Genomes and Genomics 3 Techsession7

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Molecular Phylogenetic Analysis:

Horizontal Gene Transfer, or

Are there bugs in our genome?

Mark Blaxter

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10: Maximum parsimony analysis of the alignment

The alignment was imported into a phylogenetic analysis program called PAUP* (Phylogenetic analysis using parsimony * and other methods) written by david Swofford (see here for more about PAUP).

First, we carried out a Maximum Parsimony analysis.

This analysis is character-based, and attempts to find the best possible tree (defined as the one with the fewest inferred amino acid changes) by comparing trees with each other, and selecting the "shortest". As the number of trees that are possible with 36 sequences is very, very large, we used a search method that doesn't test ALL trees, but carries out a carefully planned traverse of all the possible trees, trying to find the best it can.

The final, best tree found was:

* What sort of a tree is this (cladogram/phylogram)?

* Is it fully resolved or partially resolved?

* Is the rooting of the tree a problem? Why?

* Why might this NOT be the best POSSIBLE tree?

* What can you infer about the evolutionary origins of

the human N-acetylneuraminate lyase?

the Trichomonas N-acetylneuraminate lyase?

* We included two sequences from the zebra fish Danio rerio. What are their relationships to the other vertebrate sequences? What might explain this odd pattern?

* We included two sequences from Actinobacillus pleuropneumoniae (labelled 1 and 2). What are their relationships to the other bacterial sequences? What might explain this odd pattern?

 

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