Difference between revisions of "Ntesfaio Week 2"

From LMU BioDB 2019
Jump to navigation Jump to search
(→‎Methods: Added to C steps)
(→‎Acknowledgements: Added table reference)
 
(43 intermediate revisions by the same user not shown)
Line 1: Line 1:
−
=Naomi Tesfaiohannes Week 2 Assignment=
 
  
−
==Protocol==
+
==Electronic Lab Notebook==
−
===Part IV. Evolution===
 
  
−
The Evolution tab uses a population size of 100 flowers that contribute to the gene pool for the next generation based on fitness.
+
===Purpose===
  
−
===Question A===
+
The purpose of the '''Evolution''' section was to explore evolving digital organisms. The evolution tab used 100 flowers that are annual. These flowers live for one year and die after producing seeds for the next generation. The flower contributes to the gene pool for the next generation and is based of fitness. All parents die and the offspring begin crossing with one another. All that this simulation focuses on is fitness.
−
Selecting for red
 
  
−
A4) Prediction: What should happen to the number of red and the number of white flowers after several generations with this selection?
+
===Methods===
  
−
By making the fitness of red the highest (10) and all other fitnesses 0 the number of red flowers should dominate and the number of white flowers should be little to none. There should definitely be no other color shown.
+
All instructions came from [[File:Tesfaiohannes_Aipotu.pdf|Aipotu Link]]
  
−
A6) Result: What happens to the counts of red and white flowers as you stimulate more generations? Roughly, how many generations does it take to get to pure red. Some all-red can still have some white offspring (why)?
+
1. Open '''Aipotu''' download
  
−
Number of white and red by generational stimulate:
+
2. Click on '''Evolution''' located on the top of the screen next to '''Molecular Biology'''
 +
 
 +
3. Turn off mutation by clicking file, preferences, mutation rate, and unchecking the '''mutations enabled checkbox'''.
 +
 
 +
A) Select for '''Red'''
 +
 
 +
A1) Click on the '''red''' and '''white''' organisms while holding down the shift button so that both are highlighted by a green box
  
−
1 stimuate: 27 white and 73 red
+
A2) Load the two by clicking on the '''"Load"''' button on the bottom left of the screen
  
−
2 stimulate: 20 white and 79 red
+
A3) Set the fitness of the red flower to 10 while making all other fitnesses 0. This is located on the top left of the screen with boxed numbers that have up and down arrows to direct whether to add or subtract the fitness of the flower. 
  
−
3 stimulate: 19 white and 81 red
+
A5) '''Test:''' Click the '''One Generation Test''' button in the bottom left of the screen. Continue doing this to observe multiple generations.
  
−
At 9 generations there were 100 red and 0 any other color. All red generations can also have white offspring since white can be autosomal recessive and if one recessive genes is taken from each parent then the recessive trait can show.
+
B) Selecting for '''White'''
  
−
===Question B===
+
B1) Click on the '''red''' and '''white''' organisms while holding the shift button so that both are highlighted by a green box
−
Selecting for White
 
  
−
B4) Prediction: What should happen to the number of red and white flowers after several generations with this selection?
+
B2) Load the two by clicking on the '''"Load"''' button on the bottom left of the screen
  
−
With the selection being white (10) and all other colors (0) the white flower has the greatest fitness and should dominate the grid.
+
B3) Set the '''fitness''' in the setting panel so that the fitness of '''white''' is 10 and all other colors are 0. The instructions to do this are similar to A3, however how the white column should have a 10.  
  
−
B6) Result: What happens to the counts of red and white flowers as you stimulate more generations? Roughly how many generations does it take to get to pure white?
+
B5) '''Test:''' Click the '''One Generation Only''' button in the bottom left of the screen. Continue doing this to observe multiple generations.
  
−
The number of white significantly increases by large amounts when selecting for white
+
Check the genotype of each flower by checking the "Show colors of both alleles" in the "World Setting" part of preferences.
  
−
With 1 stimulate there were 100 white flowers. No other color appeared. 
+
C) '''Hardy-Weinberg Equilibrium & Natural Selection'''
  
−
Why does it take more generations to get to pure red than it does to get to pure white?
+
C1) Load the world with only '''red''' organisms. The entire world should be red.
  
−
===Question C===
+
C2) Show colors of both alleles by going to '''Settings''' and selecting the designated tab '''show colors of both alleles'''.
  
−
C3) Is this population at Hardy-Weinberg Equilibrium?
+
C3) Set all fitnesses to 5.
  
−
Genotype  Number  #R's  #r's
+
C7) Run one generation only.
  
−
RR        0      0    0
+
C8) Set the fitness to select for red. Set the fitness of red to 10 and all other color's fitness to 0
  
−
Rr        100    50    50
+
C10) Click the '''one generation only''' button
  
−
rr        0      0    0
+
===Results===
 +
====Question A====
 +
Selecting for '''Red'''
  
 +
A4) '''Prediction: What should happen to the number of red and the number of white flowers after several generations with this selection?'''
  
−
Frequency of R (p): 50
+
By making the fitness of red the highest (10) and all other fitnesses 0 the number of red flowers should dominate and the number of white flowers should be little to none. There should definitely be no other color shown unless a mutation were to occur (which is not the case here since the mutation tab was disabled for this fitness test).
  
−
Frequency of r (q): 50
+
A6) '''Result: What happens to the counts of red and white flowers as you stimulate more generations? Roughly, how many generations does it take to get to pure red. Some all-red can still have some white offspring (why)?'''
  
−
C5) Calculate the genotype frequency expected at HWE:
+
Number of white and red by generational stimulate:
  
−
Frequency of RR= p^2=
+
1 stimulate: 27 white and 73 red
  
−
Frequency of Rr= pq=
+
2 stimulate: 20 white and 79 red
  
−
Frequency of rr=q^2=
+
3 stimulate: 19 white and 81 red
  
−
Is the population at HWE? Why or why not?
+
At 9 generations there were 100 red and 0 any other color. All red generations can also have white offspring since white can be autosomal recessive and if one recessive genes is taken from each parent then the recessive trait can show. Each red flowered parents can be Rr and Rr, and the offspring can take the r from both parents to be white. Throughout the generations the number of red selecting flowers increased.
  
−
C7) Run one generation only. Is the population at HWE?
+
====Question B====
 +
Selecting for '''White'''
  
−
33 white and 67 red.
+
B4) '''Prediction: What should happen to the number of red and white flowers after several generations with this selection?'''
−
 
−
RR 23
 
−
Rr 44
 
−
33 rr
 
  
−
C9) With fitness set to 10 for red what should happen to p and q?
+
With the selection being white (10) and all other colors (0) the white flower has the greatest fitness and should dominate the grid.
  
−
There should be more p than q present on the world grid
+
B6) '''Result: What happens to the counts of red and white flowers as you stimulate more generations? Roughly how many generations does it take to get to pure white?'''
  
−
C11) Result: Calculate p and q as you did in part (d)
+
The number of white significantly increases by large amounts when selecting for white.
  
−
Generation 7
+
With 1 generation stimulate there were 100 white flowers. No other color appeared. 
 +
 
 +
'''Why does it take more generations to get to pure red than it does to get to pure white?'''
 +
 
 +
With the fitness set for white, the recessive alleles (r) are more prominent to survive. Their fitness is the greatest and this allows for more pure white genotypes. When the fitness is set for red, the r allele is still included since the Rr makes a red flower with a white carrier allele. This allows for red flowers to be made, expressed by the R allele, but with the white allele present. This is why it is difficult to get pure red as the red flowers, Rr, has the potential to bring in a white flower when making offspring with another Rr. However, when selecting for white, a white flower does not have R at all, making it easier to express the r allele as dominant since it is the allele given the greatest fitness.
 +
 
 +
====Question C====
  
−
88 red and 12 white
+
C3) '''Is this population at Hardy-Weinberg Equilibrium?'''
  
 +
{|Genotype
 +
|-
 +
! Genotype
 +
! Number
 +
! #R's
 +
! #r's
 +
|-
 +
|RR
 +
|0
 +
|0
 +
|0
 +
|-
 +
|Rr
 +
|100
 +
|50
 +
|50
 +
|-
 +
|rr
 +
|0
 +
|0
 +
|0
 +
|
 +
|-
 +
|
 +
|
 +
Total =
 +
|50
 +
|50
 +
|}
  
−
Genotype  Number    #R's    #r's
+
Frequency of R (p): 50/100 or 1/2
  
−
RR        40
+
Frequency of r (q): 50/100 or 1/2
  
−
Rr        48
+
C5) '''Calculate the genotype frequency expected at HWE:'''
  
−
rr        12
+
Frequency of RR= p^2= (1/2) (1/2)= 1/4 but in this case RR genotype is 0
  
−
Frequency of R (p)=
+
Frequency of Rr= 2pq=  2(1/2)= 2/4    but in this case Rr genotype is the only one present
  
−
Frequency of r (q)=  
+
Frequency of rr=q^2=  (1/2) (1/2)= 1/4 but in this case rr genotype of 0
  
−
C12) Does the result match your prediction? Why or why not?
+
'''Is the population at HWE? Why or why not?'''
  
−
==Electronic Lab Notebook==
+
No, because the only genotype to appear was Rr. There were no RR or rr genotypes. It was assumed to be (1/4) of RR, (1/2) of Rr, and (1/4) rr. 
  
−
===Purpose===
+
C7) '''Run one generation only. Is the population at HWE?'''
  
−
The purpose of the Evolution section was to explore evolution with evolving digital organisms. The evolution tab used 100 flowers that are annual. These flowers life for one year and die after producing seeds for the next generation. The flower contributes to the gene pool for the next generation and is based of fitness. All parents die and the offspring begin crossing with one another. All that this simulation focuses on is fitness.  
+
25 white and 75 red. This is very close to Hardy Weinberg, RR being (1/4) approximately 25 flowers, Rr being (2/4) approximately 50 flowers, and rr (1/4) approximately 25 flowers. The data I collected is very close to these points as seen below.
 +
{|Genotype
 +
|-
 +
!RR
 +
!21
 +
|-
 +
!Rr
 +
!54
 +
|-
 +
!rr
 +
!25
 +
|}
  
−
===Methods===
+
I do believe this follows the Hardy Weinberg Equation.
  
−
1. Open Aipotu download
+
C9) '''With fitness set to 10 for red what should happen to p and q?'''
  
−
2. Click on evolution
+
There should be more p than q present on the world grid. Allowing for more red flowers to be produced.  
  
−
3. Turn off mutation by clicking file, preferences, mutation rate, and unchecking the mutations enabled checkbox.
+
C11) '''Result: Calculate p and q as you did in part (d)'''
  
−
A) Select for Red
+
Generation 7
  
−
A1) Click on the red and white organisms so that both are highlighted by a green box
+
88 red and 12 white
  
−
A2) Load the two by clicking on the "Load" button on the bottom left of the screen
+
{|Genotype
 +
|-
 +
! Genotype
 +
! Number
 +
! #R's
 +
! #r's
 +
|-
 +
|RR
 +
|40
 +
|40
 +
|0
 +
|-
 +
|Rr
 +
|48
 +
|24
 +
|24
 +
|-
 +
|rr
 +
|12
 +
|0
 +
|12
 +
|-
 +
|
 +
|Total =
 +
|64
 +
|36
 +
|}
  
−
A3) Set the fitness of the red flower to 10 while making all other fitnesses 0.  
+
Frequency of R (p)= 64/100 = .64
  
−
A5) Test: Click the One Generation Test button in the bottom left of the screen. Continue doing this to observe multiple generations.  
+
Frequency of r (q)= 36/100 = .36
  
−
B) Selecting for White
+
For Hardy Weinberg the equation would be:
  
−
B1) Click on the red and white organisms so that both are highlighted by a green box
+
Frequency of RR= p^2= 1/4 but in this case it is (.64) (.64)= (.04096)
  
−
B2) Load the two by clicking on the "Load" button on the bottom left of the screen
+
Frequency of Rr= 2pq=  2/4 but in this case it is (2) (.64) (.36)= (.4608)
  
−
B3) Set the fitness in the setting panel so that the fitness of white is 10 and all other colors are 0.
+
Frequency of rr=q^2=  1/4 but in this case it is (.36)(.36)= (.1296)
  
−
B5) Test: Click the One Generation Only button in the bottom left of the screen. Continue doing this to observe multiple generations.
+
C12) '''Does the result match your prediction? Why or why not?'''
  
−
Check the genotype of each flower by checking the "Show colors of both alleles" in the "World Setting" part of preferences.
+
I predicted there to be more red coding alleles when the fitness for red is set to 10 and all other fitness is set to 0. However, this does not follow the Hardy Weinburg equation because it does not follow the RR (1/4) Rr (2/4) rr (1/4) since there were 40 RR, 48 Rr, and 12 rr
  
−
C) Hardy-Weinberg Equilibrium & Natural Selection
+
===Scientific Conclusion===
  
−
C1) Load the world with only red organisms. The entire world should be red.  
+
This week's assignment supported the idea, proposed by Mendel, that the alleles of both parents being passed down to offspring (one from each parents) is what determines the offspring's trait. The purpose of the Evolution assignment was fulfilled since the purpose was to observe the different offspring traits when comparing fitness of each organism (white or red). Everything was based on fitness. Having the greatest fitness, for example when one flower would have a fitness of 10 and all other flowers had a fitness of 0, allowed for one flower to dominate and after a few generations appear as the only color available. Although, having one color does not mean it will be this way for all resulting offspring. For example, a red flower can have the genotype Rr but if two flowers with this genotype were to have an offspring it can have rr which is white. Although Rr is expressed as red it holds the allele for white.
  
−
C2) Show colors of both alleles by going to Settings and selecting the designated tab
+
==Data and Files==
  
−
C3) Set all fitnesses to 5.
+
To complete this assignment I used the method enlisted on pages 5-9 of the '''Evolution''' section [[File:Tesfaiohannes_Aipotu.pdf | Aipotu Link]]
  
−
===Results===
+
The only other Data collector I used was the Aipotu download which can be located on the website [[http://aipotu.umb.edu | Aipotu Download]]
  
 
==Acknowledgements==
 
==Acknowledgements==
  
 
My homework partner this week was Iliana Crespin. We sat together in the class periods to discuss the week 2 assignment.   
 
My homework partner this week was Iliana Crespin. We sat together in the class periods to discuss the week 2 assignment.   
 +
 +
I was unaware of how to add a table to wikipedia. To do this, I searched on wikipedia how to add a table. The wiki syntax was then read over and used for my datapoint on total genotypes. I got the wikipedia syntax from the page [[https://en.wikipedia.org/wiki/Help:Table | Wikipedia Table]].
  
 
"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
 
"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
Line 156: Line 232:
 
==Reference==
 
==Reference==
  
 +
[[Week 2]] Assignment page is: LMU BioDB 2019. (2019). Week 2. Retrieved September 10, 2019, from [[https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_2]]
 +
 +
[[Template:Ntesfaio]]
  
 
[[User:Ntesfaio]]
 
[[User:Ntesfaio]]
Line 164: Line 243:
  
 
[[Category: Journal Entry]]
 
[[Category: Journal Entry]]
 +
 +
[[Category: Shared]]

Latest revision as of 15:46, 11 September 2019

Electronic Lab Notebook

Purpose

The purpose of the Evolution section was to explore evolving digital organisms. The evolution tab used 100 flowers that are annual. These flowers live for one year and die after producing seeds for the next generation. The flower contributes to the gene pool for the next generation and is based of fitness. All parents die and the offspring begin crossing with one another. All that this simulation focuses on is fitness.

Methods

All instructions came from File:Tesfaiohannes Aipotu.pdf

1. Open Aipotu download

2. Click on Evolution located on the top of the screen next to Molecular Biology

3. Turn off mutation by clicking file, preferences, mutation rate, and unchecking the mutations enabled checkbox.

A) Select for Red

A1) Click on the red and white organisms while holding down the shift button so that both are highlighted by a green box

A2) Load the two by clicking on the "Load" button on the bottom left of the screen

A3) Set the fitness of the red flower to 10 while making all other fitnesses 0. This is located on the top left of the screen with boxed numbers that have up and down arrows to direct whether to add or subtract the fitness of the flower.

A5) Test: Click the One Generation Test button in the bottom left of the screen. Continue doing this to observe multiple generations.

B) Selecting for White

B1) Click on the red and white organisms while holding the shift button so that both are highlighted by a green box

B2) Load the two by clicking on the "Load" button on the bottom left of the screen

B3) Set the fitness in the setting panel so that the fitness of white is 10 and all other colors are 0. The instructions to do this are similar to A3, however how the white column should have a 10.

B5) Test: Click the One Generation Only button in the bottom left of the screen. Continue doing this to observe multiple generations.

Check the genotype of each flower by checking the "Show colors of both alleles" in the "World Setting" part of preferences.

C) Hardy-Weinberg Equilibrium & Natural Selection

C1) Load the world with only red organisms. The entire world should be red.

C2) Show colors of both alleles by going to Settings and selecting the designated tab show colors of both alleles.

C3) Set all fitnesses to 5.

C7) Run one generation only.

C8) Set the fitness to select for red. Set the fitness of red to 10 and all other color's fitness to 0

C10) Click the one generation only button

Results

Question A

Selecting for Red

A4) Prediction: What should happen to the number of red and the number of white flowers after several generations with this selection?

By making the fitness of red the highest (10) and all other fitnesses 0 the number of red flowers should dominate and the number of white flowers should be little to none. There should definitely be no other color shown unless a mutation were to occur (which is not the case here since the mutation tab was disabled for this fitness test).

A6) Result: What happens to the counts of red and white flowers as you stimulate more generations? Roughly, how many generations does it take to get to pure red. Some all-red can still have some white offspring (why)?

Number of white and red by generational stimulate:

1 stimulate: 27 white and 73 red

2 stimulate: 20 white and 79 red

3 stimulate: 19 white and 81 red

At 9 generations there were 100 red and 0 any other color. All red generations can also have white offspring since white can be autosomal recessive and if one recessive genes is taken from each parent then the recessive trait can show. Each red flowered parents can be Rr and Rr, and the offspring can take the r from both parents to be white. Throughout the generations the number of red selecting flowers increased.

Question B

Selecting for White

B4) Prediction: What should happen to the number of red and white flowers after several generations with this selection?

With the selection being white (10) and all other colors (0) the white flower has the greatest fitness and should dominate the grid.

B6) Result: What happens to the counts of red and white flowers as you stimulate more generations? Roughly how many generations does it take to get to pure white?

The number of white significantly increases by large amounts when selecting for white.

With 1 generation stimulate there were 100 white flowers. No other color appeared.

Why does it take more generations to get to pure red than it does to get to pure white?

With the fitness set for white, the recessive alleles (r) are more prominent to survive. Their fitness is the greatest and this allows for more pure white genotypes. When the fitness is set for red, the r allele is still included since the Rr makes a red flower with a white carrier allele. This allows for red flowers to be made, expressed by the R allele, but with the white allele present. This is why it is difficult to get pure red as the red flowers, Rr, has the potential to bring in a white flower when making offspring with another Rr. However, when selecting for white, a white flower does not have R at all, making it easier to express the r allele as dominant since it is the allele given the greatest fitness.

Question C

C3) Is this population at Hardy-Weinberg Equilibrium?

Genotype Number #R's #r's
RR 0 0 0
Rr 100 50 50
rr 0 0 0

Total =

50 50

Frequency of R (p): 50/100 or 1/2

Frequency of r (q): 50/100 or 1/2

C5) Calculate the genotype frequency expected at HWE:

Frequency of RR= p^2= (1/2) (1/2)= 1/4 but in this case RR genotype is 0

Frequency of Rr= 2pq= 2(1/2)= 2/4 but in this case Rr genotype is the only one present

Frequency of rr=q^2= (1/2) (1/2)= 1/4 but in this case rr genotype of 0

Is the population at HWE? Why or why not?

No, because the only genotype to appear was Rr. There were no RR or rr genotypes. It was assumed to be (1/4) of RR, (1/2) of Rr, and (1/4) rr.

C7) Run one generation only. Is the population at HWE?

25 white and 75 red. This is very close to Hardy Weinberg, RR being (1/4) approximately 25 flowers, Rr being (2/4) approximately 50 flowers, and rr (1/4) approximately 25 flowers. The data I collected is very close to these points as seen below.

RR 21
Rr 54
rr 25

I do believe this follows the Hardy Weinberg Equation.

C9) With fitness set to 10 for red what should happen to p and q?

There should be more p than q present on the world grid. Allowing for more red flowers to be produced.

C11) Result: Calculate p and q as you did in part (d)

Generation 7

88 red and 12 white

Genotype Number #R's #r's
RR 40 40 0
Rr 48 24 24
rr 12 0 12
Total = 64 36

Frequency of R (p)= 64/100 = .64

Frequency of r (q)= 36/100 = .36

For Hardy Weinberg the equation would be:

Frequency of RR= p^2= 1/4 but in this case it is (.64) (.64)= (.04096)

Frequency of Rr= 2pq= 2/4 but in this case it is (2) (.64) (.36)= (.4608)

Frequency of rr=q^2= 1/4 but in this case it is (.36)(.36)= (.1296)

C12) Does the result match your prediction? Why or why not?

I predicted there to be more red coding alleles when the fitness for red is set to 10 and all other fitness is set to 0. However, this does not follow the Hardy Weinburg equation because it does not follow the RR (1/4) Rr (2/4) rr (1/4) since there were 40 RR, 48 Rr, and 12 rr

Scientific Conclusion

This week's assignment supported the idea, proposed by Mendel, that the alleles of both parents being passed down to offspring (one from each parents) is what determines the offspring's trait. The purpose of the Evolution assignment was fulfilled since the purpose was to observe the different offspring traits when comparing fitness of each organism (white or red). Everything was based on fitness. Having the greatest fitness, for example when one flower would have a fitness of 10 and all other flowers had a fitness of 0, allowed for one flower to dominate and after a few generations appear as the only color available. Although, having one color does not mean it will be this way for all resulting offspring. For example, a red flower can have the genotype Rr but if two flowers with this genotype were to have an offspring it can have rr which is white. Although Rr is expressed as red it holds the allele for white.

Data and Files

To complete this assignment I used the method enlisted on pages 5-9 of the Evolution section File:Tesfaiohannes Aipotu.pdf

The only other Data collector I used was the Aipotu download which can be located on the website [| Aipotu Download]

Acknowledgements

My homework partner this week was Iliana Crespin. We sat together in the class periods to discuss the week 2 assignment.

I was unaware of how to add a table to wikipedia. To do this, I searched on wikipedia how to add a table. The wiki syntax was then read over and used for my datapoint on total genotypes. I got the wikipedia syntax from the page [| Wikipedia Table].

"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

Ntesfaio (talk) 11:44, 10 September 2019 (PDT)

Reference

Week 2 Assignment page is: LMU BioDB 2019. (2019). Week 2. Retrieved September 10, 2019, from [[1]]

Template:Ntesfaio

User:Ntesfaio

Week 2

Class Journal Week 2

Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2019/index.php?title=Ntesfaio_Week_2&oldid=1516"