Python Programming for Biology: Bioinformatics and Beyond

Figure 12.3.  A cartoon phylogenetic tree, illustrating the evolutionary relationship

of a few ape species. We often build phylogenetic trees using biological sequences by

finding the arrangement of taxa (which here represent ape species) which would involve

the simplest genetic changes, thus predicting the order of evolutionary divergence and

grouping the most similar taxa together. The illustrated tree is a rooted tree, to show the

relationship of the taxa to their last common ancestor. In this stylised diagram the line

lengths do not convey any special meaning, but in general branch lengths are used to

represent evolutionary distance (dissimilarity). The example DNA sequences are the same

part of the mitochondrial cytochrome c oxidase gene COX1 from each of the species.

Often the family trees of one or more genes will be used to construct a family tree for a

group  of  whole,  distantly  related,  organisms.  Accordingly,  by  studying  slowly  changing

features,  like  the  genes  for  ribosomal  RNA  and  large  DNA  insertion  events,

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 we  can

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determine  how  most  of  the  major  groups  of  living  organisms  are  related  to  one  another.

Also, if we use a multitude of genes to build a consensus as to how a group of organisms

is  related  to  one  another,  then  we  can  determine  where  in  the  tree  a  particular  change

occurred. It is also possible to seek genes that do not follow the main evolutionary trend.

Such  rogue  genes  are  often  the  result  of  genetic  material  being  transmitted  by  some

method other than normal reproduction; examples of this include transfer via viruses and

during symbiosis.

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Although  genetic  trees  of  sequences  are  made  possible  by  doing  alignment,  they  are

special enough to get their own section. Hence, for more detailed information and Python

programming examples of how simple genetic trees may be constructed see

Chapter 14

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