F. Phylogenetic analysis:
Sequence conservation across evolution

There are some assumptions about evolution that underlie the science of molecular sequence analysis.

DNA sequences of species (and sub-groups within species) change over time due to mutation.
two species that have genes that are more similar in sequence are phlogenetically closer (and therefore separated by less evolutionary time) than are two species that have less sequence similarity.

It should be possible to gather some sequence data from several different organisms, total up the differences, and determine their relationships.

However, there are a number of hotly contested issues that interfere with this simplistic analysis.

First, not all DNA sequences mutate at the same rate: protein coding regions mutate more slowly than non-coding regions.
Second, some positions is protein coding DNA sequences are more free to mutate than others due to the redundancy of the genetic code.
Beyond this lie the religious wars between adherents of parsimony vs. maximum likelihood methods of measuring distance.

 
Given these problems, it is still possible to take a set of sequences and calculate phylogenetic distances and create a tree.

                           +----Thermosipho africanus
                           !
                           !               +---Fervidobacterium nodosum
                      +--8       +-----5
                      !    !        !       !    +--Fervidobacterium gondwanense
                      !    !        !       +--4
                      !    +-----6            +---Fervidobacterium islandicum
                      !             !
                      !             !       +---Petrotoga miotherma
                      !             +-----2
             +----10                     !    +---Geotoga subterrenea
             !        !                      +--1
             !        !                           +---Geotoga petrae
             !        !
             !        !         +---Thermotoga subterrenea
             !        !    +--7
   +------9        !    !    +--Thermotoga elfii
   !         !        +-12
   !         !             !    +---Thermotoga hypogea
   !         !             +-11
   !         !                  +----Thermotoga thermarum
   !         !
   !         +----Thermotoga maritima
   !
   3------Aquifex pyrophilus
 
 

The problem faced by the researcher is to choose which of nearly 100 different software tools to use.

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Computers in Molecular Microbiology
Bharat Patel, Biomolecular & Biomedical Sciences, Griffith University, Australia
Comments to: bharat@trishul.sci.gu.edu.au