Molecular Taxonomy and phylogenetic trees

Molecular Taxonomy and Phylogeny/Bioformatics

This paper involves a discussion about two phylogenetic trees in which highlighting of the existing differences are done. Each of the two phylogenetic trees shows inferred evolutionary relationships specifically among various biological species or even other entities. Basically, tree one has some major structural and alignment differences among other differences.

Tree 1 has 20 taxa with an average sequence length of 305, but ranging from 104 to 480. Regarding the same aspect, tree 2 has 15 taxa and an average sequence length of 331 that ranges from 114 to 413. Other aspects include computation alignment of 11 seconds, duration of 11 seconds, and a phylogeny period of 15 seconds for tree 1. The rendering period for tree 2 is 5 seconds. Its overall time is 42 seconds. This is completely different from tree 2 which has an alignment and phylogeny durations of 13 seconds and 116 seconds respectively. The rendering period for tree one is 5 seconds while the overall time is 134 seconds. Based on the differences in the number of taxa and the alignment durations in the two trees, it can be depicted that the two trees show descends from two different ancestors (Desper and Gascuel, 2004).

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In both tree 1 and tree 2, the sequences seem to be aligned with muscles that have been configured for the highest accuracy possible. For tree 1, the reconstruction was done using the maximum likelihood method that has been implemented in the PhyML program (Desper and Gascuel, 2004). The WAG substitution model is selected with an assumption of an estimated invariant sites proportion. Furthermore, 4 gamma-distributed categories of rate have been used to ensure accounting for the rate heterogeneity all across sites.

For tree 2, ambiguous regions are removed, after alignment, with Gblocks using parameters such as minimum length of blocks after gap cleaning. Besides, there are no gap positions that are allowed within the final alignment. The minimum sequence number for flank positions is much less at 85%. The two trees do not have a specific point that translates where the protein sequence begins. The start codons are therefore not clear in this case. The reason for this is that the start codon should be the first codon for a messenger RNA transcript that is translated by a respective ribosome. It usually codes for methionines in eukaryotes as well as a modified Met in prokaryotes (Kelchner and Thomas, 2006).

The start codon should have been mostly AUG or ATG, but this was not the case for either of the two trees. With reference to the typical genetic code, there is no way a start codon could have existed. The Genetic code refers to a set of instructions within a gene that tells the specific cell the way forward to making a certain protein (Michel, 2007). The key letters used in the genetic code are A, T, G, and C, and they represent chemicals adenine, thymine, guanine, as well as cytosine respectively.  With this regard, it is thus difficult to predict them because they do not seem to appear properly. Basically, the trees appeared to show surprises in clustering the species although computer software is used instead of true homologs.


Desper R, Gascuel O. 2004. Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol      Biol Evol, Volume 21: pp.587–598

Kelchner SA, Thomas M.A., 2006. Model use in phylogenetics: nine key questions. Trends Ecol   Evol, Volume 22: pp.87–94

Michel C. J., 2007. Codon phylogenetic distance. J Comput Biol Chem Volume 31: pp.36–43

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