DNA Subway Lab Notebook Template

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James Madison University *

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140

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Biology

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Apr 3, 2024

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Name: Lab Section: Unknown name (if used): Items to include in your Canvas Lab Notebook - to be submitted AS INDIVIDUALS! When taking screenshots, include only the portion of the screen that has to do with DNA Subway. Don’t include your laptop toolbar or other tabs open in your internet browser. For Mac computers try using “Command + Shift + 4.” For PCs try using the Snipping Tool. Make sure the pasted image is large enough to read. 1. Title and Date: An informative project title. Think ahead to what might make a good title for your poster next week. Also, give the date your DNA Subway analysis was completed. 2. DNA subway Blue Line Project Info: Your DNA subway login and blue line project title in the format provided at the beginning of the lab handout, and your project ID#. 3. Consensus sequence: A screenshot of your consensus sequence. Be sure the image includes the length of the consensus sequence . If you only have one sequence, include a screenshot of the length of that sequence. 4. BLAST hits : A screenshot of your top ten BLAST hits. This should include all columns (alignment length, bit score, e-value, and mismatches) for each hit. Also make sure you include the column headers in your screenshot. 5. Taxonomic Table: Fill in the table with information about the top three taxonomically unique hits (three different species) in your BLAST search. You can find the required information by checking Wikipedia (taxonomic information is on the right) or www.itis.gov. Remember to italicize both words of the species name. The genus should also be capitalized. Taxonomic info Alignment length Bit score e-value mismatches K: P: C: O: F: G: S: * O: F: G:

S: * O: F: G: S: K=Kingdom, P=Phylum, C=Class, O=Order, F=Family, G=Genus, S=Species * Assume K, P, and C are the same as the first table entry. If your unknown is a plant , you may delete Phylum or P and replace it with ‘Clade.’ Under clade (a generic term) enter the most inclusive taxa below Kingdom found when you research your species; for example ‘Angiosperms’. You can also replace Class or C with ‘Clade’ and enter the taxa from your research that is the next more inclusive than the Order; for example the clade within Angiosperms might be ‘Eudicots’. 6. BLAST Best match: Give the species name for the BLAST hit that is the BEST match to your specimen. Explain how you know this is the best match. Your answer must be in a complete sentence(s) and include discussion of alignment lengths, mismatches and bit scores. Species name: How do you know it is the best match? 7. MUSCLE alignment: A screenshot of your trimmed MUSCLE alignment. 8. Sequence similarity matrix: A screenshot of your sequence similarity matrix. Your screenshot must include the numbered species names on the left as well as the matrix. 9. Most similar MUSCLE match: Which BLAST hit showed the highest percent similarity to your sample after your MUSCLE alignment? What % similarity did it have? Blast Hit: % Similarity 10. Least similar MUSCLE match : Which sample showed the lowest percent similarity to your sample after your MUSCLE alignment? What % similarity did it have? Make sure you understand why you should use this as the outgroup for your trees.

Blast Hit: % Similarity 11. NJ tree: A screenshot of your NJ tree with the correctly-selected outgroup and YOUR SAMPLE HIGHLIGHTED. Based on only the NJ tree, name the most specific taxonomic group (e.g. Canis ) to which you are confident your specimen belongs. You must list taxonomic information for taxa on the tree not in the top 3 Blast hits (from question #5 above) if it is needed to name the most specific group you are confident your specimen belongs to. Taxonomic info for additional Blast hits not included in #5 above, if needed: Most specific taxonomic level (Species? Genus?...) Taxon name 12. ML tree: A screenshot of your ML tree with the properly selected outgroup and YOUR SAMPLE HIGHLIGHTED. Based on only the ML tree, name the most specific taxonomic group (e.g. Canis ) to which you are confident your specimen belongs. You must list taxonomic information for additional taxa on the tree if it is needed to name the most specific group you are confident your specimen belongs to (only if not included in #5 or #11 above). Taxonomic info for additional Blast hits not included in #5 or #11 above, if needed: Most specific taxonomic level (Species? Genus?...) Taxon name 13. Images(s) of your specimen and Google/Wikipedia images of top three BLAST hits: Include at least one photo of YOUR specimen. For students working with the unknown samples, image files are included in your unknown folder. Also include Google/Wikipedia images of the top three BLAST hits. You can do fewer than three Google/Wikipedia images if there aren't three obviously different species. Label your images. Compare your image(s) with the BLAST hit images to see which BLAST hit image your unknown most closely resembles to prepare you to answer Question 14.

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14. Organism ID: Based on the results from your BLAST search (question 6 above), MUSCLE alignment (question 9 above), phylogenetic trees (questions 11 and 12 above), and your image search (question 13 above), fill in the table immediately below with the most specific taxonomic level to which you are confident your specimen belongs. Include the taxonomic level (Order, Family, Genus, Species, etc.), and the taxon name. Taxonomic Level Taxon name Fill in the table below with the higher level taxonomic information for the taxon you named immediately above; only fill in rows down to and including the level to which you are confident your unknown belongs. Kingdom Phylum Class Order Family Genus Species

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