1' The Tree of Life

1
1. The Tree of Life View a http//tolweb.org/tree/
phylogeny.html at the Tree of Life. Search for
Proboscidae, Decapodiformes, and anteater.
Describe these oprganisms. 2. Draw a tree with
the following sequences HGLCSHALCSHAICSPAICSPA
ICT 3. Maximum parsimony Informative sites are
defined as columns in an alignment that favours
one tree topology over another. Find the number
of informative sites in the following alignment
1 ATGTA 2 TAGTA 3 CGCTG 4 GCCTG Which tree
would be found by the maximum parsimony for this
alignment?
2

• 4.
• Get set of sequences from the attached word file
• Create a multiple alignment using ClustalW at
  http//www.ch.embnet.org/software/ClustalW.html
• Retrive sequence alignment in a proper format and
  
• Create a tree using
• http//bioweb.pasteur.fr/seqanal/interfaces/protpa
  rs-simple.html
•  You can create a phenogram and a tree.
• Submit the ClustalW file (watch for proper
  format) to
• http//bioweb.pasteur.fr/seqanal/interfaces/protdi
  st.html
• to create a distance matrix
• which can be submitted directly to neighbor (NJ
  and UPGMA trees NJ UPGMA)
• (just in case you want to transfer file by
  yourself-http//bioweb.pasteur.fr/seqanal/interfac
  es/neighbor-simple.html)
• fitch

3
5.
Consider the following sequences for five taxa
1-5 and the known outgroup O, which has the
ancestral states
Infer the UPGMA tree for these sequences from
your matrix. Label the branches with their
lengths (no computers). To derive this tree,
start by clustering the two species with the
lowest pairwise difference -- 1 and 3 -- and
apportion the distance between them equally on
the two branches leading from their common
ancestor to the two taxa. Treat them as a single
composite taxon, with distances from this taxon
to any other species equal to the mean of the
distances from that species to each of the
species that make up the composite (the use of
arithmetic means explains why some branch lengths
are fractions). Then group the next most similar
pair of taxa and apportion the distance equally.
Repeat until you have the whole tree and its
lengths.