Lab8: Phylogeny

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Lab 8: Phylogeny

I would like this lab to be short, and I am afraid that this may give the mistaken impression that phylogenetic analysis is impossible! There are fascinating aspects of biology to explore phylogenetically, but asking good, focused questions is remarkably tough.

Anyway, here is an interesting protein with which you have worked, please give the following a try.

There are some interesting comments, terms, etc. in "old" BIO520 materials.

I have downloaded, in fasta format, the sequences of the SRY polypeptide, thought to be a major male-determining polypeptide in mammals, from a variety of mammals: human, marmoset, horse, pig, sheep, European bison. Please complete the following analyses:

Perform a multiple alignment of these SRY proteins (Pileup or Clustal). Save as a .msf file
Use Paupsearch and Paupdisplay, heuristic search, (please note, PAUPSTAR on the Mac is a much easier program to use, but our version is not usable due to its expiration), to find at least one tree relating these polypeptides to one another and save as a yourname1.gif
Repeat with the same .msf file, but do an exhaustive search. You may notice a modest increase in processor time. Display the tree and save as yourname2.gif.
Now, trim the alignment (lineup will work, but is quirky to learn) or trim the sequences to include only the region of greatest similarity, from QDR (consensus) to YKYRPRR. Repeat the exhaustive search. Save tree as yourname3.gif.
Add the SRY sequence from the marsupial animal, the dunnart. Repeat the alignment and the exhaustive search. Display the tree as yourname4.gif.
Repeat the display, but produce a phylogram rather than a cladogram. In a phylogram, the branch lengths are related to a distance or difference characteristic. Save this as yourname5.gif.

Genhelp on Paupsearch and Paupdisplay will be helpful and informative. We will not try maximum likelihood methods (which are applied only to DNA sequences due to the uncertainty in the substitution matrices for proteins and the computationally intensive nature of likelihoods), bootstrapping, etc. If you would like to do this, because of your profound interest in phylogeny, try to align some rDNA sequences, like the representative dataset for the eukaryotic BIG TREE.. The best place to get pre-aligned rDNA is the Ribosomal Database Project-but be warned that their info is tricky. If you do this, download the aligned file, then use pileup, then paup. Be forewarned that this is a BIG dataset.

Submit printed versions of these .gif files. Directly on the relevant .gif file, please answer the following questions VERY briefly. A good answer to #1, for example, would include a hand-drawn version of what you think the phylogeny is (and the basis for this thought):

yourname1.gif Does this phylogeny agree with your impression of the phylogeny of this group?
yourname2. gif Is this phylogeny different from the heuristic search. If so, give a reason why this might be so.
yourname3.gif Is this phylogeny different from yourname2.gif. If so, give a reason why this might be so.
yourname4.gif Does this phylogeny agree with your understanding of the phylogeny of mammals?
yourname5.gif Why does yourname5.gif look different from yourname4.gif?
If you examined SRY gene evolution, you might find that the SRY coding region evolves MORE rapidly at codon positions 1 and 2 than in position 3. How would you interpret this finding? Relate, in 1 or 2 sentences, this finding to your answers to question 1 and question 4. The data from question 5 may also be helpful in this answer.

Please submit these by Friday, November 6.