Today's Practical:
You will be given a dataset containing 6 aligned sequences (ribosomal RNA). The total length of the alignment is 1,273 positions.
The correct set of relationships is:
There is a systematic bias in this dataset (note: we are intentionally using a dataset like this in an effort to demonstrate the kinds of problems that might be encountered).
What does systematic bias mean?
- In this instance there is a base compositional effect. Not all of the sequences have similar base compositions. In fact two closely related species (Thermus and Deinococcus) have sequences that differ quite substantially in base composition.
- This bias has the ability to confound accurate phylogenetic reconstruction.
- First you will use the dataset without the taxon 'T_ruber' (Thermus ruber), which has an intermediate base composition.
- You will use a number of different phylogenetic reconstruction methods. It is important to become familiar with the command syntax when using PAUP.
- You will see that the correct set of relationships can be difficult to reconstruct, unless you use an appropriate method.
- It is possible to include
the
T. ruber sequence (with an intermediate base composition) and
you will then see that is quite easy to reconstruct the correct set of
relationships.