AP Biology Name AP Lab Three: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST In the 1990 s when scientists began to compile a list of genes and DNA sequences in the human genome it became abundantly clear that we were eventually going to need a place to put all of these sequences. One of the systems developed was BLAST, or Basic Local Alignment Search Tool. The BLAST computer program uses complicated algorithms to search through over 21 million DNA, RNA and protein sequences of a maximum 10,000 base pairs. With a few clicks of a mouse students and scientists alike can compare known and unknown DNA sequences, establish common relationships between organisms, and look for similar protein structures in different organisms. All in a matter of seconds. This lab is an activity introducing you to using this amazing computer program. Parts of the activities are required; others are extra credit. THIS LAB DOES NOT GO IN YOUR AP LAB NOTEBOOK. Activity #1: Constructing a cladogram from known traits Cladograms are visual trees that quickly show an evolutionary relationship between organisms based on a specific trait. Cladograms typically show established, linked relationships, but they may also be simply based on guesses. As a cladogram line increases up, the relationships between organisms become closer. In the above cladogram, the closest relationship is that of the crocodiles and birds while the least-related organisms are the sharks and the birds. Amphibians are more closely related to primates than to rodents and rabbits, and sharks emerged earlier in earth s history than ray-finned fish did. Cladograms also provide a hypothesis for what evolutionary trait separated different groups of organisms. In the above example, all organisms in the cladogram have vertebrae, but the sharks do not have a bony skeleton. Primates, rodents and rabbits, crocodiles and birds all have eggs, but only crocodiles and birds have eggs with shells.
Part A: Below are 8 species of animals, organized alphabetically. Use the pictures or research different traits that these organisms have. Then, hypothesize which organisms are the oldest/youngest on the planet and what traits arose first in history. Hypothesize which trait separated each species and which species are the oldest/newest. Show your hypotheses by filling in Cladogram #1, placing the species and the traits in their appropriate locations. BARNACLE CRAB LAMPREY SEA SLUG SEA URCHIN SKATE SQUID STARFISH Part B: Below is a table of traits and whether or not each of the plant organisms has that particular trait. Use these traits to determine which organisms are the oldest/youngest on the planet and what traits arose first in history. Write your answers on the second cladogram (Cladogram #2). Enclosed Embryo Flowers Fruits Leaves Seeds Stomata Vascular Tissue Conifer YES NO NO YES YES YES YES YES Cycad YES NO NO YES YES YES YES NO Fern YES NO NO YES NO YES YES NO Horsetail YES NO NO NO NO YES YES NO Liverwort YES NO NO NO NO NO NO NO Moss YES NO NO NO NO YES NO NO Peach YES YES YES YES YES YES YES YES Wood Rose YES YES NO YES YES YES YES YES
Activity #2: Constructing a cladogram from known and unknown DNA sequence Using BLAST, a scientist compared a human copy of GAPDH (glyceraldehyde-3-phosphate dehydrogenase), an important reaction in glycolysis. The data table below shows the similarities between the DNA sequences and the protein sequences of human GAPDH and the GAPDH of other organisms. Species Gene Percentage Similarity Protein Percentage Similarity Chimpanzee (Pan troglodytes) 99.6% 100% Dog (Canis lupus familiaris) 91.3% 95.2% Fruit Fly (Drosophila melanogaster) 72.4% 76.7% Roundworm (Caenorhabditis elegans) 68.2% 74.3% 1. On a separate sheet of paper, draw a phylogenetic cladogram of all five species (including humans) according to the gene percentage similarity. 2. On the paper, answer the following question: Why is the percentage of similarity in the gene always lower than the percentage of similarity in the protein for each of the species? Activity #3: Constructing a cladogram using BLAST A team of scientists has uncovered a fossil specimen near Liaoning Province, China. Little is known about the fossil. It appears to be a new species. Upon careful examination of the fossil, small amounts of soft tissue have been discovered. Normally, soft tissue does not survive fossilization; however, rare situations of such preservation do occur. Scientists were able to extract DNA nucleotides from the tissue and use the information to sequence several genes. Your task is to use BLAST to analyze these genes and determine the most likely placement of the fossil species on Figure 4. 1. Obtain a card with one of the four gene sequences written down. This will be the fossil you research and build your cladogram from. 2. At the top of the page, click on the tab marked Saved Strategies. 3. Under Upload Search Strategy, click on Browse. Follow the instructions on the board or website to locate Marshall s shared drive. Click on the gene sequence that matches your assigned gene. 4. The screen will appear pre-loaded according to the necessary parameters you will use. Scroll down and click the button on the bottom left marked BLAST. DO NOT CHANGE ANY PARAMETERS. 5. When the results page appears, scroll down to the section titled Sequences producing significant alignments. This is a list of all gene sequences that show similarities to the fossil sequence, the most similar being on top. 6. Identify the unknown species of fossil according to BLAST.
7. Choose any four sequences on the list (feel free to scroll down as far as you d like). Each sequence includes information about the species it was taken from, including the scientific name. Research these scientific names and construct a table to display the following data: a. Common names b. Similar characteristics to at least one other species on your list. c. Similarity to the unknown fossil based on the Ident number. 8. Construct a cladogram showing the evolutionary relationships of these five species. 9. After you have a completed cladogram, look up the distance tree of results at the top of the screen to view the actual cladogram, which you can compare to yours. a. What similarities did your cladogram and the actual one have? What differences? b. If you were constructing a cladogram based on physical relationships rather than genetic relationships, what similarities would it share? What differences? To earn credit for AP Lab 3, you will need to submit the following items 1. From Activity #1 a. Cladogram #1 b. Cladogram #2 2. From Activity #2 a. Phylogenetic cladogram b. Answer to question #2 3. From Activity #3 a. BLAST data table b. BLAST cladogram c. Unknown species identity from BLAST results d. Answers to the two BLAST cladogram questions.
Cladogram #1: Animal Phylogeny PLANTS HETEROTROPH
Cladogram #2: Plant Phylogeny ALGAE CLOSED EMBRYO