Exercise 5 - Molecular Phylogenies
Aims: compute different phylogenies and interpret the results
1- Insulin phylogeny
Starts the Phylo_win: in the command shell, type: /home/enseignt/gueguen/phylo_win
Open the multiple
alignment containing vertebrate insulin proteins in MASE format that you
previously created during Exercise 4.
Compute the molecular phylogeny of vertebrate insulin proteins using the
Neighbour-Joining (NJ)
method and the Poisson
distance.
Bootstrap the tree with 500 replicates. The correspondence between SWISS-PROT
sequences and species names is available here.
Identify the different gene duplication in the tree. In which species did they
occur? Does the tree correspond to the expected vertebrate phylogeny?
2- Universal phylogeny
File 28sfrags.mase
contains a set of
prealigned rRNA sequences from the large (LSU) and the small (SSU) subunits:
- Save it in text format on your computer.
- Load it with Phylo_win.
- Visualize the set of reliably aligned sites called
all sequences
.
- Build the universal phylogeny using the
transversion-only
evolutionary distance, bootstrap it with 500 replicates.
- Is the position of the Euglena chloroplastic sequence expected?
3- A 250 MY old bacterium: is it possible?
Vreeland et al. have published the isolation of
a 250 million years-old bacterium from a salt crystal. Their data are reproduced
in a file of aligned bacterial 16S rRNA sequences:
permians.mase
.
- Compare usage of parsimony and of distances + NJ methods.
- What is the very important information vehiculed by the branch lengths in the
NJ analysis?
- What do you think of the conclusions of Vreeland et al.?
The results of Vreeland et al. have been severely critized by
Graur and Pupko, who concluded that the isolated
bacterium is most probably recent in age.
4- The evolutionary origins of HIV-1 and HIV-2 viruses
Gao et al. have published a phylogenetic
analysis of the pol gene of HIV-1 and HIV-2 viruses and of their simian
homologs (SIV).
File hivpol.mase
contains public protein
sequences with which it is possible to attempt to reproduce their results.
Sequence FIV/Oma (Feline Immunodeficiency Virus) is used as an outgroup for the
analysis. File hivpol-dna.mase
reproduces
the same alignment at the DNA level:
- Identify which simian species are at the origin of HIV-1 and HIV-2 viruses?
- Conduct analyses on Ka and on Ks distances when possible.
File hivpol.pdf
contains the (nearly) complete
article by Gao et al. (there is a problem with its first page!)
If you have problems or comments...
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