We will use the on-line lab called PopGenLab, which simulates the evolution of moths.  We will perform simulations of experiments designed to study factors that can lead to changes in genotype frequency in a population resulting in population genetic changes that influence the evolution of moths. By manipulating genetic and environmental parameters that influence the genetics of these moths, you will learn about important principles of population genetics and the factors that can affect population genetics for any species.

This lab is similar to the Populus simulations that we used last time in that both use the Hardy-Weinberg principle to understand microevolutionary changes.  However, they are different in that the Populus models looked at natural selection, mutation, and genetic drift, whereas our main focus this time will be on assortative mating, migration, and population bottlenecks.

Below you will find some general introductory material on the simulation as well as the experiments we will work on. Please read these materials beforehand and submit answers to the three questions that are italicized. Your answers should be e-mailed, as usual, to your section's TA by noon, on Saturday or Sunday.  In the lab, we will see whether what you predict to happen actually occurs when we run the simulation.

Introduction

One particularly well-characterized example of natural selection in a population involves British moths called peppered moths (Biston betularia). These moths are found in two different colors or morphs. One morph has light, almost white-colored wings with small flecks of brown, while the other morph is predominantly black and brown in color. Because birds are predators of peppered moths, wing color is an important camouflage for moths. White morphs can blend well into the light, peppered appearance of lichen-colored trees.

In the early 1800s the black morph began to appear in greater frequencies in cities throughout England, particularly highly industrialized cities, while the white morph dominated populations in rural areas. The increased frequency of the black morph coincided with the industrial revolution occurring in England. It was determined that the increase in soot released from coal-burning plants killed many species of lichen growing on trees in industrialized areas of England and blackened tree bark to a much darker color than lichen-covered trees in rural areas. As a result of this pollution-induced change in the environment, white morphs became much more visible and more vulnerable to predation by birds. Black morphs began to dominate populations in industrialized areas because they were less likely to be seen and eaten by birds. In some industrialized areas, genotype frequencies for black morphs approximated 100% of the population. The selective advantage by black morphs disrupted Hardy-Weinberg equilibrium conditions for moths in industrialized areas. The story of Biston betularia is a classic case of natural selection in a population and an example of how evolution can proceed via strong selection pressures.

You will use PopGenLab to learn how changes in important parameters of population genetics can influence evolution in simulated populations of moths that resemble peppered moths. You are provided with moths living in tree stands. A single gene with two alleles controls wing color of these moths, and each genotype produces a different color pattern. Moth survival depends on the insect's ability to blend against the bark of the trees they are living in. Different tree types are provided with bark colors that match the colors of the moths in the simulation. The experiments that you set up and analyze in PopGenLab will provide you with an important understanding of the factors influencing Hardy-Weinberg equilibrium and natural selection. By varying parameters such as allele frequencies and survival rates of each genotype, population numbers, population carrying capacity, mating patterns, and the frequency of population crashes due to natural disasters, you will design experiments to help you understand how each parameter can affect evolution within the population of moths.

Experiments

Experiment 1: The Influence of Mating Patterns on Population Genetics
One of the conditions required for maintaining Hardy-Weinberg equilibrium in a population is random mating. When individuals select mates with a particular heritable trait-for example, color or size-this is a form of nonrandom mating known as assortative mating. Similarly, inbreeding is another form of nonrandom mating in which closely related individuals within a population mate. In this experiment, you will examine how different forms of mating among moths influence Hardy-Weinberg equilibrium.

1. Assortative Mating
Set up an experiment at default conditions for Hardy-Weinberg equilibrium for all parameters except the number of tree stands. Set tree stand number to 100. Carry out the first experiment with random mating. Then conduct a number of experiments where there is assortative mating. Use the slider to choose different degrees of assortative mating in values ranging from 0% (random mating) to 100% (only like phenotypes mate).

What is the effect of assortative mating on genotype frequencies? Allele frequencies? Heterozygosity? Explain your answers.

2. Disassortative Mating
Conduct a series of experiments where there is disassortative mating. Choose different degrees of disassortative mating at values between 0% (random mating) and 100% (only unlike phenotypes mate).

What is the effect of disassortative mating?

3. Genotype Frequencies and Mating Style
For both assortative and disassortative mating, conduct more experiments where you vary the initial genotype frequency. Try experiments where the initial allele frequency is not equal to 0.5.

Based on the results of these experiments, can you draw any other conclusions about the effects of assortative and dissassortative mating on allele frequency?

Experiment 2: Migration
Random genotypic and phenotypic changes in isolated populations can be overcome by migration. Both movement of organisms into a population and the migration of organisms out of a population can influence genotype frequencies. Migration can result in new alleles being introduced into a population. Conversely, when organisms migrate out of a population the frequency of certain alleles in the population can decline.

Run an experiment with a large amount of genetic drift (i.e., with very small stand size to allow only very small population size) occurring in 100 isolated populations by setting the number of stands to 100. To create migration among these populations, click on the Migration button and use the slider to change migration rate (for example, 0, 1, 5, and 20%). Design and carry out experiments where there are different levels of migration occurring among the populations. For each of these experiments, carefully study what has happened to the populations by analyzing each category of results (genotype frequency, allele frequency, allele distribution, etc.).  Make sure to compare between the average trends across all populations and the results in single populations.

Does migration modify the effects of genetic drift? If so, how? Explain.

Experiment 3: Population Bottlenecks
Occasionally populations undergo "crashes," when the population size gets too small. For example, a rapid reduction in population size can occur due to natural disasters such as flood, fire, tornadoes, drought, and other extreme weather conditions. These natural disasters are frequently unselective in nature--they kill individuals throughout the population and are not selective for a particular phenotype. Even if population numbers recover, the effect of a natural disaster can have an impact on the gene pool in a population for many generations because the range of genotypes (both frequency and number) in the population that survived the disaster may not be the same as it was in the original population. Biologists call this effect a bottleneck effect.

Conduct an experiment in which there is very little genetic drift (i.e., with large stand size to allow large population size). Repeat the experiment with moderate and high frequencies of "disasters" that reduce population numbers to small values.

What is the genetic impact of these population bottlenecks?

How do these disasters affect the probability of population extinction?

Can these effects be mitigated by allowing migration to occur among the population? Yes or no? Design and carry out experiments to examine this idea. Based on your results from these experiments, if you were a conservation biologist, what would these data suggest to you about the design of natural reserves?