Solved by a verified expert:M4A1: Lab Assignment: Mendelian Pigs
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Worksheet
· Complete the work sheet as you work
through SimBio lab activities.
· Type answers into the worksheet or
copy and paste from the SimBio application.
· Address all parts of each section.
You may submit bullet statements or full sentences. Keep statements short and
concise (100 words or less).
· The lab has three sections, sections
1 and 2 will each add 50 points to your lab grade. Section 3 will be evaluated
as part of the lab report M4A3.
There are
two ways to study genetics. Mendelian genetics focuses on the
rules of inheritance and the expression of an individual’s alleles. Population
genetics examines how allele frequencies change in populations. In
this lab, you’ll use both approaches to explore the genetics of coat color in
pigs and how these traits are passed down within families and through
populations.
Section 1: Breed your bacon
1.
How many generations does it take to
have pure breeding brown and black pigs in your selected pens?
2.
Summarize first back cross
experiment:
Parents
A
B
Genotype
Phenotype
Punnett
Square
Gamete A – 1
Gamete A-2
Gamete B-1
Genotype
Phenotype
Gamete B-2
Genotype
Phenotype
Summary of
outcome:
Prediction
Genotype
Phenotype
Result:
Genotype
Phenotype
3. Summarize second back cross
experiment:
4.
Parents
A
B
Genotype
Phenotype
Punnett
Square
Gamete A – 1
Gamete A-2
Gamete B-1
Genotype
Phenotype
Gamete B-2
Genotype
Phenotype
Summary of
outcome:
Prediction
Genotype
Phenotype
Result:
Genotype
Phenotype
Section 2:
Pigmented Pigs
1.
What is the difference between
eumelanin and pheomelanin?
2.
What is the role of MC1R in the
production of each type of melanin?
3.
Explain the function of the W Allele
4.
Explain the function of the B Allele
5.
Explain the function of the R Allele
6.
Explain the function of the SAllele
7.
What is a loss of function mutation and
how does loss of function of S affect coat color of pigs?
8.
What type of pigs would you cross to
produce light spotted red pigs?
Section 3
(This part
of the lab simulation will be graded as the lab report M4A2):
Going Hog Wild
In the
previous exercise (Pigmented Pigs), you used the principles of Mendelian
inheritance to make predictions about how traits would be passed down in
families of pigs based on the genotypes of the parents. In section 3, you will
make predictions about inheritance in whole populations, not just families. By
studying the genetics of populations, you will discover whether a particular trait
such as hair color can disappear over time.
1. Genes in populations
Complete the first simulation.
What is your starting allele frequency and ending allele frequency for the alleles
you chose?
Phenotype/Allele
Initial frequency
Ending frequency
Phenotype/Allele
Initial frequency
Ending frequency
You founded
the first population with a rare dominant allele and a common recessive allele,
and you looked at how allele frequencies changed over time (Qu. 37-Qu. 40).
Now consider the following questions:
How
are dominance relationships of alleles related to allele frequencies in
apopulation? That is, does knowing an allele is dominant tell you whether it
iscommon or rare? Does knowing an allele is common tell you whether it is
dominant or recessive?
Propose a hypothesis for the
questions above as well as describe how you would set up a study to test your
hypothesis. Run your experiment and save your results, you will need them later.
Hypothesis:
Experimental Design: What type
pigs are you planning to cross? How many generations?
Phenotype/Allele
Initial frequency
Ending frequency
Phenotype/Allele
Initial frequency
Ending frequency
Hypothesis Accepted/Rejected:
How does the starting
frequency of an allele affect changes in frequency for that allele over time?
Generate a hypothesis andexperiment for
this question. Make sure you keep yourresults forlater.
Hypothesis:
Experimental Design: What type
pigs are you planning to cross? How many generations?
Phenotype/Allele
Initial frequency
Ending frequency
Phenotype/Allele
Initial frequency
Ending frequency
Hypothesis Accepted/Rejected:
2. Gene frequencies for populations (Lab tutorial page 7)
Set up a population, with at least 30 pigs, that contains two alleles,
with any allele frequencies you like. Record which two alleles you use:
1. Allele (p) Frequency
#pigs:
2. Allele (q) Frequency: # pigs:
Predicted frequency after 270 months, we estimate a
population of a 1000 pigs:
1. Allele (p) Frequency: # pigs:
2. Allele (q) Frequency: # pigs:
Observed frequency after 270 months, we estimate a population
of 1000 pigs:
1. Allele (p) Frequency: # pigs:
2. Allele (q) Frequency: # pigs:
After finishing all parts of this lab simulation,
return to your results and check if the alleles for coat color were in Hardy
Wein-Berg Equilibrium at the beginning and end ofthe simulation. You will need to
compare calculated and observed allele frequencies (see lecture notes and
assigned videos) and test results by Chi-Square for significance. You find an
example at the end of this worksheet. Results will be part of lab report M4A3.
3. Hungry wolves or Will Blondes Really Disappear
(Lab Tutorial p. 12)
Predation
The
researchers also believe that so-called bottle blondes may be to blame for the
demise of their natural rivals. In terms of pigs and our simulation – this
means, certain coat colors are more vulnerable to predation.
Design and conduct an experiment(s),
using the pigs, to test whether this idea could be true.In designing your experiment,
consider which pig phenotypes to use for representing hair color genetics
in people, where bottle blonds are not naturally blond and therefore have
a hair color, like brown or black, which is dominant to blond.Also consider that being so
unattractive that you fail to find a mate is, in an evolutionary sense,
the same as being eaten by a wolf before you reach puberty. In both cases
you fail to leave descendants. So giving one color of pig a higher death
rate is equivalent to making them less attractive to mates.When you have finished your
experiment(s) and come to a conclusion, your instructor may ask you to
write this as a short scientific paper, so take notes on what you do and
the results you observe.
Hypothesis:
Set up a population, with at least 100 pigs, that contains three or more
alleles to produce the phenotypes you choose. Add to tables as needed. Record
which alleles you use:
1. Phenotype: Allele (p) Frequency: #pigs:
2. Phenotype: Allele (q)
Frequency: # pigs:
3. Phenotype: Allele (p) Frequency: #pigs:
4. Phenotype: Allele (q)
Frequency: # pigs:
Predicted frequency after 270 months, we estimate a
population of a 10000 pigs:
1. Phenotype: Allele (p) Frequency: #pigs:
2. Phenotype: Allele (q)
Frequency: # pigs:
3. Phenotype: Allele (p) Frequency: #pigs:
4. Phenotype: Allele (q)
Frequency: # pigs:
Observed frequency after 270 months, we estimate a population
of 10000 pigs:
1. Phenotype: Allele (p) Frequency: #pigs:
2. Phenotype: Allele (q)
Frequency: # pigs:
3. Phenotype: Allele (p) Frequency: #pigs:
4. Phenotype: Allele (q)
Frequency: # pigs:
Hypothesis Accepted/Rejected:
After finishing all parts of this lab simulation, return to your results
and check if the alleles for coat color were in Hardy Wein-Berg Equilibrium at
the end of the simulation. You will need to compare calculated and observed
allele frequencies (see lecture notes and assigned videos) and test results by
Chi-Square for significance. You find an example at the end of this worksheet.
Results will be part of lab report M4A3. Double check your math with the online
X-square calculator,QuickCalcs.
The alleles
and phenotypes in your virtual pigs are all found in real pigs as well. Meiying
Fang and colleagues found that wild pigs are virtually all homozygotes for
the W allele, whereas genotypes that include the B, S,
and R alleles are common among domestic pigs. Could these data
help us to determine the history of domestication of pigs?Include this
information in the discussion and conclusion of the lab report M4A3.
Resource:
Fang, M., G.
Larson, et al. 2009.Contrasting
mode of evolution at a coat color locus in wild and domestic pigs. PLoS Genetics 5:e1000341
Chi-Square
Test (Goodness of Fit)
This
statistical analysis will test if your data fit gene frequencies under expected
conditions, in this case the Hardy-Weinberg equilibrium.
The
Chi-square is calculated by the formula:
X2= ?
Observed
values are frequencies of coat color alleles in our simulation, and expected
values are the calculated values of allele frequencies based on a
Hardy-Weinberg distribution (p2 + 2pq + q2 = 1)
X2
test requires degrees of freedom, which is the number of classes of characters
-1.
For example:
Set up a population, with at least 30
pigs, that contains two alleles, with any allele frequencies you like.
Record which two alleles you use:
4. Allele (p) Frequency: 0.6 # pigs: 18
5. Allele (q) Frequency: 0.4 # pigs: 12
Predicted frequency:
Homozygotes P2: 0.36
Heterozygotes 2pq: 0.48
Homozygotes q2: 0.16
Predicted frequency after 270 months, we estimate a
population of a 1000 pigs:
3. Allele (p) Frequency: 0.6 # pigs: 600
4. Allele (q) Frequency: 0.4 # pigs: 400
Observed frequency after 270 months, we estimate a population
of 1000 pigs:
3. Allele (p) Frequency: 0.625 # pigs: 625
4. Allele (q) Frequency: 0.375 # pigs: 375
Homozygotes P2:
0.389
Heterozygotes 2pq: 0.424
Homozygotes q2: 0.14
Calculation: X2= = + = 1.04 + 1.56 = 2.6
We have two
classes (2 alleles) in our analysis, which means 1 degree of freedom. If our
Chi-square value is less than the value at the 0.05 probability level, we
accept our hypothesis.
Our X2value (2.6)
is smaller than 3.84, so our hypothesis is correct, and the population
is in Hardy-Weinberg Equilibrium.
A
Chi-Square Table
Probability
Degrees
of
Freedom
0.9
0.5
0.1
0.05
0.01
1
0.02
0.46
2.71
3.84
6.64
2
0.21
1.39
4.61
5.99
9.21
3
0.58
2.37
6.25
7.82
11.35
4
1.06
3.36
7.78
9.49
13.28
5
1.61
4.35
9.24
11.07
15.09
Reference:
GraphPad
(2016) QuickCalcs. Retrieved from http://graphpad.com/quickcalcs/chisquared1/
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