BIO 211 CSULB Genetic Drift Discussion

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California State University Long Beach

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Student name _____________________________________________________ Exploring genetic drift (and other evolutionary mechanisms) using driftR driftR is a simulation that allows you to explore the effects of mutation, natural selection, migration (~gene flow), and routine genetic drift on allele frequency over time in one or more populations. Change in allele frequency over time in a population IS EVOLUTION! The basic approach to explore any one of these evolutionary mechanisms is to minimize the effects of all other mechanisms except the one you’re interested in, then adjust the strength of the one you’re interested in, simulate, adjust, simulate, etc. So, if you’re interested in exploring genetic drift, set the mutation rate and migration rate to zero, and make the fitness of all three genotypes the same as each other. Then mutation, migration, and natural selection won’t affect the outcomes. Then adjust things you think might affect genetic drift – starting allele frequency and population size, for example. Once you understand each mechanism separately, you can also explore how they interact with each other! This simulation was originally written by Joe Felsenstein and colleagues, and more recently implemented in another form by CJ Battey (both from the University of Washington). If you’re interested in the underlying math, feel free to ask me – I can send you the original reference. 2 Basic instructions on running driftR Go to this URL: https://brunopernet.shinyapps.io/driftr-master/ To run the simulation, you can just click “Run Simulation” at the top left, and the output (frequency of allele A in each population over generations) is shown in the graph to the right. What parameters can you control? Parameter Starting allele frequency Mutation rate Fitness of each genotype Migration rate Number of populations Population size Number of generations Output on the y-axis Description Starting frequency (p) of an allele (A) in a one-locus, two-allele system (like we’ve discussed in class). P must range from 0-1. The frequency of the other allele (B) is 1-p. Here you can use one starting frequency, or more separated by commas. The default is two initial frequencies. When you use more than one initial frequency, the number of populations (see below) is divided between those frequencies. E.g., if you choose 10 populations and two frequencies, 5 populations start at one frequency, and 5 at the other. This describes the rate of mutation of one allele into the other each generation. If it’s zero there is no mutation; if it’s 0.1, it means there is a 10% chance that allele A will mutate into allele a that generation (and vice versa). I think. You can set the three genotypes to each have equal relative fitness or vary them. A fitness of zero means that genotype cannot survive; 1 is the highest fitness possible. If you are simulating more than one population, you can control the amount of migration between them. Zero is no migration; 0.2 is the highest level allowable (I do not know what the units are… proportion of the population moving to other populations each generation?). Migration is symmetrical among all populations. You can simulate processes in just one population, or in many at a time. Each line on the plot will represent p in one of your populations. If you click the “legend” box near the bottom, a legend will show up to the right of the graph identifying each population as 1, 2, 3, etc. How large do you want each of the populations to be (in terms of numbers of individuals)? You can click the “infinite population” checkbox if you want to rule out genetic drift occurring in your population(s). How many generations do you want the simulation to run? I would stick with something like 100-200, since that’s a lot but still allows you to see details of what each population is doing over the generations. Once you get to 200 or more, data are too compressed on the the x-axis, in my opinion. Leave this set to p, the frequency of allele A. The other possibilities are population genetic parameters we are not discussing in Biol 211. 3 1) Basic observations of genetic drift As a start, set up driftR with a starting allele frequency of 0.5, zero mutation rate, fitness of all three genotypes=1, migration rate=0, number of populations=1, population size=100, and 200 generations. Under these conditions only genetic drift should affect allele frequencies. Run the simulation. Look at the main output window. [To make this a little less abstract, when you think of a “population,” please picture a population of your favorite eukaryote! So, for some of you this will be about xenophyophores, or gray whales, or California poppies, or horseshoe crabs, or dumbo octopus. Whatever you like.] a) What happens to the frequency of allele A over time? Does it always go up? Does it always go down? What if you run the simulation again? And again? And again? (Rather than running it over and over again you could set the number of starting populations to 5 or so. Above 5 it gets hard to track each individual population because the graph gets crowded.) b) Is the ending (after 200 generations) allele frequency in a population the same as the starting allele frequency in that population? Or is it always lower? Or always higher? How would you describe this pattern of change in words? c) After 200 generations, have any populations become fixed for allele A (that is, p=1; they’ve lost allele B), or have any populations ever lost allele A (p=0)? (The simulation keeps track of this for you: look at the “fixed/lost” counter at the bottom left of the main output window.) If you run the simulation with the settings above but for 50 populations (either run it 10 times with n=5 populations, or run it once with number of populations set to 50), what percentage of the populations are left with only one allele (A or B)? d) What is the cause of this pattern of change? Define genetic drift in your own words. 4 e) Say you start with 10 populations, all with p=0.5. Does genetic drift cause variation in allele frequency among populations to increase, or decrease? f) With the settings you’ve been using, all three genotypes have the same fitness, so we know that natural selection cannot be acting. Neither are migration or mutation. But allele frequency still seems to be changing over time. Are these populations evolving? 5 2) How does population size affect genetic drift? Set up driftR with a starting allele frequency of 0.5, zero mutation rate, fitness of all three genotypes=1, migration rate=0, number of populations=50, and 200 generations. Now… see how population size affects the magnitude of genetic drift effects! Start with small population size (say 10?) and work your way up to something bigger (maybe 100,000)? Each time you run it, keep track of the results in a table like the one below: Population size Verbal description of how much variation there is in p among the populations after 200 generations Number of populations left with only one allele (where either the A or B alleles are lost from the population) Looking at those results… a) How does population size affect the likelihood that a population will deviate from its initial allele frequency over time, just by genetic drift? b) How does population size affect the likelihood that a population will lose an allele over time just by genetic drift? This would be clearest if you graphed it, with population size on the x-axis and # of populations (or percent of the 50 initial starting populations) left with only one allele on the y-axis. You can do that by hand or using a program like Excel if you want. 6 3) How does initial allele frequency affect the chances of that allele being lost or fixed by genetic drift? Set up driftR with zero mutation rate, fitness of all three genotypes=1, migration rate=0, number of populations=50, population size=100, and 200 generations. Now… see how initial allele frequency affects the likelihood that an allele will be lost (or fixed) by drift! Start with an allele at frequency 0.1 and work your way up to 0.9. Each time you run the simulation, keep track of the results in a table like the one below: Initial p Percent of initial populations where allele A was fixed Percent of initial populations where allele A was lost Looking at those results… a) How does initial allele frequency affect the likelihood that an allele will be lost from a population just by genetic drift? Again, this might be clearest if you graph initial allele frequency on the x axis against the dependent variable of interest on the y axis.
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Explanation & Answer

Attached.

EXPLORING GENETIC DRIFT OUTLINE

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Exploring genetic drift (and other evolutionary mechanisms) using driftR
Outline
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Necessary observations of genetic drift

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What happens to the frequency of allele A overtime?

2

Is the ending allele frequency in a population the same as the starting allele frequency in that
population?

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After 200 generations, have any populations become fixed for allele A

2

What is the cause of this pattern of change? Define genetic drift in your own words.

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Say you start with ten populations, all with p=0.5. Does genetic drift cause variation in allele
frequency among populations to increase, or decrease

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With the settings you’ve been using, all three genotypes have the same fitness, so we know that
natural selection cannot be acting

3

How does population size affect genetic drift?

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How does population size affect the likelihood that a population will deviate from its initial allele
frequency over time, just by genetic drift?

4

How does population size affect the likelihood that a population will lose an allele over time just
by genetic drift?

5

How does initial allele frequency affect the chances of that allele being lost or fixed by genetic
drift?

6

EXPLORING GENETIC DRIFT OUTLINE

2

How does initial allele frequency affect the likelihood that an allele will be lost from a
population just by genetic drift?

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EXPLORING GENETIC DRIFT

1

Exploring genetic drift (and other evolutionary mechanisms) using driftR
Name

EXPLORING GENETIC DRIFT

1.

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Necessary observations of genetic drift

a. What happens to the frequency of allele A over time? Does it always go up? Does it ever
go down? What if you rerun the simulation? And again? And ...


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