Evolution, drift and selection with beads and toothpicks

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 hands-on 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

For help with terms, check chapters 18-20 of Biology and chapter 11 of Concepts of Biology from OpenStax.

Objectives

Explain the concepts of natural selection and drift, including being able to predict changes in gene frequencies due to these processes

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. Unless mutations occur, genes do not change across an organism's lifespan. 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.

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 in a population.

Genetics: Drift and Selection

Methods

Materials

styrofoam (or corkboard, anything you can push a toothpick into)
toothpicks (10)
beads (100 each of two different colors)
- the instructions below assume you have black and white beads, but any 2 colors will work
jar/beaker

Simulation Assumptions

Simulations require a clear set of assumptions to be made. While these often simplify what happens in the real world, they should also resemble the real world (or at least a part of it) so that results are useful. For our work we'll study population genetics in Betula toothpickius (toothpicks are made of birch trees from the genus Betula). We'll make the following assumptions for our simulation about these organisms:

B. toothpickius have two-part (bipartite) life cycle (like many invertebrates). The larvae live in another habitat, then they settle and metamorph to a sessile form on our styrofoam plots (this is how many marine invertebrates like oysters and mussels operate).
The settlement phase represents a limit on population growth for the species. B. toothpickius adults are space-limited , and our plots can only hold 10 organisms. The 10 that land on the plot and metamorph are a random subset of the larvae from the existing environment.
After metamorphing, B. toothpickius advance through a juvenile phase to an adult phase. They then release a lot of gametes (sperm and eggs) into the surrounding environment and die (they are semelparous!). The gametes combined to form larvae that are retained locally (this is important, as it connects genetic frequencies across generations!) . The space adults occupied is immediately available for colonization by new larvae of the species.
For our experiments we will only focus on a single gene. There are two alleles for this gene. We will represent this by placing two beads on each toothpick. For demonstration we will assume you are using black and white beads, but any two colors will work!
One allele is dominant over the other. Remember, this means we get a dominant phenotype in individuals that only have the dominant allele (homozygous dominant) and that have an allele/bead of each color (heterozygous). For demonstration we will assume black beads represent the dominant allele.

Genetic Drift

We will first simulate genetic drift, or the chance changes in gene frequencies, by making a small population of organisms and following it for several generations. Drift can occur in populations of any size but it has the largest impact on small populations, so our plot of 10 organisms is a good start.

We'll start our simulation by placing 10 toothpicks into our Styrofoam plots. These are our adult B. toothpickius. We will determine the genotype of these individuals by randomly selecting two beads to place on them. To simulate the large larval pool these 10 adults may have come from (and that previous generations produced), place 50 white beads and 50 black beads in a jar. Mix them up, and then randomly select and place two beads on each toothpick. This represents the space limitation we noted above. The large larval pool has been pared down to only 10 individuals that will eventually produce the next generation by chance selection.

Now count the number of black and white beads you see on adults. Record these observation as the # of black and white beads on adults for generation 1 on the Genetic Drift Data Sheet (you'll need to download this or make a copy in Google sheets to enter data!). Next, we'll find the frequency of black and white beads in the population. In Hardy-Weinberg terms, we can call rename these frequencies as p (proportion of black beads) and q (proportion of white beads). To find these frequencies, divide the number of beads you observed for a given color by the total number of beads (20!). The final answer must be between 0 and 1. The provided spreadsheet checks the calculations for you in the yellow cells!

Next, we'll simulate the gametes these adults would have produced. Since gametes should reflect the gene frequencies of the adults they come from, empty your current larval pool (jar of beads). Many invertebrates produce lots (in the thousands or millions of gametes), but we'll limit our larval pool to 100 gametes. Since gametes (eggs or sperm) are haploid, we can represent them with a single bead. To do this, place a 100 beads total back in the jar so that they reflect the current frequency of each allele in the adult population. For an example, if you had 9 adult black beads, p = .45 (9/20), and the number of black beads you should add to the new larval pool is 45 (.45 * 100).

Finally, end generation one by letting the current adults die. Remove the toothpicks from the plot and place their beads back in with the extra beads (not the larval pool). You have just ended round 1 of your simulation.

Now repeat this for 9 more rounds. For each round, place 10 toothpicks back on the plot, randomly select two beads from the larval pool you created at the end of the last round to place on the toothpicks. We are effectively skipping the larval phase by doing this, and also assuming there is no difference in settlement probability based on genotype. After "making" your adults, calculate the p and q frequencies, make a new larval pool that matches these proportions, and then kill the adults.

After completing this exercise, graph how p changes over time. What do you expect or notice?

Genetic Drift Data Sheet

Natural Selection

Next we'll simulate natural selection. To do we'll add one small twist to our previous instructions. We'll assume that homozygous recessive individuals (those with 2 white beads) manifest a lethal mutation after they have metamorphed into adults. How do you think this will impact q (the frequency of white beads) over time?

We'll once again start our simulation by placing 10 toothpicks into our Styrofoam plots. We will again determine the genotype of these initial individuals by randomly selecting two beads to place on them from a jar that has 50 white beads and 50 black beads.

Here's the twist: After you "create" your adults, immediately remove any that have two white beads. These individuals die before reproducing and thus can't contribute to the next generation.

Now count the number of black and white beads you see on adults. Record these observation as the # of black and white beads on adults for generation 1 on the Natural Selection Data Sheet (you'll need to download this or make a copy in Google sheets to enter data!). Next, we'll find the frequency of black and white beads in the population. In Hardy-Weinberg terms, we can call rename these frequencies as p (proportion of black beads) and q (proportion of white beads). To find these frequencies, divide the number of beads you observed for a given color by the total number of beads remaining in the population during reproduction (20 - the beads you removed due to homozygous individuals). The final answer must be between 0 and 1. Round it to two decimal places sot the provided spreadsheet can check the calculations for you in the yellow cells!

Next, we'll simulate the gametes these adults would have produced. Since gametes should reflect the gene frequencies of the adults they come from, empty your current larval pool (jar of beads). Many invertebrates produce lots (in the thousands or millions of gametes), but we'll limit our larval pool to 100 gametes. Since gametes (eggs or sperm) are haploid, we can represent them with a single bead. To do this, place a 100 beads total back in the jar so that they reflect the current frequency of each allele in the adult population. For an example, if you had 10 adult black beads and 6 adult white beads, p = 10/16 = .625, and the number of black beads you should add to the new larval pool is 63 (.625 *100, rounded to the nearest whole number).

After completing this exercise, graph how p changes over time. What do you expect or notice?

Natural Selection Data Sheet

Review Questions

Compare the changes in p across generations in the drift and selection simulations. What did you expect to happen in each? Why?
Why does drift have a larger impact on small populations? Relate your answer to the simulations you performed.
How could you incorporate mutations into your simulation?

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.

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