Phylogenetic trees

[HELISA]

Evolutionary tree diagrams have become familiar in the literature. These trees are often presented as factual depictions of historical events. However, a more sophisticated scientific view point is that trees depict hypotheses of historical events. How a tree, viewed as hypothesis is a different interpretation than a tree viewed as a depiction of historical fact?

[AstusAleator]

Need a little help with your homework eh? Well I'll make sure to mispell and have lots of typos so you can't copy and paste .

a phylogeneatic tre, when vewed as hstrical fakt becums unscientific. The natur of hypotheses is to constanly be questioned, analyzed, and tsted.

[HELISA]

Thanks
Actually this is not a homework, but my will to discus this topic.
I'm studying right now molecular evolution, and this is a topic for our future discussion. UI do not have any experience with this subject of study, so if somebody give me some useful hints I will be gratefull.

[alextemplet]

Astus is right. To view such a tree as fact is a bad idea because we don't know for certain that it is fact; all it represents is our best guess as to how the lineage in question evolved. Many phylogenetic trees are constantly being revised to account for new discoveries.

[HELISA]

Is there any value of the viewpoint of phylogenetic tree as a depiction of historical fact?

[alextemplet]

Not that I can think of. It's sort of like drawing a map of the world without having fully explored it yet.

[HELISA]

So, in other words I can conclude from your opinions that phylogenetic trees are completely unscientific graphs which must be continuously tested and improved. They are just hypothetical pictures of evolutionary relationships among organisms which can not be understood as a fact. Hmm, so why bother phylogenetic trees? What is their real value? I know that phylogenetic trees can be based on differences between some sequences which underwent several substitutions during evolution, is this kind of information can not be considered as a fact?

[alextemplet]

No, I didn't say they're unscientific. They're actually very scientific because part of the nature of science is to constantly ask questions. I suppose you could attach a certain sort of "factuesque" quality to them, and certainly they represent our best guess that we can currently conceive as to how the lineage evolved. However, they should not be taken as absolute fact because some new discovery might cause our ideas to change. In other words, they're as close to fact as we're able to currently achieve, but some future discovery might bring us closer.

[HELISA]

So, finally I could say that phylogenetic trees are some kind of models of life’s history. They are based on historical events i.e. number of mutations in certain sequences, they represent the best guess of evolutionary relationships among various taxa, but….as a depiction of hypotheses, they should be all the time tested and improved if new evidences are available. Correct me, if I am wrong…?

[alextemplet]

Exactly right.

[HELISA]

I would like to thank you, Alextemplet for your patient to explain me everything! Thank you a lot!

[HELISA]

Ok, so I have an example of phylogenetic tree which depicts genetic relationships between the serotypes of RNA virus based on comparison of the sequence of part of the capsid-coding region of the genome.
This dendrogram could be intrepreted as a historical fact and a hypothesis.
As far as I understand correctly, this tree considered as a depiction of historical fact provides information about the percentage difference in nucleotide sequence of different serotypes of the virus and that is all what I can consider as a fact, right?
On the other hand, if this dendrogram is interpreted as a hypothesis, one may suggest that the high mutation rate observed within capsid-coding region is due to its relevant role in determining the virus host range, or it could be concluded that some regions where this virus occured represent some factors which cause specific mutation pattern for this virus.
My conclusions are based on that what I understand from our discussion. Do you have any other ideas about different interpretation of this tree?