Evolutionary Biology Gene Flow & Selection | Assignments Evolutionary biology

Gene Flow and Selection

Simulating Genetic Drift

Avida-ED Lab Book

Exercise 4: Exploring Population Change without Selection

Page 37

The population always begins with 9 different individual Avidians. Do you expect the

relative frequency of each descendant type to stay the same, increase, or decrease over

the course of each experimental replicate? Do you think this will be the same or different

across the different population sizes? Why? Please draw your predictions on the graph

below. You can graph your prediction for each population size on the same graph using

different types/colors of lines.

I expect the relative frequency of each descendent type to decrease over the course of each

experimental replicate because one descendant type will become more dominant over the course

of the experiment. I think this will be different across different population sizes because this may

increase the chance that more than one descendant type become more frequent.

1The population always begins with 9 different individual Avidians. Do you expect the

diversity of descendant types (number of colors) present at the end of each replicate of

300 updates to stay the same, increase, or decrease? Do you think this will be the same or

different across the different population sizes? Why?

I expect the diversity of the descendant types at the end of each replicate to decrease because one

descendent type will become more frequent than the other types. I think that each replicate will

continue to decrease in different population sizes, but more than one descendent type will

become frequent as the population size increases because with a bigger population size

1If you repeated the experiment do you think you would get the same result? Why?

I believe that if I repeated the experiment then I would get similar results but not exactly the

same results because if we repeat the experiment and get a different result, then we know that

there is something about the test that we are not considering. If we repeat the experiment

multiple times, we should get the same or similar results in order to build confidence in our

results and ensure our data is credible.

Updates Number of single

ancestral type present

(i.e. rxfl_ancestor)

for3x3dish

Number of single

ancestral type present

(i.e. rxfl_ancestor) for

9 x 9 dish

Number of single

ancestral type present

(i.e. rxfl_ancestor) for

19 x 19 dish

0 9 9 9

50 2 9 9

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Gene Flow and Selection Simulating Genetic Drift Avida-ED Lab Book Exercise 4: Exploring Population Change without Selection Page 37  The population always begins with 9 different individual Avidians. Do you expect the relative frequency of each descendant type to stay the same, increase, or decrease over the course of each experimental replicate? Do you think this will be the same or different across the different population sizes? Why? Please draw your predictions on the graph below. You can graph your prediction for each population size on the same graph using different types/colors of lines. I expect the relative frequency of each descendent type to decrease over the course of each experimental replicate because one descendant type will become more dominant over the course of the experiment. I think this will be different across different population sizes because this may increase the chance that more than one descendant type become more frequent.  The population always begins with 9 different individual Avidians. Do you expect the diversity of descendant types (number of colors) present at the end of each replicate of 300 updates to stay the same, increase, or decrease? Do you think this will be the same or different across the different population sizes? Why? I expect the diversity of the descendant types at the end of each replicate to decrease because one descendent type will become more frequent than the other types. I think that each replicate will continue to decrease in different population sizes, but more than one descendent type will become frequent as the population size increases because with a bigger population size  If you repeated the experiment do you think you would get the same result? Why? I believe that if I repeated the experiment then I would get similar results but not exactly the same results because if we repeat the experiment and get a different result, then we know that there is something about the test that we are not considering. If we repeat the experiment multiple times, we should get the same or similar results in order to build confidence in our results and ensure our data is credible. Updates Number of single ancestral type present (i.e. rxfl_ancestor) for3x3dish Number of single ancestral type present (i.e. rxfl_ancestor) for 9 x 9 dish Number of single ancestral type present (i.e. rxfl_ancestor) for 19 x 19 dish 0 9 9 9 50 2 9 9

Discussion Questions and Wrap-up. After examining the course data, work with your lab team to respond to the following questions.  How does this experimental setup test the sole influence of genetic drift on the evolution of a population? Avida Ed experimental setup allows us to test genetic drift by seeing the varying affects genetic drift has on small populations versus larger ones.  Did the same descendant types (colors) go extinct for each of your runs? The same descendant types did not go extinct for each run, it changed every time because all ancestors are equally able to adapt to the environment.  Thought experiment – How much final descendant type diversity would you expect to find if you ran your replicates of population size 361 for 10,000 more updates (i.e., a much longer time)? If the population size of 361, if replicated for 10,000 more updates then I would expect there to be only one final descendant type to be available.  What impact does genetic drift have on diversity in an evolving population? Genetic drift can impact diversity in an evolving population because it decreases diversity by making one descendant type more dominant or frequent over time.  How does population size influence the effects of genetic drift? The population size influences the effects of genetic drift because in a smaller population, there’s less diversity and in a larger population, there’s more diversity available.  Thought experiment – How would Figure 1 be different for a population of smaller size (for example, 5 organisms)? And for a much larger population size? You are able to understand that in a small size population, there is only one descendent type that becomes dominant and at a sooner rate than a larger population size which has greater diversity which allows for more than one descendent type to become more dominant or frequent and will happen in a longer time.

evolution will not be able to occur. If the NOT function occurs only after 500 updates then we would have to assume that the individual adapted and did not evolve.  When competing the evolved ancestors in each of their ancestral environments, do you predict the same ancestor will “win” (that is, contribute a greater frequency of descendants to the population) in both environments? Why or why not? When competing the evolved ancestors in each environment, I do not think the same ancestor will “win” in both environments because that specific ancestor is more adapted and evolved to the use the specific resources found in their ancestral environments and will have traits that are benefical to their specific environment. Respond to the following before proceeding to step 9:  In this environment with all resources absent, use the concept of adaptation to describe and compare the starting fitness values of each ancestor. In this environment with all resources absent, the ancestor has a higher fitness because in this environment, the ancestor has a offspring cost proportionate to its energy attainment while the notose ancestor has a high offspring cost and low energy acquisition rate making fitness low. The ancestor with no resources is better suited to this environment because it can adapt to more conditions and is not limited to one resource.  Use the concept of fitness to predict which ancestor will contribute a greater proportion of descendants to the population after 300 updates. I predict that the no resource ancestor will contribute a greater proportion of descendants to the population because the ancestor will survive better to produce more offspring. After completing Competition Treatment 1: Compare the relative frequencies of the descendants of the ancestors by observing the two colors on the Map. Does this match your prediction? Explain. The results of the experiment matched my prediction because it shows that natural selection favors one ancestor type in each environment. We saw one ancestor type with a higher frequency in each environment due to natural selection. Competition Treatment 2 – Competing ancestors when notose present. Repeat steps 1-11 of Competition Treatment 1 using the same parameters and procedures, except add notose to the environment by marking notose with a check. Respond to the following before proceeding to step 9:  In this environment with notose present, use the concept of adaptation to describe and compare the starting fitness values of each ancestor.

In the environment with notose present, the notose ancestors has a higher fitness because the energy acquisition is proportionate to the offspring cost however no resource ancestors will have a higher energy cost due to its inability to thrive in this environment.  Use the concept of fitness to predict which ancestor will contribute a greater proportion of descendants to the population after 300 updates. I predict that the notose ancestor will contribute a greater proportion of descendants to the population because the ancestor will survive better to produce more offspring. After completing Competition Treatment 2: Compare the relative frequencies of the descendants of the ancestors by observing the two colors on the Map. Does this match your prediction? Explain. The experimental test matches my prediction because it shows that natural selection favors one ancestor type in each environment. We saw one ancestor type with a higher frequency in each environment due to natural selection. How does this differ from what you observed in Competition Treatment 1? The result from this experiment is different from Competition Treatment 1 because the no resource ancestor was able to be more adapt to that environment while in this environment the notose ancestor has the advantage. Discussion Questions and Wrap-up. After examining the course data, work with your lab team to respond to the following questions.  How does this experimental setup test the influence of selection on leading to the increased frequency of certain phenotypes? This experimental setup tests the influence of selection because by observing the number of offspring produced in each environment shows the influence on the increased frequency.  On average, how does the final frequency of individuals performing NOT compare in the different environments? In environments that reward Notose, there is a higher frequency with the phenotype. In the environment where notose was present, the majority of organisms had the notose phenotype while the minority did not while in the environment with no resources, there was a 50/50 chance.  Describe a mechanism that could explain this result.

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