Midterm Exam #1. MB 451 Microbial Diversity. Honor pledge: I have neither given nor received unauthorized aid on this test.

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1 Midterm xam #1 M 451 Microbial iversity Honor pledge: I have neither given nor received unauthorized aid on this test. Signed : ate : Feb 5, 2007 Name : KY 1. What are the three primary evolutionary branches of life? (5 points) rchaea, acteria, and ukarya Multiple choice (2 points each) 2. Which of the following is not an aspect of a taxonomy?. Grouping. Naming. Identifying. Isolating. None of the above 3. Which describes a phylogeny?. a genealogy. a tree. evolutionary pathways. natural relationships between organisms. ll of the above 4. Species evolve by.... diversification. progression. linear advancement. magic. none of the above 5. Which of these evolutionary representations is both objective and quantitative?. the 5-Kingdom tree. the volutionary Ladder. the Prokaryote/ukaryote dichotomy. the 3-omain molecular phylogenetic tree. None of the above 6. Which if the following is not an algorithm for generating phylogenetic trees from molecular data?. Neighbor-joining. Parsimony. Maximum likelihood. Jukes & antor. all of the above 7. photoheterotroph gets its energy from X and its carbon from Y.. X= light ; Y= carbon dioxide. X= light ; Y= organic compounds. X= inorganic compounds ; Y= carbon dioxide. X and Y both = organic compounds. none of the above Page 1 of 5

2 Short answer & fill in the blank (points as indicated) 8. Usually the best single molecular sequence for phylogenetic analysis is ssu-rrn. (2 points) 9. 2-dimensional matrix of molecular sequences is called a(n) sequence alignment. (2 points) 10. Molecular sequences may be alignable using structural superimposition even if they are so different from one another that they cannot be reliably aligned based on the sequence alone. (2 points) 11. bootstrapping is a way to judge the reliability of the branches in a tree. (2 points) 12. Why is an understanding of phylogeny important? (4 points) oth to make predictions about the properties of an organism, and to prevent inappropriate comparisons between unrelated organisms. 13. What are the main steps of a molecular phylogenetic analysis? (4 points) 1. ecide on organisms and sequences 2. Obtain this data 3. Identify homologous residues 4. perform phylogenetic analysis 14. Why is raw sequence similarity an underestimate of evolutionary distance? (5 points) ecause of the occurrence of multiple substitutions at a single site that are only counted as a single difference, or in the case of reversion, as no difference at all. Page 2 of 5

3 Tree interpretation : answer the following questions based on this ssu-rrn-based phylogenetic tree. The scale bar (0.10) represents evolutionary distance. Sequences/organisms without names (i.e.p, Nak_9, SRI-240, and V2.1bac27) are from uncultivated species. (2 points each) 15. Is this a dendrogram or a phenogram? phenogram 16. Which sequence(s) is/are presumably the outgroup? Methanococcus jannashii 17. Which sequence is most closely related to acillus subtilis? scherichia coli 18. What is the evolutionary distance between Persephonella marina and Hydrogenobacter thermophilus? _ ircle (on the tree above) the last common ancestor of acillus subtilis and Thermus thermophilus. 20. xcept for the outgroup, which two sequences in this tree are the most distantly related? Flexibacter flexilis and p 21. Which branch(es) would you have the least confidence in? The one between the 2 Persephonella species, and the one between.coli and.subtilis (the one between p and NK_9 is also right up there). Page 3 of 5

4 Problem-solving (points as indicated) 22. lign the following sequences: (8 points) Sequence 1 G G G G U U G U - G G G G U U G U Sequence 2 G G G U U G U U G G G U U - G U U Sequence 3 G G G U G U G G G U - G U - Sequence 4 U G G G U G U U G G G U G U 23. Generate a similarity matrix from the following alignment: (10 points) Sequence 1 G U G U G Seq1 XX XX XX XX Sequence 2 G U G U G Seq2 0.9 XX XX XX Sequence 3 G G G Seq3 _ _ XX XX Sequence 4 G G U G G Seq4 _ _ XX 24. onvert the following similarity matrix into a distance matrix using the Jukes & antor curve: (10 points) Similarity matrix istance matrix Seq1 XX XX XX XX Seq1 XX XX XX XX Seq XX XX XX Seq XX XX XX Seq XX XX Seq XX XX Seq XX Seq XX Similarity JUKS & NTOR URV volutionary distance Page 4 of 5

25. onvert the following phenogram into a dendrogram. (10 points) 26. Generate a tree using the neighbor-joining method from the following distance matrix. SHOW YOUR WORK!

5 25. onvert the following phenogram into a dendrogram. (10 points) 26. Generate a tree using the neighbor-joining method from the following distance matrix. SHOW YOUR WORK! You need only solve the structure of the tree; you do not need to solve the branch lengths. (10 points) reduced matrix X X X X X / 0.3 X X X X / X X X X X X X 0.55 X X X X X X X X X The nearest neighbors are and, so these are joined: verage distances in the matrix to /; the nearest neighbors are then between / and, so these are joined: The nodes are completely resolved - you re done! Page 5 of 5

Honor pledge: I have neither given nor received unauthorized aid on this test. Name :

Midterm Exam #1 MB 451 : Microbial Diversity Honor pledge: I have neither given nor received unauthorized aid on this test. Signed : Date : Name : 1. What are the three primary evolutionary branches of