Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST

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1 Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST INVESTIGATION 3 BIG IDEA 1

2 Lab Investigation 3: BLAST Pre-Lab Essential Question: How can bioinformatics be used as a tool to determine evolutionary relationships and to better understand genetic diseases? 1

3 Lab Investigation 3: BLAST Pre-Lab Learning Objectives: You will be able to - create cladograms that depict evolutionary relationships analyze biological data with a sophisticated bioinformatics online tool use cladograms and bioinformatics tools to ask other questions of your own and to test your ability to apply concepts you know relating to genetics and evolution 2

4 Lab Investigation 3: Pre-Lab Background Information: Read pages S41 to S44. Answer the following on your pre-lab handout. 1. Explain why being able to identify the location and sequence of genes is important. 2. Why is bioinformatics considered a powerful tool? Provide 2 pieces of evidence to support your claim. 3. What is a cladogram? How are cladograms used? 4. Draw a cladogram that depicts the evolutionary relationship among humans, chimpanzees, fruit flies, and mosses. 3

5 Lab Investigation 3: Pre-Lab 5. Use data in Table 1 to construct a cladogram of the major plant groups. (page S43) 6. Look at Table 2. Percentage Similarity Between the GAPDH Gene and Protein in Humans and Other Species on page S44 that compares the % similarity between the GAPDH gene and protein in humans with the other species in the table. a. Why is the percentage similarity in the gene always lower than the percentage similarity in the protein for each of the species? (Hint: Think about how a gene is expressed to produce a functional gene product, in this case a protein.) b. Draw a cladogram depicting evolutionary relationships among the 5 species according to percent similarity 4

6 5

7 Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST INVESTIGATION 3 BIG IDEA 1 6

8 Lab Investigation 3: BLAST Lab Procedure Read the paragraphs at the bottom of page S44. This is an enlarged photo of Figure 3. This fossil specimen was found near the Liaoning Province in China. It is a newly discovered species. (Remember: DNA nucleotide sequences were extracted from soft tissue in this fossil.) Source: American Museum of Natural History, Mick Ellison 7

9 Lab Investigation 3: BLAST Lab Procedure It s uncommon for any soft tissue to survive fossilization, but DNA nucleotides were extracted from small amounts of soft tissue in this fossil. Scientists used that information to sequence several genes. Your task is to use BLASTn to analyze these genes and determine the place where the fossil species is most likely to be placed on the cladogram. 8

10 Lab Investigation 3: BLAST Lab STEP 1: Using Figure 4. Fossil Cladogram, form an initial hypothesis as to where you think the fossil specimen should be placed on the cladogram based on the morphology (form and structure of an organism) you made earlier. Write your hypothesis to the right of the cladogram. Remember to draw where you think the fossil specimen should be on the cladogram in Figure 4 on page 2 of your lab handout. 9

11 Lab Investigation 3: BLAST Lab STEP 2: Highlight and copy one of the 4 genes* on the handout provided. STEP 3: Upload one of the gene sequences into BLAST by going to the BLAST homepage. *4 different DNA nucleotide sequences extracted from soft tissue in the fossil. 10

12 Home page for BLAST at NCBI THIS IS WHAT THE BLAST HOME PAGE LOOKS LIKE. 11

13 Home page for BLAST at NCBI BEGIN by Clicking on Nucleotide BLAST. 12

14 This is the next page you ll see. 13

15 Uploading a Gene Sequence Choose your first gene. Copy and paste the nucleotide sequence of that gene (1, 2, 3, or 4) into the Enter Query Sequence box. 14

16 Uploading a Gene Sequence Here s the nucleotide sequence. * * Be sure to add a job title so you know which gene nucleotide sequence you uploaded. 15

17 Click on BLAST Scroll to the bottom of the page. Click on BLAST button. 16

18 Results You ll see the results in 2 forms as a Diagram, which you see below, and a Table. Click on Graphic Summary to see the Table of your BLAST results. 17

19 Results The list of species that appears in this section are those with sequences identical to or most similar, to the gene you uploaded. The sequences become LESS similar are you go down the list. 18

20 Results Click on a particular species to find out more specific information, including the classification scheme (scientific name), the protein that the sequence codes for, and the sequence of bases that appear to align with your gene of interest. Copy and paste the scientific name of that species and google it to find out the common name. 19

21 Results You must click on the box of the species you want to use to create the Distance Tree of Results. See the next slide. 20

22 Make a Distance Tree of Results Scroll back to the top of the page and click on Distance tree of results. Watch what happens! 21

23 The Cladogram This is the gene you uploaded.

24 You will be provided with a legend with that includes a Label Color Map and a BLAST names color map so that you can better understand the cladogram your search produced. The Legend This is the gene you uploaded. 23

25 Modifying the View Change Change the the Max Max Seq Seq Difference from Difference 0.75 to 0.15 from to see a close-up of the tree. Your gene is highlighted in yellow below. Using the legend, you can determine evolutionary relationships. 24

26 You will What s next? Repeat this process for 2 other genes of interest. Analyze your results. Decide whether or not the data from the BLAST search supports your hypothesis about the placement of the fossil species on the cladogram. Compare and discuss your cladogram with other students. 25

27 Design and Conduct Investigation You will Find and BLAST your own genes of interest. Use example procedure provided. Possibly use one or more of the suggested genes to explore. 26

28 27

29 FOR TEACHERS: You can use other resources like those found at the ENSI, UCMP, and BioInteractive sites before or after doing this lab. Adapted by C. Hollinger from AP Biology Investigative Labs: An Inquiry-Based Approach. Copyright 2012 by The College Board, revised 2015,

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