Describe phenotypic and genotypic traits of organisms

Describe phenotypic and genotypic traits of organisms

Describe phenotypic and genotypic traits of organisms 150 150 Nyagu

Lab 4 Competition and Natural Selection Goals and Objectives At the end of this laboratory you should be able to: 1. Describe phenotypic and genotypic traits of organisms. 2. Distinguish purely genetic from purely environmental effects on phenotype. 3. Describe the three conditions for natural selection. 4. Explain the concept of relative fitness in the context of natural selection. 5. Explain how relative fitness may be influenced by the environment. 6. Explain how relative fitness may be influenced by intraspecific competition. 7. Explain how differences in relative fitness lead to differences in allelic frequencies across generations. 8. Understand how statistics can be a tool to help us analyze our data. Pre-lab Introduction for Lab 4 Read and complete the pre-lab exercise before Monday 9 a.m. of lab week. Read the rest of the lab to get a general idea of what you will be doing. This week’s lab will give you an opportunity to think about natural selection. You will be working with two forms of radish plants in the family Brassicaceae. Did you know that one plant species, ๐˜‰๐˜ณ๐˜ข๐˜ด๐˜ด๐˜ช๐˜ค๐˜ข ๐˜ฐ๐˜ญ๐˜ฆ๐˜ณ๐˜ข๐˜ค๐˜ฆ๐˜ข, has produced many of the vegetables we eat such as cauliflower, cabbage, brussel sprouts, broccoli, kohlrabi, kale, and collards? All these vegetables belong to one species, but humans have selected different lineages for particular morphologies. Cauliflower was selected for tight flower buds, whereas kale was selected for large leaves. If humans can alter morphology so drastically by artificial selection (controlling the types that are allowed to mate and the forms of the offspring that survive), are there similar processes that go on in nature? Did you know much of Darwin’s insights on natural selection came from selective breeding experiments? It seems likely that natural selection will favor morphologies different from those humans prefer–you will have a chance to see how two forms of one species differ and to decide which form is likely to predominate in nature. As you think about natural selection, you must draw on information from past labs. In lab 2, you learned some basic plant biology and what happens when plants are malnourished. In lab 3, you discovered that the growth rate of a population depends on the average birth and death rates of individuals within it. Birth and death rates are influenced by the availability of food and space in which to live. The availability of food and space is determined by the quality of the environment, but it is also affected by local population density. In this lab you will observe the effects of density on plant growth and development, and you will infer how competition is likely to affect natural selection by acting on the survival and reproduction of different genotypes. In all naturally occurring populations, individuals vary genetically (๐—ด๐—ฒ๐—ป๐—ผ๐˜๐˜†๐—ฝ๐—ฒ) and in the resulting physical expression of those genes (๐—ฝ๐—ต๐—ฒ๐—ป๐—ผ๐˜๐˜†๐—ฝ๐—ฒ). When individuals make gametes (sperm and egg if we are talking about animals), they pass some part of their genetic makeup to their offspring. The exact genetic makeup of the offspring depends on the versions of genes (๐—ฎ๐—น๐—น๐—ฒ๐—น๐—ฒ๐˜€) present in the pair of fusing gametes. The parental generation contains a range of genotypes and phenotypes. After the processes of meiosis (gamete formation) and mating, the offspring will contain different genotypes and a range of phenotypes. You can imagine this yourself. You are a product of your biological parents. You share some traits with both parents, but you are not identical to them. The same will be true at the population level. The offspring can be similar to the parental generation, but likely not identical. Then what happens if natural selection is acting on the population? What changes will result in the following generation? This is what we will explore in this lab. In a non-evolving natural population, the frequency of alleles and genotypes in the offspring generation will be the same as it was in the parental generation. In Lab 5 we will go into this in much more detail. In an evolving population, allele frequencies change across generations. The allele frequencies change because there will be variation in the number of offspring each parent has that survives to reproduce. Individuals that leave more offspring that survive to reproductive age than other individuals will have increased the frequency of their particular alleles in the next generation as compared to those who have fewer offspring. In this lab you will be studying natural selection, which is the driving force behind adaptation. Natural selection is inevitable when the possession of a particular genotype and resulting phenotype has consequences for the survival and reproduction of individuals. You will not be measuring particular allele frequencies in this lab, but you will be looking for ๐˜ท๐˜ข๐˜ณ๐˜ช๐˜ข๐˜ต๐˜ช๐˜ฐ๐˜ฏ ๐˜ช๐˜ฏ ๐˜ฑ๐˜ข๐˜ณ๐˜ฆ๐˜ฏ๐˜ต๐˜ข๐˜ญ ๐˜ค๐˜ฐ๐˜ฏ๐˜ต๐˜ณ๐˜ช๐˜ฃ๐˜ถ๐˜ต๐˜ช๐˜ฐ๐˜ฏ๐˜ด and make predictions as to what the population will look like in the next generation. In preparation for this lab, you planted radish seeds where the genetic makeup (๐—ด๐—ฒ๐—ป๐—ผ๐˜๐˜†๐—ฝ๐—ฒ) for body color was known. The genotype of each seed produces a plant of ๐˜ฆ๐˜ช๐˜ต๐˜ฉ๐˜ฆ๐˜ณ a ๐˜€๐˜๐—ฎ๐—ป๐—ฑ๐—ฎ๐—ฟ๐—ฑ white ๐—ฏ๐—ผ๐—ฑ๐˜† or a purple ๐—ฏ๐—ผ๐—ฑ๐˜†. We will be using the term “morph”, which means form, to describe the different phenotypes. And so in this case we have a purple morph and a white morph. We know something about the genetics of these plants, too. The purple morph is homozygous recessive (rr) for the gene for body color. We can depict its genotype for color as rr. The white morph is the dominant phenotype. Donโ€™t be too worried about this terminology now. We will discuss these ideas in more detail in the genetics lab. Figure 4-1 The BIG QUESTION we will try to answer in this lab is: ๐——๐—ผ๐—ฒ๐˜€ ๐—ฏ๐—ผ๐—ฑ๐˜† ๐—ฐ๐—ผ๐—น๐—ผ๐—ฟ ๐—ถ๐—ป๐—ณ๐—น๐˜‚๐—ฒ๐—ป๐—ฐ๐—ฒ ๐—ฎ ๐—ฝ๐—น๐—ฎ๐—ป๐˜’๐˜€ ability to ๐—ฟ๐—ฒ๐—ฝ๐—ฟ๐—ผ๐—ฑ๐˜‚๐—ฐe under different types of competition? If so, then alleles causing the purple morph are likely to change in frequency (increase or decrease) from generation to generation due to natural selection. What kinds of differences among plants are likely to be important? We are interested in differences that matter evolutionarily. If evolution requires a change in the frequency of alleles and genotypes from parents to offspring, then we must look for differences in performance that will cause such changes. Letโ€™s think about what this means in real terms. Is it true that there will be no evolutionary change in allele frequencies if purple and white genotypes achieve exactly the same total weight? What if they produce exactly the same number of seeds? Before you answer, consider the subtle ways in which plants may alter the ways they grow and reproduce. What if one genotype grew less and made a smaller plant but allocated more energy to flowers than the other genotypeโ€”could it still set as many seeds? What if one genotype made fewer flowers than the other and set fewer seeds, but each seed was larger than seeds of the other type and hence more likely to germinate? One genotype could produce a smaller number of relatively more vigorous offspring than the other type, couldnโ€™t it? The bottom line here is that to really assess the relative survival and reproductive value of these two parental genotypes at the body color locus, we would want to know how many offspring of each parental plant genotype will survive long enough to produce โ€œgrandchildren.โ€ By the time the grandchildren are born, we will have a good idea whether the two genotypes are making equal contributions to later generations. If they are, then neither allelic frequencies nor genotypic frequencies are expected to change from generation to generation. If they are not making equal contributions to succeeding generations, then allelic and genotypic frequencies will change and evolution is occurring. The term fitness describes the number of an individualโ€™s offspring that survive to reproduce. Thus, an individualโ€™s fitness is measured when he or she has offspring that reproduce. However, the actual number of offspring is not very importantโ€”making 100 offspring sounds like it might result in high fitness, but if every organism in the population makes 100 offspring, then producing this number offers no advantage. What matters to evolution is an individualโ€™s relative fitnessโ€”the number of its offspring that survive to reproduce (make grandchildren) in comparison to the population average (mean). If an individual has high relative fitness, then the alleles it carries will become more frequent than other alleles in the next generation. Many characteristics of plant growth, such as height, flower number, flower size, and seed size, contribute to the relative fitness of individual plants. These characters are considered components of fitness. (Note that even flowers that do not produce fruit may contribute to fitness by fertilizing other flowers with their pollen.) In one lab, we cannot follow individual plants until โ€œgrandchildrenโ€ are produced, but we can compare some components of fitness for two genetically determined body color forms or morphs of the radish. We would like you to discover whether there are costs and benefits in terms of relative fitness to possessing a particular genotype. In other words, we are asking you to look for evidence of natural selection in action. Recall the three conditions for evolution by natural selection: 1. Individuals vary with respect to phenotype. 2. Phenotypic variation is heritable. 3. Phenotypic variation results in differential reproduction (in other words, it results in differences in relative fitness among organisms). Pre-lab Questions Q1. Variation is the raw material on which natural selection can act. The two radish morphs used in this lab differ at the root color locus. List three other aspects of phenotypic variation that you might reasonably expect to see among plants: a. b. c. Q2. If a population had no phenotypic variation, why would we not expect natural selection to act on this population? Q3. Humans artificially select many kinds of plants and animals through controlled breeding programs. Why is a heritable trait crucially important for a successful breeding program? If the plant morphs you study are going to respond to natural selection, they must vary in phenotype, and this variation must be heritable. This variation must also result in differences in relative fitness among the morphs. For example, the size of leaves a plant produces could affect relative fitness by determining how much energy a particular plant collects. The amount of energy collected could affect investment in reproduction. Leaf size is measurable trait. Q4. Suggest three other measurable plant traits that could affect relative fitness and explain them briefly. a. b. c. Physiological Attributes of the Two Phenotypes In the second lab of this quarter, you spent some time thinking about resource acquisition in plants. As you recall, plants collect energy through photosynthesis by using pigments to harvest light. You may need to look back at your notes from Lab 2 in this manual, or in your text, to answer some of the questions below. Q5. What is the primary pigment that makes leaves green in land plants? Q6. There may be more than one pigment in a plant. For example, the purple morph that you will study this week has a purple coloration on its roots, and other parts. The purple color indicates the presence of the pigment anthocyanin. What does a plant gain from having more than one pigment? Q7. Develop a simple hypothesis regarding how the presence of anthocyanin affects the relative fitness of the two radish morphs. Q8. Herbivory on radish plants can induce the production of defensive chemical such as glucosinolates. For example, one effect of these chemicals is the inhibition of growth of caterpillars feeding on the plant. Do a web search to learn more about glucosinolates and describe another way in which they can provide a defense for plants against being eaten. Be sure to write the function in your own wordsโ€”do not just copy and paste from your source. Q9. A plant has to divide its energy among many different functions. Briefly outline one reason that a plant might not produce glucosinolates. Adaptations Variation among individuals arises through sexual reproduction and mutation. In sexual reproduction the processes of crossing over and independent assortment during gamete formation result in new combinations of alleles in zygotes. As the zygote becomes an organism, each new genetic combination is exposed to an environment where its relative fitness will be tested. We can think about the fitness value of the entire collection of genetic traits, or we can consider individual traits such as body color. A trait might have no effect on fitness (a neutral trait), it might have a positive effect on fitness (a beneficial trait), or a negative effect on fitness. If the trait has a consistently negative effect on fitness, then organisms possessing the trait will leave fewer offspring than others in the population, and the alleles for the trait will decline in frequency. We say this trait is โ€œselected against.โ€ If the trait has a positive effect on fitness, then organisms possessing the trait will leave more offspring than others in the population. The alleles underlying this trait will increase in frequency. We refer to a trait that increases fitness as an adaptation. Natural selection should result in a high frequency of adaptations within each population. This is the basis for what biologists often observe as a good fit between organisms and their environment. Q10. Assume that the ability to produce glucosinolates appears in 1% of the individuals in a population. Outline a situation in which the ability to produce glucosinolates would be adaptive based on analysis of the benefits and costs of glucosinolates. That is, what would result in the increase in frequency of individuals that can produce glucosinolates? Environmental Effects on the Measurement of Fitness The goal of this weekโ€™s lab is to evaluate the relative fitness of the two morphs of radish plants in different environments. A trait that results in high fitness in one environment may not confer high fitness in another environment. Each morph will be grown in three different environments (treatments): each morph will be grown alone (single plant); each morph will be grown with neighbors of its own morph (intramorph competition); and each morph will be grown with neighbors of the other morph (intermorph competition). You will have six pots of plants to study, one for each morph in each environment, as shown in Fig 4.2 below. In each pot, you will measure one target plant we call the ๐—ณ๐—ผ๐—ฐ๐—ฎ๐—น ๐—ฝ๐—น๐—ฎ๐—ป๐˜, circled in Figure 4.2. If other plants are present, they constitute the environment for the focal plant. R = white morph; r = purple morph Suppose we were interested in one of the components of fitness such as number of seeds per plant. We would measure this on the focal plant in each pot. If we replicated the planting scheme 12 times and measured 12 focal plants, we could get the average number of seeds for each morph in each environment by taking the mean of our 12 replicates for each morph in each treatment. Q11. When plants are grown with neighbors, it is possible that they will compete for resources. They can compete at the root level or the shoot level. Looking back to lab 2 if necessary, place the resources from the left side of Figure 4-3 in the boxes for the shoots or the roots depending on where competition for each is likely to occur. . Figure 4-3 ยฉ Hamamoto 2008. Used with permission There are different kinds of competition. Intraspecific competition occurs when an organism competes for resources with members of its own species. Interspecific competition occurs when an organism competes for resources with members of another species. Competition might be the most intense if an organism is competing with others who need exactly what it needs. Competition might not be intense if the needed resources are quite abundant. Figure 4-4 ยฉ Chu 2008. Used with permission Q12. In our radish experiment we do not have two species, but we do have two morphs. We know that the morphs differ genetically at the body color locus, so we could have intra-morph and inter-morph competition. In one of the treatments, each focal plant has no competition. Which treatment corresponds to which type of competition? Treatment 1: a) No competition b) intermorph competition c) intramoprh competition Treatment 2: a) No competition b) intermorph competition c) intramoprh competition Treatment 3: a) No competition b) intermorph competition c) intramoprh competition Q13. Suppose we wanted to know whether the white morph produced more seeds than the purple morph under the best possible conditions. We have data on the average number of seeds produced by each morph in each treatment. Which data set would we use? (1) the average number of seeds per plant for each morph collected from Treatment 1 (2) the average number of seeds per plant for each morph collected from Treatment 2 (3) the average number of seeds per plant for each morph collected from Treatment 3 Q14. What is the null hypothesis for the experimental test described in the question above? (1) the average number of seeds per plant for the white morph is greater than the average number of seeds for the purple morph (2) the average number of seeds per plant for the white morph is less than the average number of seeds for the purple morph (3) the average number of seeds per plant for the white morph is equal to the average number of seeds for the purple morph Q15. Suppose you wanted to test whether competition had any effect on the white morph. What is the correct null hypothesis for this experimental test? (1) the average number of seeds per white plant grown alone equals the average number of seeds per white plant when grown with neighbors (2) the average number of seeds per white plant grown alone is less than the average number of seeds per white plant when grown with neighbors (3) the average number of seeds per white plant grown with intramorph neighbors equals the average number of seeds per white plant when grown with intermorph neighbors Q16. Suppose you wanted to test whether intramorph competition was greater than intermorph competition for the standard plants. What is the correct null hypothesis for this experimental test? (1) the average number of seeds per white plant in Treatment 1 equals the average number of seeds per white plant in Treatment 2 (2) the average number of seeds per white plant in Treatment 2 equals the average number of seeds per white plant in Treatment 3 (3) the average number of seeds per white plant in Treatment 1 is greater than the average number of seeds per white plant in Treatments 2 and 3 Q17. Suggest a mechanism that would allow a plant to grow better if it had intermorph neighbors than if it had intramorph neighbors. Think about the degree of genetic similarity between the focal plant and its neighbors and make a link between genetic similarity and resource use. Q18. When biologists study natural selection they are looking for changes in genotype or allele frequencies across generations in the real world. You will see this in more detail in lab next week. However, based on the thinking you have just done about plant growth, density, and neighbors, which experimental treatment(s) is (are) most likely to give you information about relative fitness of the two …
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