Questions for Biodiversity II Lab and Cladogram Worksheet

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After viewing the four organisms in Exercise 1 and completing Exercise 2, now it is time to draw some conclusions. Answer the following questions. You also have the cladogram activity found after these questions to complete. Submit ONE Word or PDF file in Canvas BEFORE lab next week. ALL ANSWERS ARE INDIVIDUAL REPSONSES. No incomplete sentences or one-word answers. Exercise 1: A) Locomotion Have the four organisms evolved novel mechanisms for locomotion? What is the basis for your conclusion? B) Gas exchange Compare and contrast the gas exchange mechanisms in the four organisms. Do you see any common themes? What variations did you encounter? C) Vascular systems Discuss the similarities and differences between an open circulatory system and a closed circulatory system. Do you see a connection between the circulatory system and the gas exchange system in each species? Why does a squid have two hearts? D) Digestive System Consider the organization of the digestive systems in the four species. Do you see any common themes? Why does the tube in each organism have specialized regions, and what are functions of these specialized regions? Would you predict that the basic design of the digestive system is an ancestral trait that was present in the common ancestor to all of these organisms? Exercise 2: Set 1 Describe the three types of body plans that you reviewed in this exercise. List the Phyla observed and which body plan they possess.

Evolutionary Relationships with Cladograms Using morphological data to make cladograms: 1. Using character sets provided in the laboratory handout, determine which of the character sets each animal has. In the Data Table provided in this write-up, place an "X" in the box if the animal has the character set. Amphioxus Lamprey Shark Carp Frog Lizard Opossum Cat Set #1 Set #2 Set #3 Set #4 Set #5 Set #6 Set #7 Set #8 2. Draw a cladogram in the space below to illustrate the ancestry of these animals using your complete table above. The diagram should reflect shared characteristics as time proceeds. (Your teaching assistant will show you an example of a cladogram. Notice how the different animals shown in the cladogram are all placed at the same time level (across the top) since they are all alive today.)

3. Several unknown vertebrates are provided in the lab. After carefully studying this material, place these animals on your cladogram and explain why you placed them where you did. Using molecular data to make cladograms: You have already constructed a cladogram based upon morphological similarities. You have been provided a chart (posted on Canvas) showing the amino acid sequences of a protein that is homologous for the 20 organisms shown, including several of the organisms already used to make your morphology-based cladogram (or at least very similar to the organism you used). As stated in the handout, the protein is cytochrome-c. It is an enzyme that is important in the oxidation of food molecules by the mitochondria. It helps release the energy in food molecules so that it can be used by the cell. Each amino acid is represented by a unique letter in the chart. The amino acid represented by this letter code is indicated in the box that accompanies the data set. Compare the sequence of amino acids (letters) in the human cytochrome-c to the sequences for each of the following 7 animals shown in the data set (rhesus monkey, rabbit, kangaroo, chicken, snapping turtle, bullfrog, and tuna) by counting the number of differences . HINT: Highlight or underline the organism being checked, then circle each amino acid which is different from the one above it in the human sequence (use pencil). It helps to use a ruler or other straight edge. Notice that the amino acids showing no differences in any of the organisms are highlighted in blue, so you can just ignore them when you scan the line of letters. When an organism has a "-" instead of an amino acid, it means that there is no amino acid there. When comparing a "-" to an organism that has an amino acid at the position, it should be considered as a difference . When both organisms have a "-" at that spot, it is not considered as a difference.

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4. Record the number of differences from the human sequence next to each animal's name below. Compare your numbers with those of your lab mates. If there is a discrepancy, repeat the scan and count. Number of amino acid differences Human vs. Rhesus monkey _________ Human vs. Rabbit _________ Human vs. Kangaroo _________ Human vs. Chicken _________ Human vs. Snapping turtle _________ Human vs. Bullfrog _________ Human vs. Tuna _________ 5. Now, using the data you just obtained, construct a molecular cladogram in the space below showing the relationship among the 7 species for which you have cytochrome-c sequence data. Use the same procedure that you used to construct the morphological cladogram. Even though the species used to make your molecular cladogram were different from those used to make the morphological cladogram, they fall into similar categories (e.g., the tuna and the carp are both bony fishes, the opossum and the kangaroo are both marsupials, and the rabbit and cat are both placental mammals). 6. In general, do the two cladograms show the same relationships among these species? Explain.

Testing your cladograms: One of the reasons that biologists consider the current evidence for evolution so convincing is because of what you have just observed – that is, the confirmation of the theory by two independent data sets. In this case, we have used a morphological data set and a molecular data set to derive the same basic set of relationships among several groups of vertebrate animals. Yet, the two data sets are completely independent of each other. However, we do not want to leave you with the impression that everything we observe in nature is so easily resolved. 7. According to the morphological cladogram you constructed, what is the predicted relationship between lampreys, carp, and humans (i.e., who should be more closely related to us, lamprey or carp)? For what reasons? 8. Likewise, if the molecular cladogram is correct and we are able to obtain the cytochrome-c sequence for lampreys, which sequence should show more differences compared to the human sequence – lamprey or tuna? For what reasons? 9. The amino acid sequence shown below is from lamprey cytochrome-c. Compare it to the human sequence. How many differences do you observe? _______ 5 10 15 20 25 30 1 G D V E K G K K V F V Q K C S Q C H T V E K A G K H K T G P 31 N L S G L F G R K T G Q A P G F S Y T D A N K S K G I V W N 61 Q E T L F V Y L E N P K K Y I P G T K M I F A G I K K E G E 91 R K D L I A Y L K K S T S E

10. Does your result provide unequivocal evidence concerning the relationship among humans, tuna, and lamprey sequences? Explain. In science, when we obtain data that are equivocal, one potential solution is to get more data. In many cases of sequence data, this can easily be done today by accessing the national and international sequence databases. For example, the data table below shows the number of amino acid differences observed when β-globin chains (one of the protein chains that make up hemoglobin found in red blood cells) from several species of vertebrates are compared to the human molecule. Human β-globin chains have 146 amino acids. Species Number of amino acid differences vs. human β-globin Gorilla 1 Gibbon 2 Rhesus monkey 8 Dog 15 Horse 25 Cow 25 Mouse 27 Chicken 45 Frog 67 Carp 71 Lamprey 125 11. Do these data help to resolve the question raised by comparing the sequences of human, tuna, and lamprey cytochrome-c? Explain why or why not. 12. In general, the probable validity of molecular trees can be increased by adding more gene sequences to the comparisons being made. How is this illustrated in this example?

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Questions for Biodiversity II Lab and Cladogram Worksheet

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