Take home quiz #4

(Please return a hardcopy of your answers by Friday, October 12th)

Correct answers will be posted on Friday during the late afternoon.

  1. A group of organisms that is defined be a shared primitive character is
    A) monophyletic
    B) paraphyletic
    C) polyphyletic
     
  2. An autapomorphy of group of organisms is useful to establish the relation between this group and other groups. correct / incorrect
     
  3. According to Hennig a natural taxonomy should be based on (circle all that apply, more than one might be correct)
    clades,
    monophyletic groups,
    paraphyletic groups,
    shared derived characters,
    autapomorphies,
    a Hennigian comb
      
  4. A shared derived character characterizes a
    A) monophyletic
    B) paraphyletic
    C) polyphyletic
      
  5. If you have an unrooted tree (i.e. you don't know where inside the tree the ancestor is located), can you define clades using this tree?
      
  6. Which of the following statements is correct:
    A) All homologous sequences show significant similarity in a pairwise sequence comparison.
    B) All complex sequences that show significant similarity in a pairwise sequence comparison are homologous.
    C) Both of these statements are correct.
       
  7. You compare two circular genomes from closely related organisms using a Genome Dot Plot. How would you detect an inversion that occurred symmetrically around the origin of replication.
     
  8. How would the plot change, if for one of the genomes the origin of replication were not coinciding with the origin of the coordinate system?
       
  9. How could you assess, if an alignment between two sequences is reliable?
       
  10. What might be the reason that a multiple global sequence alignment is more reliable than a pairwise alignment.
       
  11. In an in vitro selection system, how could you couple the selection for a protein function to the encoding poly nucleic acid?
       
  12. Why does recombination accelerate evolution? (hint: check out Muller's ratchet)
         
  13. In defining protein space JALVIEW uses
    A) the presence or absence of a conserved sequence motif to define protein space
    B) each alignment column as a dimension to define protein space
    C) a tree based on percent identity to define a groups that have to close to each other in sequence space
       
  14. In comparing two genomes using the gene plot program at the NCBI,
    A) All blast hits better than a cutoff value are displayed
    B) Only best reciprocal blast hits are displayed
    C) Only genes located on the main chromosome are included in the analyses
      
  15. Molecular phylogenies are usually calculated as unrooted trees. Correct/incorrect
    (sorry, this question had a typo in the earlier version)
      
  16. Most of the ORFs identified with the ORF finder program at the NCBI are real, i.e., these are actually transcribed and translated. Correct/incorrect
      
  17. Programs like Glimmer
    A) identify most "real" ORFs
    B) frequently identify ORFs that are not real
    C) both A and B are correct
     
  18. Extra credit for undergraduate students:
    Which molecule(s) was/were first used to determine the root of the tree of life?
      
  19. Extra Credit: The name(s) of the person re-discovering the endosymbiont hypothesis is
    Carl Woese and George Fox
    Lynn Margulis
    Günter Wächtershäuser