Tiffanie Begin
Spring B 2021
Bio 345: Evolution
March 16, 2021
Activity 1.1: Natural Selection of Alleles
Getting Started
-Type all your answers into this worksheet in blue text. This will make grading much
quicker.
- Download the following three model files:
Simple Birth Rates Fixation 2.0.nlogo
Simple Death Rates Fixation.nlogo
Random Mating Diploid Selection.nlogo
These are located in Canvas, where you found this same worksheet. Make sure to save
them somewhere on your computer where you can find them later (e.g. Desktop)!
- Go to the following website: https://ccl.northwestern.edu/netlogo/. Please use the
NetLogo Web version to run the simulations. You might encounter issues if you run
them on the downloaded program.
Exercise 1: Birth Rates
In the top right corner click on “Choose File” to Upload a Model. Find the Simple Birth
Rates Fixation 2.0.nlogo where you saved it and upload it to NetLogo.
Click on the “Model Info” tab at the bottom of the page to access important information
and answer the following questions about the “Birth Rates” simulation:
1. What do the red and blue colors signify? The red and the blue represent the two
populations (Blue-fertility/population of blue turtles and Red-fertility/population of
red turtles)
2. What do the triangles (a.k.a. “turtles” in simulation-speak) signify?
ANSWER: The triangles are the individuals in the populations.
(Note for myself, please disregard when grading totally for me 😊 thank you so
much!!! : This ‘turtles” is a term for the shape of the symbol that pops up in the
modeling software {this particular modeling software} or the shape of the
individuals that pop up in the model we are using/dealing with.) [This is my note
to self please disregard]
3. What does carrying capacity signify? The carrying capacity is the maximum
number of individuals in the terrain, or the maximum size of populations,
Tiffanie Begin
Spring B 2021
Bio 345: Evolution
March 16, 2021
indicating that this is the top number of individual organisms that can be
contained within this model at a time.
4. What causes turtles to “die” in the simulation? Random chance causes the turtles
to die in this simulation
5. Is it possible for a red turtle to have a higher or lower chance of dying than a blue
turtle? No because in this simulation the chance of dying is completely
randomized, so that the red and the blue have an equal chance of dying within
the simulation, and that happens once the total number of organisms has
reached the capacity for the terrain.
6. How does changing the blue-fertility slider affect the simulation?
It changes the number of offspring produced by each blue turtle in each
generation.
Let’s look at how strong the difference in birth rate has to be in a small population in
order to consistently get one population going extinct.
Set:
carrying capacity to 100
red fertility to 2.0
blue fertility to 2.1 (giving blues a 0.05 reproductive advantage).
Start the initial population to be half blue (starting-proportion-blue = 0.5)
Run an experiment (at least 10 runs) by clicking on setup, and then run-experiment
(which will run the experiment multiple times). The results of each experimental run will
pop up in the yellow textbox.
7. How many times does blue go extinct? 1:10 (1 out of 10 times, or 10% of the
time)
Now set the blue fertility to 2.01 and run an experiment (at least 10 runs). Make sure to
click the setup button after changing the blue fertility value.
**Hint: Always click the setup button before starting a new experiment or after changing
any parameters.**
8. How many times does blue go extinct? 2:10 (2 out of 10 times, or 20% of the
time)
9. Compare your results for questions 7 and 8. Are they different? Why did/didn’t
changing the fertility affect the proportion of times reds went extinct? Hint:
random number of each color die every round. Yes they are different. In
Tiffanie Begin
Spring B 2021
Bio 345: Evolution
March 16, 2021
changing the fertility from 2.10 children to 2.01 children, it made the fertility of the
blue population closer to the same number that the red population had which was
2.0. In doing so, this did change the blue fertility of the population to go extinct
10% more than in the previous experiment. When going from 10% to 1%
difference in advantage, the red still had a better chance at competition either
way however when they were at 2.10 children, they had a higher fitness
advantage than when we changed it to 2.01. Either way the red population still
had an advantage however it was more competitive since the children were
closer to the same number. Yes the models were different. When the fertility
advantage was reduced from 10% to 1%, the number of random deaths
impacted both populations more equally. When the blue fertility advantage were
higher, the impact of the random death was lower because there were more of
them to start with.
10. Refer to the definition of adaptation in CogBooks. Is higher fertility an adaptation?
Why or why not? “Adaptation is a central concept in biology. The word has two
related meanings. “Adaptation” means the evolutionary process by which, over
the course of generations, organisms are altered to become improved with
respect to features that affect survival or reproduction. “An adaptation” is
a characteristic of an organism that evolved by natural selection. Both meanings
are difficult to define precisely[1, 2]. An adaptation is a characteristic that
enhances the survival or reproduction of organisms that bear it, relative to
alternative character states.”
I believe that in this experiment that the higher fertility was not an adaptation
because we were told the populations and outcomes were completely
randomized. There were no advantages besides having a starting point for one of
the populations higher than the other. If we were told there was a mutation,
natural selection to where a trait had given one of the two populations an
advantage or even a disadvantage over the other, then I would say that I believe
the higher fertility in having an adaptation caused a significant outcome due to
the fitness (or lack there of) in one of the two populations we are experimenting
through the simulation.
Let’s examine what happens if a new advantageous allele for better fertility enters a
population, perhaps by mutation (i.e. it is initially rare). In this scenario, the original
population will be red, while the individual with the new, more advantageous allele will
be blue.
Set:
carrying capacity to 100
staring-proportion-blue to 0.01, so there is only 1 blue organism and 99 reds at
the start.
blue fertility back to 2.1
Tiffanie Begin
Spring B 2021
Bio 345: Evolution
March 16, 2021
Hit setup and run-experiment until the simulation reaches an outcome at least 10
times.
11. How many times does blue go extinct? 9:10 (9 out of 10 times, or 90% of the
time)
12. Compare your results in question 11 to your answer for question 7. Are they
different? Why did/didn’t changing the rarity of the advantageous trait affect the
proportion of times reds went extinct? Yes they are extremely different. For
question number 7, the blue went extinct 1 out of 10 times as opposed to this
time the blue population went extinct 9 out of 10 times, making a difference of
80% which is a dramatic/drastic difference. The impact of any of the individuals
with that particular trait dying when there’s only a few of you has a massive
impact as opposed to having a very large population that only a few were with
this dying trait, most likely wouldn’t impact the larger population immediately or
quickly, if it did at all (possibly wouldn’t do anything over generations, it
would/could just fade/fall off). When the fertility rate is high, that is a great
advantage, but when there is very few in the population, it makes it harder to out
compete the red population. The impact of the random deaths is much higher on
the population.
Exercise 2: Survival
In the top right corner click on “Choose File” to Upload a Model. Find the Simple Death
Rates Fixation.nlogo where you saved it and upload it to NetLogo.
So far, we have only simulated selection based on reproductive/fertility differences. But
survival is also important in natural selection. In this model, you can set the relative
survival probability of the blues compared to the reds. Note: the survival advantage only
makes an individual more likely to survive, but it does not guarantee their survival.
Click on the “Model Info” tab at the bottom of the page to access important information
about the simulation and answer the following questions:
13. Is it possible for red and blue turtles to have different fertility rates in this
simulation? No because in the model information it states that the red and blue
populations “will move around and reproduce with the same birth rates”, meaning
that the fertility rates will be the exact same thing. We are experimenting with a
focus of natural selection as opposed to birth rates.
14. Is it possible for red and blue turtles to have different likelihoods of death in this
simulation? Yes because we are using this simulation to experiment the
probabilities of advantages and disadvantages of the number of blue
organisms/individuals as opposed to the red. This variable will not be kept
Tiffanie Begin
Spring B 2021
Bio 345: Evolution
March 16, 2021
constant since this is what we are trying to experiment/observe the cause and
effects of death rates via natural selection etc.
15. What causes turtles to “die” in the simulation? The turtles in this simulation “die”
when the carrying capacity of the terrain is exceeded.
Set:
starting proportion of blues to 0.5 (half)
carrying capacity to 100
blue survival advantage to 1.1 (maximum)
Hit setup and run-experiment until the simulation reaches an outcome at least 10
times.
16. How many times does blue go extinct? 0:10 (0 out of 10 or never/it does not go
extinct at all)
Now set the blue survival advantage to 1.01, hit setup and run-experiment until the
simulation reaches an outcome at least 10 times.
17. How many times do blues go extinct? 1:10 (1 out of 10 times, or 10%)
18. Compare your results for questions 16 and 17. Are they different? Why did/didn’t
changing the survival advantage affect the proportion of times reds went extinct?
Yes they are different. When the blue survival advantage was 1.1 (the maximum)
the blues never went extinct whereas when the blues survival advantage was
changes to 1.01 (a 0.09 difference) it does create a big difference, even though it
may not seem like a big difference but going from zero/not going extinct at all to
going extinct 10% or 1 out of 10 times is a significant difference. It is not huge,
but it is definitely something you need to be aware of and take note of.
19. In both the Birth Rates and Survival simulations, the blue population many times
grew faster than the red, eventually pushing the red to extinction. Compare and
contrast how increased fertility or survival affected the way the blue population
increased in the different simulations. The increase in fertility affected the way
the blue population increased their survival in the different simulations based
upon the numbers we worked with. For example, given even the slightest change
in the survival advantage actually makes a really big deal of going from not going
extinct at all/survival rate of being 100% as opposed to changing the survival rate
from 1.10 to 1.01 (a difference of 0.09) made the survival rate of the blue
population go from 100% to 90%. Which also changed how the red population’s
survival rate was. They went extinct 100% of the time when the blue survival
advantage rate was 1.10 to their survival rate being 10% when we changed the
blue survival advantage rate to 1.01. Going from not surviving at all to at least
surviving by 10% is very significant as well. Thinking more about it, basically it is
Tiffanie Begin
Spring B 2021
Bio 345: Evolution
March 16, 2021
either going extinct or endangered are two totally different things. It is existing or
not. Even surviving the 10%, technically you could end up being the ultimate
survivor by possibly evolving and adapting by mutation, genetic drift or natural
selection etc. Who knows anything could happen, especially sometimes with the
luck of the ‘draw, whichever card you pick you may be lucky’ kind of like winning
the lotto.
Exercise 3: Random Mating
In the top right corner click on “Choose File” to Upload a Model. Find the Random
Mating Diploid Selection.nlogo where you saved it and upload it to NetLogo.
The dynamics of evolution change slightly from the previous scenarios when organisms
are diploid and may have recessive and dominant alleles. This is because different
genotypes can create the same phenotype, and phenotype is what natural selection
acts on.
In this model, you can set the fitness (i.e. offspring produced) of each genotype; AA
(red), Aa (blue), or aa (green), as well as the frequency of each genotype in the
population. This time, the colors do not represent different populations, but instead
represent different genotypes within a population. Once the population reaches carrying
capacity, random blue, red, or green turtles die.
First, we will explore how long it takes for a dominant allele with a fitness advantage to
reach fixation when it is rare.
Set:
carrying capacity to 100
starting frequency of homozygous AA to 0
starting frequency of the heterozygotes (Aa) at 0.01 frequency (this means you
are starting with just 1 A allele in the population).
fitness of aa to 1
fitness of AA and Aa to 2 so that the A allele is dominant and has a HUGE
advantage
20. If AA is set to 0, and Aa is set to 0.01, what is the frequency of aa? 0.99
Hit setup and run-experiment until the simulation reaches an outcome at least 10
times.
21. How many times does the A allele go to fixation (i.e. there are no Aa or aa
individuals left, therefore the a allele is no longer in the population)? 8:10 (8 out
of 10 or 80% of the time), apparently there had to be some in the population that
Tiffanie Begin
Spring B 2021
Bio 345: Evolution
March 16, 2021
either had the recessive allele hiding somewhere or that a mutation/genetic drift
occurred to where a recessive allele appeared.
Now set the starting heterozygote frequency to 0.1 (10%) instead of 0.01, so that the A
allele is less rare, and thus less likely to be lost due to random deaths (i.e. genetic drift –
we will learn more about genetic drift in the next module). Hit setup and run-
experiment until the simulation reaches an outcome at least 10 times.
22. How many times does A go to fixation in this case? 10:10 (10 out of 10 times, or
100%)
Compare this to when the advantageous allele is recessive.
Set:
fitness of AA to 1
fitness of Aa to 1
the fitness of aa to 2
the starting frequency of AA to 0.9
leave the starting frequency of Aa at 0.1
Hit setup and run-experiment until the simulation reaches an outcome at least 10
times.
23. How many times does the a allele go to fixation? 6:10 (6 out of 10, or 60%)
24. Compare your answers to questions 21, 22, and 23. What factors are at play that
cause the answer 21 to be more similar to 23 than 22? i.e., why does a rare
dominant allele have the same fate as a more frequent but recessive allele? If a
rare dominant allele and a recessive allele are being compared, they both are
rare in themselves. The recessive allele is 20% more likely to occur than the rare
dominant allele so that makes sense why those calculations came to be: for the
rare dominant allele it was 80%, for the recessive allele it was 60% and for the
heterozygote it was 100%. The factors at play are that the common ‘pop ups’ or
more likely to occur scenarios/alleles are what come forward more often than not,
which yet again shows with the numbers and simulation experiments.
25. Describe evolution of a trait when it is conferred by a recessive allele and when it
is conferred by a dominant allele. The evolution of a trait when it is a dominant
allele is advantageous because it is dominant so you only need one of the alleles
to have this trait passed down as opposed to the recessive allele needing two (or
both) of the alleles to be recessive since it is not dominant. It is much harder for a
recessive allele and trait to be passed down as well as expressed due to it being
recessive. For example, in a Punnett Square between a Homozygous Dominant
parent and the other parent being Heterozygous parent, the possibility of the
Tiffanie Begin
Spring B 2021
Bio 345: Evolution
March 16, 2021
outcomes of their offspring would be: 25% Homozygous Dominant, 50%
Heterozygous and 25% Homozygous Recessive.
