<p>AP Biology Lab 3</p><p>Comparing DNA sequences to understand evolutionary relationships with BLAST (Basic Local Alignment Search Tool)</p><p>I. Read the introduction on p. S41 and do Question 2.a-b on pages 43-44. a.) b.) (sketch a cladogram here)</p><p>II. Read the Procedure section on Page 44. Write down your observations and do Steps 1-4 as explained in the lab book List your Observations of the fossil on p.44: </p><p>Step 1: Your initial hypothesis (write FOSSIL on the cladogram where you think it should be placed)</p><p>STEP 2: (follow lab book instructions) Download three gene files from http://blogging4biology.edublogs.org/2010/08/28/college-board-lab-files/ Note that the files do not open on your computer. They only work when uploaded on the BLAST website.</p><p>STEP 3: Use your lab book for the instructions http://blast.ncbi.nlm.nih.gov/Blast.cgi (note: when you get to step 3c--your downloaded files are probably located in your downloads folder). Go to Step 4 and see ‘Analyzing Results’ on pages 46-48 before loading and viewing any of the other genes. Fill in the following table for each of your three downloaded fossil genes:</p><p>STEP 4 and Analyzing Results:</p><p>Fossil’s genes of Species & gene name that most closely Click ‘Distance tree of results’: found at the top in ‘Other interest (Gene matches the gene of interest (look up the Total E value Identities (%) Reports’ (make observations, hypotheses, and /or sketches #’s choose only 3) common name online) Score here) 1 Species name: common name: gene name: Query length: 2 Species name: common name: gene name: Query length: 3 Species name: common name: gene name: Query length: 4 Species name: common name: gene name: Query length: </p><p>Based on the results gathered for the three genes, revisit your initial hypothesis and explain where you would place the FOSSIL organism on the cladogram and why.</p><p>What limitations does this evidence have? How would you strengthen your conclusion? </p><p>III. Whale Evolution Lab Using a second program known as COBALT, you will compare the gene sequences of the cytochrome b protein between whales and different mammals to develop a hypothesis related to whale evolution. Use the handout and Access the Google Form on the webpage to record answers as you work through the lab.</p><p>IV. EXTRA CREDIT Using either the BLAST or COBALT program, develop a question of your own to investigate a gene or protein (such as Actin, Catalase, Myosin, Keratin. You can look at the relatedness (phylogenetics) of that gene/protein amongst organisms (say maybe the evolution of river dolphins?), search for normal versus mutant forms of the gene/protein related to a disease, or ????</p><p>Submit your question, data records/observations and final conclusions in a one page summary for up to 3 points of Extra Credit.</p>