Hi, everyone! I'm an undergraduate student, and I'm having troubles in interpreting the Phylogenetic tree of Neuroglobin sequences that I constructed using MEGA X. Could anyone help me interpret the tree that I made? Thank you in advance!
How are we supposed to interpret the tree we have never seen?
If you mean how to interpret the trees in general, a simple Google search for how to interpret phylogenetic tree will give you plenty of clues. Briefly, the closer the trees entries are, the more related they are in terms of evolution. Adding the horizontal length of all branches that connect any two entries (ignore the vertical connections) tells you how distant they are. So if you connect any two entries in the tree by their shortest path and ignore the vertical connections, that tells you about their relative evolutionary distance.
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What does the tree look like? What is the question you're trying to answer? What was the method used to construct the tree?
Its impossible to answer without at least this much information.
The tree looks like this. I'm looking for the evolution of neuroglobin through the 5 selected vertebrate classes which are: Osteichthyes, Amphibia, Reptilia, Aves, and Mammalia. The method that was used in this tree is ML, with 1000 bootstrap replicates, and aligned by clustal W. I hope you'll be able to help me sir.
But what is it youre hoping to learn from this?
this serves as our final project in Bioinformatics subject. Since I'm no professional in reading trees like this, I can not provide such information that might be wrong. That is why I'm asking for help sir.
There's very little of consequence you can say from this tree as-is, other than "yeah, these are related" because the branches are well supported generally - but that's not really a 'finding' since it was a basically a known predicate of the data going in in the first place.
You can maybe say a few specifics such as "human neuroglobin is closest to canine neuroglobin" based on this tree, but that's really about it.
You can perhaps annotate on the tree where the groupings/splits are (e.g roughly where the Aves vs mammals clades split off). But this is all using information from outside the tree itself since you already know something about the evolution of those taxa.
You can't date any of these relationships, since you don't have a molecular clock, you can only say how many substitutions separate them (but that would be almost easier and more enlightening to obtain from the alignment than the tree anyway).