The tips of the tree represent groups of descendent taxa (often species) and the nodes on the tree represent the common ancestors of those descendants. Two descendents that split from the same node are called sister groups. ... Many phylogenies also include an outgroup — a taxon outside the group of interest.

Nikunj Patel okay I see! So could you please help me by explaining what is exactly happening with my series of sequences on the graphs I have shown above? Thanks!

Hello Hajar!

Why did you select those sequences? Are they amino acid or nucleotide sequences? What method did you use to generate those trees? Maximum likelihood? Bayesian? It would be helpful to root the tree on the branch leading to the Trypanosoma sequence, because it isn't an animal nor a plant, which are your more represented taxonomic groups.

Usually, sequences tend to group together according to taxonomic groups. For example, Human, house mouse, and brown rat are all sequences from mammals. In this case, they group together because the identity among them is higher than to the other sequences. In other words, the topology of your trees only reflects the taxonomy relationship (evolutionary path) of the organisms you are analysing.

The trees that you show aren't very informative as they are. I don't know how did you get those sequences, but I suggest that you build a HMM profile (hmmer3 could help) and run some searches on many more species spanning the tree of life. This could help you to get a bigger picture and make inferences about paralogy, orthology, gains (duplications), and loses. In this way you could also make some more inferences about the protein''s function (which I think is your question of interest).

Best,

Samuel