Final phylogeny project: metazoan controversies. Due Friday, May 4th. Hand it in and be prepared to share your findings with the class.

Groups: You can work in groups of 2-4 people of your choice. I strongly encourage having some cross-discipline members.
In this lab you will use the UPGMA code as well as the package PHYLIP to explore some current controversies on the deep phylogeny of metazoans (enimals, loosely speaking). In particular, there is a lot of current debate about the Coelomata vs. Ecdysozoa rival hypotheses. It is crucial for this lab to do the relevant reading.
  1. Select nucleotide (not protein) sequences and species to use for phylogenetic analyis of Metazoans. Choose 1 or more sequences common to all chosen species: I recommend using mitochondrial sequences, the 18S ribosomal subunit, histones, cytochrome subunits, and/or homeobox domains. For species, you need to choose 1 or more from each category:
    1. Chordates (recommended: Homo sapiens, Mus musculus)
    2. Arthropoda (recommended: Drosophila melanogaster, Anopheles gambiae)
    3. Nematoda (recommended: Caenorhabditis elegans, Anisakis simplex)
    4. Priapula and/or Porifera (recommended: Priapulus caudatus, Oscarella carmela)
    5. Annelida (recommended: Lumbricus terrestris, Platynereis dumerilii)
    6. Acanthocephala and/or Brachiopoda (recommended: Terebratulina retusa, Leptorhynchoides thecatus)
    7. optional: Cnidaria (Hydra magnipapillata)
    8. Outgroup (recommended: Plasmodium falciparum or Neurospora crassa).
      9. Using NCBI's Taxonomy database will probably be very helpful for this.

  2. Use a multiple alignment program such as Clustal or TCoffee to align your sequences. One source of these is the EBI-EMBL site.

  3. Use the UPGMA/Jukes-Cantor program to produce a tree and do a bootstrap analysis. How do your answers relate to the Coelomata-Ecdysozoa controversy?

  4. Use PHYLIP to construct trees by the maximum parsimony (dnapars) and maximum likelihood (dnaml) methods. When using PHYLIP, you need to convert to its input format. The EBI program READSEQ may be helpful for this. This primer on PHYLIP may be helpful as well. How do these results relate to the UPGMA trees? How do they relate to the Coelomata-Ecdysozoa controversy?