AP Biology Lab 3

Comparing DNA sequences to understand evolutionary relationships with BLAST (Basic Local Alignment Search Tool)

I. Read the introduction on p. S41 and do Question 2.a-b on pages 43-44. a.) b.) (sketch a cladogram here)

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:

Step 1: Your initial hypothesis (write FOSSIL on the cladogram where you think it should be placed)

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.

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:

STEP 4 and Analyzing Results:

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:

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.

What limitations does this evidence have? How would you strengthen your conclusion?

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.

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 ????

Submit your question, data records/observations and final conclusions in a one page summary for up to 3 points of Extra Credit.