ 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 111 ]
[ 999 999 999 000 000 000 011 111 111 112 222 222 222 333 333 333 344 444 444 445 555 555 555 666 666 666 677 777 777 778 ]
[ 123 456 789 012 345 678 901 234 567 890 123 456 789 012 345 678 901 234 567 890 123 456 789 012 345 678 901 234 567 890 ]
#Species_A TGG AAC TTT GGG TCC CTG TTA GGA GTG TGT CTG ATC TTG CAA ATC TTA ACA GGC TTA TTT CTA GCC ATA CAC TAT ACA TCA GAT ACA GCT
#Species_B ..A ... ..C ..C ... ..T C.. ... ..C ..C ..A .C. ..A ... ... C.C ..C ... C.C ... T.G ... ... ... ..C ... ... ..C ... ATA
#Species_C ..A ... ..C ..A ..G ..A ... ... A.C ..C ..A ... ..A ..G ..T C.G ... ... C.. ... ... ... ... ... ..C ... ... ..C ... A.A
#Species_D ..A ... ... ..C ..T ..C C.C ... A.T ..C T.A ..T C.A ... ... C.G ... ... C.T ..C ... ..T ... ..T ... ... ..T ... ..C ..C
10) The graph below shows the change in the frequency of an allele subject to natural selection [use your Excel worksheets].
(a) Based in the shape of the curve, is the mode of selection
i) Highly advantageous dominant
ii) Slightly advantageous dominant
iii) Highly advantageous recessive
iv) Slightly advantageous recessive
(b) Identify the characteristics of the curve that indicate this.
a) Based on a Chi-Square test [use your Excel worksheet], does the distribution depart significantly from Hardy-Weinberg expectations?
b) Give the Chi-square value, degrees of freedom, and probability (p > or < 0.05) of the result
c) Calculate the inbreeding coefficient F: does the population show Wahlund Effect? Why or why not?
*d) Which SNP variant contributes most to any observed effect? Explain.
| genotype | Count |
| AA | 90 |
| AC | 90 |
| AT | 330 |
| CC | 40 |
| CT | 200 |
| TT | 250 |
Text material © 2018 by Steven M. Carr