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Overview
Overview
In this lab we will introduce some basic information on genetics and then study the effects of genetic drift and natural selection using a computer-based simulation. Similar to our functional response lab, simulations can be used to test hypotheses about the natural world. In this lab we'll use a hands-on simulation to explore the effects of genetic drift and natural selection on the gene frequencies in a population. This lab may serve as introduction to (or replacement in case beetles don't emerge) the lab on inducing evolution in bean beetles. Much of the information is shared between the two labs.
Background
Background
For help with terms, check chapters 18-20 of Biology and chapter 11 of Concepts of Biology from OpenStax.
Objectives
Objectives
Explain the concepts of natural selection and drift, including being able to predict changes in gene frequencies due to these processes
Introduction
Introduction
Why do organisms look different from each other? And why do offspring resemble their parents? Understanding genetics provides parts of the answers to these questions.
Every somatic (body) cell in an adult (or any post-fertilization) organism contains the information that acts a blueprint for that organism; how that information is expressed determines how each cell operates. This information is carried in genes. A gene is a section of DNA that provides instructions on how to make molecules, typically proteins. Genes, along with environment, determine the traits (or phenotypes) an organism displays. Morphological, development, and behavioral traits can all be influenced by genes. Genes are located at a specific spot (a locus) on a chromosome (a long structure composed of DNA). The number of chromosomes varies among organisms. Humans have 46 total, while fruit flies have 8.
Diploid organisms, or those that are formed by the meeting of sex cells (gametes), like sperm and eggs, contain two copies of each gene (one from each parent). These genes are located on matching chromosomes (e.g,, humans have 23 pairs of chromosomes). There are often multiple forms, or versions, of a gene with-in a population. We call these forms alleles. Different versions of a gene originally arise due to mutations, or accidental changes that occur in the DNA code when a cell is replicated. If an organism receives the same allele from both parents, we consider the organism to have a homozygous genotype (genetic constitution) at that locus. If they receive different alleles from each parent, the organism is heterozygous. Unless mutations occur, genes do not change across an organism's lifespan. This also means mutations can only be passed on if they impact sex cells.
In heterozygous individuals, interactions among alleles can impact what traits organisms display. If one allele is dominant and the other is recessive, the phenotype (trait we can observe in the organism) will be the same in organisms that are heterozygous and those that are homozygous for the dominant allele (have two copies of the dominant allele). This means that traits associate with recessive alleles are only observed in organisms that are homozygous recessive (or that have two copies of the recessive allele). While the simulation we will study today focuses on a gene that only has two alleles, one being dominant and the other recessive, it should be noted that in nature most genes have multiple alleles, interactions may be more complex than simple dominance/recessiveness, and that most traits are impacted by multiple genes. Interactions among alleles explain multiple things people have observed in natural populations. For example, allele interactions can help explain why some traits appear to "skip" generations, why children can have different traits than either parents, and why some rare diseases are more common to appear in matings between closely-related individuals or in small populations.
In addition to allele interactions determining the traits we observe in organisms, some genes are only found in the chromosomes contributed by one parent. In humans, for example, the 23rd chromosome pair consists of the sex chromosomes. These chromosomes partially determine the sex of offspring. In humans males possess an X and Y chromosome, and females possess two X chromosomes. The X chromosome contains some genes that are not found on the Y chromosome. These are known as sex-linked genes, and males (with their X and Y chromosome) only have one copy of each gene. This means the allele contributed by the mother (on the X chromosome) is the only one that impacts phenotypes for some traits. This explains why some traits such as color-blindness are more common in males.
Since alleles interact to determine organismal traits, evolution can be defined as the change in allele frequency over time. The relative abundance, or frequency, of these alleles may change over generations for a variety of reasons, but they all rely on the fact that parents pass on copies of their genetic material to their offspring and that multiple forms, or alleles, exist for most genes in a population. Since genes can determine the ability of organisms to survive and reproduce (the fitness of an organism) by impacting the phenotype of organisms, genes that lead to organisms being more fit can become more common in a population through a process called natural selection. For example, if adult body mass varied in a population and the risk of predation were greater among the smallest individuals in the population, then the larger individuals would have greater survival and consequently greater reproductive success than the smaller individuals. If body mass was determined by genetic factors, or was heritable, we might expect successive populations to show larger and larger average body masses. We would call this directional selection. Besides directional selection, natural selection can also select for less variation in a trait (stabilizing selection) and for trait extremes (divergent selection).
It should be noted that evolution is a stochastic (random) process. You can't guarantee which alleles from each parent will unite in their offspring, and random events may befall any individual. However, selection tends to "favor" a certain phenotype and thus has predictable results . For example, we can predict how evolution will lead to antibiotic resistance in bacteria exposed to "fatal" levels of antibiotics.
Watch antibiotic resistance evolve | Science News
This experiment also demonstrates why bacteria are both an excellent and frightening group in which we can observe evolution. This also shows why we can define evolution as genetically-based phenotypic change that occurs over generational time spans. Both these definitions imply the importance of genetic change and that populations, not individuals, evolve.
Although natural selection is typically the most potent cause for evolution and is the principal cause for evolutionary change, other processes, such as mutation, gene flow, and genetic drift also can cause evolution (Freeman and Herron 2007). While natural selection has predictable impacts on a population, these other causes for evolution can lead to random phenotypic changes in a population. As mentioned above, mutation is the spontaneous change in the genotype of an individual that may cause a change in the phenotype of the offspring of that individual. Gene flow occurs when the frequency of an allele in a population is influenced by the movement of individuals into a population (immigration) or movement out of a population (emigration). An extreme example is when a new allele is introduced to a population. Both mutation and gene flow can introduce alleles to a population that can then be acted upon by natural selection.
The stochastic nature of evolution, however, can also lead to random changes in allele frequency over time. We call this random evolution genetic drift, and it differs from selection in that results are less predictable. These random changes tend to be larger in small populations for a number of reasons. For example, when a population contains few individuals, even random mating may result in the loss of alleles and an increased frequency of homozygous genotypes compared to populations with greater numbers (Futuyma 1986). Genetic drift is thus a form of reproductive sampling error. To the extent that random changes in genotype frequencies result in changes in phenotypes, phenotypic evolution may occur as a consequence of genetic drift. Drift can even lead to non-optimal genotypes becoming more common or even fixed (meaning only one allele is present) in a population.
Methods
Methods
You will be simulating the evolutionary processes of drift and natural selection using Virtual Biology Lab's digital fish pond (http://virtualbiologylab.org/ModelsHTML5/PopGenFishbowl/PopGenFishbowl.html). In this simulation, digital koi fish (carp) will serve as the model organism to observe these processes in action.
In this model, there are three genotypes and phenotypes for koi:
Homozygous recessive (rr) - fish are white all over
Heterozygous (Rr) - fish are mottled/white with orange spots
Homozygous dominant (RR) - fish are orange all over
You can read the Background tab from the model's homepage for review of the concepts described above.
To learn how to manipulate the parameters of the model, click on the "Tutorial" tab for instructions. Once you have finished reading the instructional pop-ups, the model will immediately begin. Right away, press "Pause" and set your parameters for the following trial.
Genetic Drift
Genetic Drift
We will first simulate genetic drift, or random change in allele frequencies, by creating a population of organisms and following it for several generations.
For the first simulation, you keep leave all parameters at their default values. Note what this means. We have a population of 200 individuals at the beginning, distributed in such a manner that the initial R allele proportion is 0.5 and the population is evenly split among males and females. The population can't go over 200 individuals (carrying capacity), and there are also default mortality (death) and brood size parameters set that should stop your population from going extinct. MIgration rate is 0, so we are dealing with a closed population. Mutation rate is 0 (alleles won't change by chance). All phenotypes have the same relative fitness (1), and no assortative mating taking place.
These conditions result in a setting where evolution (change in allele frequencies) can only occur do to chance. To see this we'll run and compare several simulations.
To begin a simulation, click the blue icon with the curved arrow (circled in red). The koi population you designed will begin moving around in their pond. Speed up time to the maximum (16x), then click on the "To Data" Arrow to watch what happens. Let it run for about 250 generations-- this will only take a few minutes. Then press pause and assess the composition of the pond.
1. What are the frequencies of the genotypes rr, Rr, and RR in your pond?
2. Look at the graph in the lower left labelled "Allele Proportion". It displays the proportion of the R allele in the population each generation. Is there any distinguishable pattern or trend in the proportion of alleles during this trial? If not, why do you think your graph looks the way it does? Take a screenshot of the graph and label it "Genetic Drift, Simulation 1".
Now run the model with the same parameters again for the same amount of time (click the blue curved arrow icon to restart the simulation; do not just continue running for another 250 generations).
3. What are the new genotype frequencies? Are they the same as your previous trial? Different? Why?
4. Take a screenshot of the "Allele Proportion" graph again and label it "Genetic Drift, Simulation 2".
Run the model with the same parameters again (click the blue curved arrow icon). Do this several times (you need to run at least 10 simulations total), saving the allele graph each time and labeling it appropriately.
5. How do the final graphs of allele proportion compare? Do you see any trends in allele proportion among or within the simulations?
Natural Selection
Natural Selection
Next we'll simulate natural selection. To do this, we'll add one small twists to our previous instructions.
Return to the Design window. You will now alter the relative fitness of the genotypes. Imagine that the homozygous recessive genotype that creates the all-white phenotype also results in less healthy fish than the other genotypes. Maybe they are more likely to be eaten by predators, or maybe they are more prone to illness.
Reduce the fitness of the rr genotype to 0.0 (extreme selection!) and run the model on maximum speed.
6. After ~250 generations, what are the frequencies of each genotype? Save an image showing the "Allele proportion" graph and label it "Natural Selection, Simulation 1"
7. Restart the simulation (click the blue curved arrow icon). Save and label the Allele proportion graph again.
8. Do this another 8 times (for 10 total trials).
Review Questions
Review Questions
9. Compare the changes in allele frequency across generations compare in the drift and selection simulations. What did you expect to happen in each? Why?
10. Why does drift have a larger impact on small populations? How could you demonstrate this in the simulation?
11. In the natural selection simulation we set the fitness of rr individuals to 0. Why does the r allele persist in the population? What would happen if selection was less extreme?
Extensions
Extensions
The simulator allows for exploration of other topics. You might want to consider
How would you model heterozygote advantage?
How does mutation impact allele frequency?
How does population size (carrying capacity) impact your findings?
How do demographic characteristics (brood size, mortality rate) impact the population over time and interact with evolutionary factor?
References
References
This lab contains information from
Blumer, L. S. and C. W. Beck. 2010. Inducing Evolution in Bean Beetles. Page(s) 25-35, in Tested Studies for Laboratory Teaching, Volume 31 (K.L. Clase, Editor). Proceedings of the 31st Workshop/Conference of the Association for Biology Laboratory Education (ABLE), 534 pages. Used with permission.
Still interested?
Still interested?
A great additional visual of how randomly genetic drift works can be found in another model here: http://udel.edu/~mcdonald/evoldrift.html
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