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Lab 9: Population Genetics Lab objectives: 1. Review Mendelian and population genetics 2. Understand genetic drift and its interplay with natural selection 3. Consider the relevance of population genetics for conservation biology Key concepts and calculations: 1. Gene: basic functional unit of heredity, made up of DNA 2. Locus: a specific, fixed position on a chromosome where a gene is located. 3. Allele: particular form or “variant” of a gene; found at a given locus 4. Genotype: the combination of alleles present in an individual (for one gene) 5. Phenotype: the resulting trait in the organism 6. Evolution: a change in allele frequencies over time 7. Population-level analyses : How to calculate allele frequencies in a population: p = frequency of one allele q = frequency of the other allele p + q = 1 Genotype frequencies in the absence of evolution (remember Hardy-Weinberg equilibrium, assuming homozygous dominant, heterozygous, homozygous recessive): p 2 + 2pq + q 2 = 1 Phenotype frequencies (but, you must know which allele is dominant): Sum to 1 8. Genetic drift: variation in the relative frequency of different genotypes in a small population, owing to the chance disappearance of particular genes as individuals die or do not reproduce. 9. Random genetic drift is non-adaptive evolution When mating is random and there is no gene flow, no selection, and no mutation, random genetic drift can still change allele frequencies. 10. No selection = “neutral” allele (equally advantageous compared with other allele) Synonymous substitutions Negligible differences in protein function 11. Under genetic drift, allele frequency fluctuates at random, but eventually one allele becomes fixed. If one allele is fixed, the other is lost (two sides of the same coin). Probability of fixation = allele frequency Probability of loss = 1 – allele frequency Genetic drift is strongest in small populations In real populations, an interplay exists between selection and drift, depending on which is stronger. 12. Relative fitness (w) indicates how fit each genotype is, relative to the other genotypes. Activities during lab period:

1. Lecture and videos on population genetics 2. Computer simulation of drift and selection Lab exercises: Deeper discussion of key concepts, led by lab instructor One of the lab TAs has recorded a short primer on these concepts, emphasizing the relevance of genetics to conservation biology. At each stage of the exercises later in lab, try to stop and think about how the results you obtain tell you something about conservation biology of populations and species at a time of local and global environmental changes. You can watch a short lecture about population genetics here: https://youtu.be/xfy7fjpH1KA We really want you to understand several key concepts about genetic drift. If nothing else, please take away these points: ● Drift is a stochastic (i.e. random) process ● Drift is stronger in small populations ● The probability of allele fixation = initial allele frequency in the population (when there is no selection) ○ So, for example, if 25% of the people in a population have an allele (frequency of 0.25), there is a 25% probability that the allele will be fixed (or the only one present in the population). That also means that there is a 75% probability that this allele will be lost (no longer present in the population), because these are two sides of the same coin. ○ If the allele is advantageous, then positive selection will lead to a greater probability that this allele will be fixed. Watch these videos on population genetics: Genetic drift: https://www.youtube.com/watch?v=W0TM4LQmoZY Hardy-Weinberg Equilibrium: https://www.youtube.com/watch?v=7S4WMwesMts And finally, a recap of natural selection: https://www.youtube.com/watch?v=7VM9YxmULuo Computer simulation of drift and selection Conduct the simulations below on the exercise worksheet. Be sure to think about both fixation and loss. You will examine the effects of population size, initial allele frequencies, and selection. Make notes regarding the questions. Reminder: Your lab instructor is available for office hours if you have any questions, need clarification, or would like to talk through these concepts!

Exercise worksheet: Population genetics Open the webpage https://evobir.shinyapps.io/wf_model/ and complete the simulations below. You will see a graph that looks something, but not exactly, like this: What you are seeing in the graph on the right is the change in the frequency of allele A in your population over time. Each line is a separate iteration of this same simulation. They are 10 replicates, each with a different result. Time is on the x axis, and is counted in generations. The y axis is showing the frequency of allele A in the population. The scale for this is 0-1, because we are interested in the proportion of the population that has allele A. So, for example, if the frequency of allele A at generation 100 is 0.5, then 50% of the population (50 people, since we have set our n=100), will have allele A. Therefore, a frequency of 1.0 will mean the allele is fixed , and is the only version of the allele present in the population. Alternatively, a frequency of 0 means the allele is lost , and is no longer found in the population. S IMULATION 1: Two alleles are present for a particular gene. Run the simulation with all selection coefficients the same (each is 1.0) . Leave n = 100 and the initial frequency of A at 0.5. Run the simulation five times (each time, the simulation will run 100 generations for each of the 10 replicates). Each time you run the simulation, record the number of replicates where f(A) = 1 or f(A) = 0 at Generation 100. # replicates with final f(A) = 1 (fixed) # replicates with final f(A) = 0 (lost) Run 1 2 2 Run 2 2 1 Run 3 1 2 Run 4 0 0 Run 5 1 0 Do you always obtain the same result? Why? You do not always obtain the same result, because selection and genetic drift causes variability in certain

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allele frequencies, where some disappear. S IMULATION 2: Increase n to 1000 and rerun the simulation five times. What do you predict will happen? Why? # replicates with final f(A) = 1 (fixed) # replicates with final f(A) = 0 (lost) Run 1 0 0 Run 2 0 0 Run 3 0 0 Run 4 0 0 Run 5 0 0 What happened? Compare with the results of Simulation 1. No alleles were lost in this trial, and no alleles were fixed. This is reasonable because the population number has increased whereas in the first simulation, the population was smaller. Genetic drift has less of an impact on large populations, and a larger population allows for more genetic variation. S IMULATION 3: Now go back to n = 100 , but set the initial frequency of A to 0.1 . Run the simulation five times. What do you predict will happen? Why? # replicates with final f(A) = 1 (fixed) # replicates with final f(A) = 0 (lost) Run 1 0 7 Run 2 0 9 Run 3 0 6 Run 4 0 5 Run 5 0 6 What happened? Compare with the results of Simulation 1. Despite sharing the same population size of simulation 1, the variance in initial frequency of A caused the overall frequency of the generations to never rise above 40%. This inability to achieve a fixed status is solely due to the lower init. frequency, leading to an increased loss in allele A. The lower initial frequency of this simulation, caused the allele to be lost in more replicates, because it is more likely to be lost due to random chance in genetic drift S IMULATION 4: Set n = 1000 and keep the initial frequency of A at 0.1 . Run this simulation five times. What do you predict will happen? Why?

# replicates with final f(A) = 1 (fixed) # replicates with final f(A) = 0 (lost) Run 1 0 1 Run 2 0 1 Run 3 0 0 Run 4 0 0 Run 5 0 0 What happened? Compare with the results of Simulation 3. Similarly to Simulation 3, none of the replicates resulted in A being fixed. However, due to the larger population size, genetic drift (allele disappearance due to random chance) has less of an impact, and the number of replicates where A was lost decreased, and the allele remained present in the larger populations. S IMULATION 5: Now, consider that the alleles are associated with different fitnesses, allowing natural selection to act. For example, imagine two different phenotypes: one where an animal blends into its environment almost perfectly; and another where the coloration of the animal makes it easier for predators to see. Think about an example like this as you go through the following exercises. Remember to link genotype to phenotype, and phenotype to fitness. Here, set n = 100 , the initial frequency of A to 0.5 , and adjust the relative fitness so that fitness of AA = 1.0, fitness of Aa = 0.9, and fitness of aa = 0.9 . Run this simulation five times. Is this selection for or against allele A? What do you predict will happen? Why? # replicates with final f(A) = 1 (fixed) # replicates with final f(A) = 0 (lost) Run 1 10 0 Run 2 10 0 Run 3 9 0 Run 4 10 0 Run 5 10 0 What happened? Compare with Simulation 1, which had equal selection coefficients. This selection is for allele A, because the phenotype allows for blending into the environment, and thus better fitness, and it is naturally selected. The genotype AA is the most fit as it results in the most fit dominant phenotype. The results of the simulation show that 9-10 out of 10 replicates resulted in the allele being fixed, and none where it was lost. This also goes to show that even when alleles show as fixed, genetic drift and hence, genetic variability still poses as an evolutionary force. We predict that this allele will be fixed in future populations as it is selected due to causing the fittest phenotype. S IMULATION 6: Repeat the previous simulation with fitness of AA = 1.0, fitness of Aa = 0.8, and fitness of aa =

0.8 . Run the simulation five times. What do you predict will happen? Why? # replicates with final f(A) = 1 (fixed) # replicates with final f(A) = 0 (lost) Run 1 10 0 Run 2 10 0 Run 3 10 0 Run 4 10 0 Run 5 10 0 What happened? Compare with the results of Simulation 5. When lowering the Aa and aa fitness by 0.1 (to 0.8), this implies that the presence of a (in aa and Aa) decreases the fitness of the phenotype. Therefore, with A being the allele resulting in the most fit phenotype (homozygous AA). The results show an average of A being fixed in all 10 replications and thus lost in 0 replications, showing natural selection of the phenotype caused by A or Aa. After completing this lab, how do you think population size affects genetic drift? Smaller populations are more prone to a higher genetic drift and have a higher chance to to lose genetic frequency quicker than larger populations. Additionally, the fitness of an allele also contributes to how genetic drift forces can affect it, and to which degree. What is the fixation probability of an allele? The fixation probability of an allele is the probability that it it will become the only allele present in a population and be 100%. How does fitness affect the fixation probability of an allele? The higher the fitness of a specific allele, the higher the probability of that allele achieving fixation. Homework - Completed Lab manual should be uploaded to Blackboard. You can write directly on this document.

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