PRABI
Rhone-Alpes Bioinformatics Center


Phylogenetics

A Simple Phylogenetic Tree Construction pt. 1

Example 1 : Ornithorhyncus anatinus

Problem :

- According to taxonomy, the duck-billed platypus (Ornithorhynchus anatinus) is a mammal, but signs could lead us to believe that this classification is wrong : amphibian, oviparous, duck-billed, etc. We will try to verify this classification using molecular data.

Objectives :

- Understand the method behind constructing a phylogenetic tree from the search for sequences to the analysis of the tree.
- Get to grips with various bio-informatic software (BLAST, CLUSTALw, SeaView and Phylo_win).
- Understand the FASTA format.
- Understand the limitations of these methods.

STEP 1 :

STEP 2 :

- Taxon IS aves

- Taxon IS amphibia

- Taxon IS eutheria

- Taxon IS monotremata

- Taxon IS squamata

- Taxon IS NOT tetrapoda

STEP 3 :

STEP 4 :

STEP 5 :


[1] FASTA format :

The FASTA format is a) a sequence name introduced by “>”, the name must be kept under 10 characters preferably as some programs will shorten it, b) the sequence. Multiple sequences may be listed one after the other in the same file.

NB  : Protein and DNA cannot both be present in the same file, only one or the other.

For example :

>A17677

GTCGACACGCCTTCTGCACGGGAAGTCCTTCTGCGGCCATCGTTGCTATGGCCGCTTACT GCCTTCTAGTCCGTGCGGCTCTCGCAACAGCTCACGGGACCTTTTTGAGGATCGCCACTT CAGGTCTTCAACTCGCGGATGCCCTCATTGGCAACGTTTGCGCCCTGCCTTGGGGCGGCC GGCAGCCACCAAGTCGAGCACTTTGCGGCGGAACTACTCGGGGTAACACTTCGGCACGGA

>U00096

MRNPTLLQCFHWYYPEGGKLWPELAERADGFNDIGINMVWLPPAYKGASGGYSVGYDSYD LFDLGEFDQKGSIPTKYGDKAQLLAAIDALKRNDIAVLLDVVVNHKMGADEKEAIRVQRV NADDRTQIDEEIIECEGWTRYTFPARAGQYSQFIWDFKCFSGIDHIENPDEDGIFKIVND YTGEGWNDQVDDELGNFDYLMGENIDFRNHAVTEEIKYWARWVMEQTQCDGFRLDAVKHI

[2] An outgroup is a group of sequences which were selected to root the tree. An outgroup has always branched off from the common ancestor of all other analysed sequences before them. This ensures that the root of the tree is on the branch between the outgroup and the other sequences.
Here, the goldfish is not a tetrapoda, this implies that it branched off at a very early date before all other sequences.
An outgroup must still remain genetically close to the anaylsed sequences for maximum efficiency.