Problem Set #12, assigned May 27th, 2003

Evolutionary Genomics Course (http://bip.weizmann.ac.il/course/evogen/)

Itai Yanai, Molecular Genetics

Weizmann Institute of Science

 

To be submitted before June 3rd, 2003 by email to course@bioinfo.weizmann.ac.il

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.