Reconciling a real life RasGEF tree.

RasGEFs are important signalling proteins that diversified predominantly in unikonts. We want to reconstruct the dynamics of this dynamic gene family in unikonts. However, this is a real life tree and real life is not so easy.
  1. Look at the tree of RasGEF(CDC25) containing proteins that has been handed out (or see here), the unresolved species tree given here and the fully resolved species tree given here. The six letter abbreviations are as follows HOMAP; human, DROMEL: fruitfly; CAEELE: nematode worm; DYCDIS: slime mold; USTMAY: basidomycete corn smut fungus; NEUCRA ascomycete read bread mould fungus; SACCER ascomycete baker's yeast.
  2. I have given an unresolved species tree because annotating the RasGEF protein tree in terms of duplications and speciations using the fully resolved species tree would yield (too) many ancient duplications and differential gene loss. So instead, annotate as many internal nodes of the RasGEF protein tree in terms of duplications and speciations where this designation is not contradictory to the unresolved (consensus) tree. (i.e. perform tree reconciliation using an unresolved species tree)
  3. Given the considerations above, mark the places where the tree seems to suggest gene loss.
  4. Now using the the correct species tree given here as a tree to project events and ancestral gene content on, reconstruct the ancestral repertoire of RasGEF proteins. i.e. how many (orthologous groups of) rasgefs where present at which ancestor. (so do not use this tree to again annotate the gene tree, only to project on) How many loss and duplications of (orthologous groups of) rasgef happened at which branch. You will now be forced to explicitly make decisions on areas in the gene tree that are "wrong" (i.e. do not reflect the species phylogeny and this inconsistency is not caused by non-parsimonious genome evolution events) and areas where indeed you fully trust the gene tree and this reflects differential loss and (non trivial) ancient duplications.
  5. Discuss the orthologous relations. Which genes in human are orthologous to which genes in fruitfly. And which genes in human are orthologous to which genes in S.cerevisiae.
  6. Which organisms contains most "ancestral" RasGEFs (i.e. already present in the unikont ancestor)? Which organism contains most RasGEFs?