Hye Lynn Chon AP Biology Trivisani 9/30/13 [Pre-lab] Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST

Purpose: To use BLAST to compare several genes and construct a cladogram To create cladograms that depict evolutionary relationships To analyze biological data with a sophisticated bioinformatics online tool To 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

Methods/procedure: 1. Form an initial hypothesis as to where you believe the fossil specimen should be placed on the cladogram based on the morphological observations you made earlier. 2. Locate and download three gene files from 3. Upload the gene sequence into BLAST by doing the following: a. Go to the BLAST homepage b. Click on saved strategies from the menu at the top of the page. c. Under upload search strategy, click on Browse and locate one of the gene files you saved onto your computer. d. Click view. e. A screen will appear with the parameters for your query already configured. NOTE: Do not alter any of the parameters. Scroll down the page and click on the BLAST button at the bottom. f. After collecting and analyzing all of the data for that particular gene, repeat this procedure for the other two gene sequences. 4. The results page has two sections. The first section is a graphical display of the matching sequences. Scroll down to the section titled sequences producing significant alignments. Hypothesis: If this fossilized organism was a heterotrophic vertebrate that had soft tissue, four legs, two-parted limbs, but no feathers or fur, then it was a crocodilian.

Variables and controls: Independent variableDependent variableControl variableExperimental variablesPre-lab questions: Background information: The Human Genome Project identified and mapped a human beings 20,00025,000 genes, along with those of other organisms. The location and gene sequence are accessible on the Internet. This is important because we can understand genetic diseases and evolutionary relationships. Many of our genes are similar to those of other species. Bioinformatics is a field that combines statistics, mathematical modeling, and computer science to analyze biological data. Entire genomes can be compared for similarities in sequences. A cladogram is a treelike diagram that depicts the branching off of different species, along with the evolution of particular physical structures (shared derived characters). The placement of the derived characters corresponds to when that character evolved. The fossil specimen in question was found near Liaoning Province, China, and it appears to be a new species. It has small amounts of small tissue. Hand-drawn data tables that will be used for data collection during the lab

[Post-lab] I. II. Title- Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST Introduction a. Background: see pre-lab b. Purpose: see pre-lab c. Hypothesis: see pre-lab Materials and procedures Materials: BLAST

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Procedures: see pre-lab Results/data collection Analysis Discussion/conclusions

GENE 1 1. 2. 3. 4. Gallus gallus Birds 100% Anas platyrhynchos

Conclusion: The new fossil species belongs on the cladogram with birds. GENE 2 1. Drosophila melanogaster 2. Insects 3. 100% 4. Drosophila pseudoobscura Conclusion: The new fossil species belongs on the cladogram with insects. GENE 3 1. Taeniopygia guttata 2. Birds 3. 100% 4. Geospiza fortis GENE 4 1. Alligator sinensis 2. Crocodilians 3. 100% 4. Alligator mississippiensis Conclusion: The new fossil species belongs on the cladogram with birds.