Problem Set #12, assigned
Evolutionary Genomics Course
(http://bip.weizmann.ac.il/course/evogen/)
Itai Yanai,
Molecular Genetics
Weizmann Institute of
Science
To be submitted before
�with
heading �EG #12�
Problem 1: Phylogenetic trees. A tree of the phenylalanine synthetases from a few organisms representing all three domains of life is given below. Bacteria are in black, archaea are in magenta and purple, and eukaryotes are in green.� Explain whether or not this tree is congruent with the universal tree. If not what can be inferred from the tree?
Problem 2: Gene loss vs. horizontal transfer. The tree below is based upon a multiple alignment of a concatenation of the ribosomal proteins from various organisms. Assume that it is the �correct tree of life�. The profile on the right indicates which kingdom each genome comes from (bacteria, yeast, archaea). For each of the three given phylogenetic distributions (a,b, and c) each representing a distinct gene family calculate:
� the minimal number of horizontal transfers that need to be postulated and indicate the (one) origin of the gene (for which this number is minimized).
� the minimal number of gene losses that need to be postulated and indicate the (one) origin of the gene (for which this number is minimized).
� Assuming that a gene loss is 4 times as common as a horizontal transfer, state which of the previous two solutions is the most parsimonious scenario.
Problem 3: Anomalous DNA composition. Why does the method of anomalous DNA composition fail to identify ancient transfers?
Problem 4: Evolutionary scenarios. Explain how in light of horizontal transfer the following two sentences are incorrect:
Problem 5: Archael evolution. Archael informational genes seem �eukaryotic� while the operation genes tend to �bacterial�. Explain this phenomenon in terms of the complexity hypothesis and horizontal transfer.