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Microsoft Word - big assignment 13 instructions.docx Big Assignment 13 aka pre-test for lab exam 2 Instructions 1. you are studying Snurfles (link to webpage) which follow a classic Mendelian...

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Microsoft Word - big assignment 13 instructions.docx
Big Assignment 13 aka pre-test for lab exam 2 Instructions


1. you are studying Snurfles (link to webpage)
which follow a classic Mendelian autosomal
dominant inheritance pattern for the following
two traits- Fur color and Fins:

In your
eeding experiments you perform a
dihy
id cross for Fur Color and Fins
It turns out that Snurfles are rather fecund, and in a short
span of time you have 200 offspring for which you have
tallied phenotypes as follows:

Phenotype Obs
Exp
prop*
Yellow, Finless XXXXXXXXXX
Green, Finned XXXXXXXXXX
Yellow, Finned XXXXXXXXXX
Green, Finless XXXXXXXXXX

*the expected proportions are from the Punnett square which gives a phenotype ratio of 9:3:3:1

Use the data on the “Snurfle” tab of the Excel Spreadsheet, or 01snurfle.csv, to complete the prompts
on the answer form.

2 You are investigating a new drug that might lower anxiety. The drug was shown to be safe in
humans, so now for some efficacy testing:


Twenty participants with clinical anxiety disorder are randomly assigned to one of four treatment
groups, in which they receive the listed treatment for 3 weeks. At the end of the trial, the participants
took an anxiety test. The scores, co
ected for initial anxiety score, are reported in the table below.
(Lower scores indicate lower anxiety levels.)
Control
Placebo
no Drug
Low
Dose
Moderate
Dose
XXXXXXXXXX
XXXXXXXXXX
XXXXXXXXXX
XXXXXXXXXX
XXXXXXXXXX
Analyze the data* to determine if there is any difference in anxiety scores between the groups, and if
there is a difference, determine and explain which treatment is most effective: record your responses
to the prompts on the Answer Sheet.
*Data is also available on the Excel Spreadsheet under the “Anxiety” tab, and the 02Anxiety.csv file.



3. The oceanic field cricket, Teleogryllus oceanicus are
invasive species on the Hawaiian archipelago. They
have an interesting relationship with an endemic fly
Ormea ochracea which serves as a wonderful
example of natural selection.. The male field crickets
chirp to attract their mates, however the chirping also
attracts the parasitoid fly, which would thus attack and
ultimately kill chirping males. This has led to a
dramatic shift in the chirping behavior of the crickets
esulting in, among other things, silent nights with no cricket
chirping on some of the Islands. You are on an island with
crickets that still chirp and are interested if abiotic differences
etween the islands such as temperature are inhibiting the
parasitism of crickets by the fly in some way. Determine if
there is a trend between the air temperature and the amount of
crickets chirps you hear to help find out how these cricket
populations are chirping without going extinct.

You collect the following set of data for chirp rates and temperatures throughout the island:

Temperature Chirp Rate
C Hz
31.4 20
22.0 16
XXXXXXXXXX
XXXXXXXXXX
XXXXXXXXXX
XXXXXXXXXX
XXXXXXXXXX
XXXXXXXXXX
XXXXXXXXXX
XXXXXXXXXX
26.4 15
XXXXXXXXXX
27.0 16
28.6 17
XXXXXXXXXX
Which is also available on the Excel sheet and as 03Crickets.csv
4. Crop rotation is a common strategy used to improve the
yields of certain crops in subsequent growing seasons. An
experiment was performed to assess the effects of crop
otation plant type and crop rotation plant density levels on
the yield of corn, the primary crop of interest. A field was
separated into 12 plots and each of the treatments was
andomly applied. After 2 months of growth of the rotated
crops, the plots were cleared and corn seeds were applied
evenly to each plot. After 5 months of growth of the corn,
the yields were assessed. The data, in kg/m2, are shown
elow, and is available on the Crop tab of the Excel
Spreadsheet, and the csv file 04Crops:


planting density
Rotation
Variety low medium high super
Pea XXXXXXXXXX
XXXXXXXXXX
XXXXXXXXXX3
Soy XXXXXXXXXX
XXXXXXXXXX
XXXXXXXXXX
Wheat XXXXXXXXXX
XXXXXXXXXX
XXXXXXXXXX


Determine if crop rotation plant type, crop rotation density, or a combination of both have any effect
on the yields of corn in this field. What treatment should the farmers use to maximize the yield?




















Record responses on the answer form…



5. In preparation for replicating an
experiment involving rats and beer, you
would like to use rats already on hand to
save costs, but they are of different colors,
and you are concerned that for rats natural
life span and color might not be
independent traits. To verify this, you
consult some old logs listing rat color and
life span, and assemble the following data
table:



And the data is also available on the Spreadsheet
“05Rats” tab, as well as 05Rats.csv

Complete the prompts on the answer form…



6. Read the linked paper;

L M Klevay, R J Moore, Beer mitigates some effects of copper deficiency in rats, The American Journal of
Clinical Nutrition, Volume 51, Issue 5, May 1990, Pages 869–872, https:
doi.org/10.1093/ajcn/ XXXXXXXXXX

And respond to the prompts about it on the answer form.

Then, consult the data on the Beer tab of the excel sheet

What can you conclude from that (spreadsheet) data?

Record your analysis on the answer form.
















lifespan

short medium long
own XXXXXXXXXX
white XXXXXXXXXX
grey XXXXXXXXXX
BONUS:

Create a data set and back-story for a real or fictitious biological study subject that serves as a model
for one of the following statistical tests:

Chi-Square
! Goodness of Fit
! Independence
! HOV

One Factor ANOVA
! Data with HOV
! Data that needs to be transformed

! Two Factor ANOVA

! Regression

! Co
elation

Create a data set that can be used in an exercise like, well, this one, or maybe an exam.

On the Answer form…

Exercise 13: Unit 2 summary Answers                    Name
Here are some symbols to copy and paste maybe: α β μ σ ν χ2 λ ρ Σ
1. For the Snurfles Punnett Square Dihy
id Cross:
A. What type of analysis are you performing? i.e. are you comparing one sample to a known set of parameters, comparing means of two samples, more than two samples, comparing variance ratios, etc. Is one factor, two factors? Are you testing an hypothesis of fit to a particular distribution, or looking for a relationship between groups (replace this text with your answer).
B. What type of data are you working with? i.e. measurements, counts, ratios, discreet or continuous, etc. (replace this text with your answer).
C. if you have probabilities or proportions, are they extrinsic to the data, or intrinsic, i.e. do you have to calculate them from the data or are they a ‘given’? (replace this text with your answer).
D. Which Statistical Test will you perform? i.e. χ2 GOF/Independence/HOV, One Factor ANOVA, Two Factor ANOVA, Co
elation, Regression, student’s t-Test, etc. (replace this text with your answer).
E. Conducting the Test:
Include a plot if appropriate
State the Null and Alternative Hypothesis, if appropriate
Results of pre-test, if appropriate (just test and p-value or calc vs. crit)
Copy and paste tables if appropriate
G. Results of the Test:
Test statistics, calc vs crit, p-values as appropriate.
Post-hoc tests results, if appropriate.
Include tables if appropriate.
Include Plots if appropriate.
H. Conclusion:
    What is your interpretation of the results of the tests? Provide detail! If you reject or fail to reject any null hypothesis, what does this mean in terms of the scientific question you are trying to answer? What does it mean if the observed data does or does not match the predicted?
In this case, the assumption in the Dihy
id cross is that the expected probabilities only hold true if there is a strict Dominance pattern (not co- nor incomplete), and that the two traits assort independently and segregate randomly. If the actual offspring counts do not match the expected, what does this tell us is happening (or not happening) with these traits in Snurfles?
2. For the Efficacy Study on the Anti Anxiety Drug
A. What Scientific Question are you answering with your study?
B. What type of analysis are you performing? i.e. are you comparing one sample to a known set of parameters, comparing means of two samples, more than two samples, comparing variance ratios, etc. Is one factor, two factors? Are you testing an hypothesis of fit to a particular distribution, or looking for a relationship between groups (replace this text with your answer).
C. if you have probabilities or proportions
Answered Same DayNov 30, 2021

Solution

Rajeswari answered on Dec 01 2021
50 Votes
01 Snurfles
    Snurfle Traits from Paper                    snurfle data, sorted with calculations
    Phenotype    Obs    Exp prop*            Yellow, No Fins    Yellow,Fins    Green, No Fins    Green, Fins    SUM
    Yellow, Finless    84    0.5625        observed #    84    54    40    22    200
    Green, Finned    22    0.1875        expected #    112.5    37.5    12.5    37.5    200
    Yellow, Finned    54    0.1875        contribution    7.22    7.26    60.5    6.4066666667    81.3866666667
    Green, Finless     40    0.0625
        200    1
                    Test Stats
                    calc=    81.3867
                    df=    3    g=    4    r=    1
                    α=    0.05
                    crit=    7.818
                    p-value=    1.547x10^(-17)
            *from Mendelian Genetics Dihy
id cross
            Since p < 0.05 reject H0
            The phenotypes are not distributed as per expected proportion.
Sheet4
    Anova: Single Facto
    SUMMARY
    Groups    Count    Sum    Average    Variance
    Control    5    171    34.2    23.2
    Placebo    5    144    28.8    31.7
    Low Dose    5    108    21.6    42.8
    Moderate Dose    5    47    9.4    25.8
    ANOVA
    Source of Variation    SS    df    MS    F    P-value    F crit
    Between Groups    1725    3    575    18.6234817814    0.0000180377    3.2388715224
    Within Groups    494    16    30.875
    Total    2219    19
02 Anxiety
    Adjusted Anxiety Score
    Control    Placebo    Low Dose    Moderate Dose
    32    35    18    16
    40    28    13    10
    38    34    27    3
    28    22    21    12
    33    25    29    6
Sheet1
    SUMMARY OUTPUT
    Regression Statistics
    Multiple R    0.8351437868
    R Square    0.6974651446
    Adjusted R Square    0.6741932326
    Standard E
or    0.9715177252
    Observations    15
    ANOVA
        df    SS    MS    F    Significance F
    Regression    1    28.287326358    28.287326358    29.9702553871    0.0001066719
    Residual    13    12.2700069754    0.9438466904
    Total    14    40.5573333333
        Coefficients    Standard E
or    t Stat    P-value    Lower 95%    Upper 95%    Lower 95.0%    Upper 95.0%
    Intercept    6.4724558986    1.8765289643    3.4491638667    0.0043150396    2.418461549    10.5264502481    2.418461549    10.5264502481
    C    0.3814650163    0.0696802169    5.4745096024    0.0001066719    0.2309300601    0.5319999725    0.2309300601    0.5319999725
03 Crickets
    Temperature    Chirp Rate
    C    Hz
    31.4    20
    22.0    16
    34.1    19.8
    29.1    18.4
    27.0    17.1
    24.0    15.5
    20.9    14.7
    27.8    17.1
    20.8    15.4
    28.5    16.2
    26.4    15
    28.1    17.2
    27.0    16
    28.6    17
    24.6    14.4
Hz    31.444444444444439    21.999999999999996    34.05555555555555    29.055555555555554    26.999999999999996    24    20.944444444444446    27.777777777777779    20.777777777777782    28.499999999999996    26.444444444444439    28.111111111111107    26.999999999999996    28.611111111111111    24.611111111111107    20    16    19.8    18.399999999999999    17.100000000000001    15.5    14.7    17.100000000000001    15.4    16.2    15    17.2    16    17    14.4    
Sheet2
    Anova: Two-Factor With...
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