Peroxisome

Interpreting some trees of peroxisomal proteins

We are going to look at two trees from the following publication by Gabaldon et al. (ref). Briefly this article discusses the evolution of proteins currently located and functioning in the peroxisome. For two typical cases the tree is shown.
  1. For the tree of the peroxisome biogenesis proteins PEX1 and PEX6 given here, discuss the following issues.
    1. Which nodes are duplication nodes?
    2. What nodes are the speciation node that more or less reflects the root of the eukaryotes?
    3. What node is the speciation node that delineates the split of eukaryotes from archaea?
    4. When did the duplications occur?
    5. What now is the biology that we can learn from this tree? (quickly read the abstract and the relevant section of the original article)
  2. For the tree of the peroxisome/mitochondria localized enzyme Npy1p given here, discuss the following issues.
    1. Which nodes are duplication nodes?
    2. What nodes are the speciation node that more or less reflects the root of the eukaryotes?
    3. On which branch is the the alpha proteobacterial endosymbiosis located?
    4. When did the duplications occur?
    5. Which losses do the duplication(s) imply?
    6. In which ways might the tree be wrong and how does it matter?
    7. What now is the biology that we can learn from this tree? (quickly read the abstract and the relevant section of the original article)