Hi there! I am a student from Germany and working on a research paper about evolution and the human's relation to other primates (bonobo, chimp, gorilla, orang-utan). I have already finished the parts of my paper where i talk about different methods to analyse relations (through morphology, average-distance method etc.) and now I am wondering whether there is a possible way to find a gene, that is in every of the organisms mentioned above and shows after comparing the sequences with the BLAST programme a tree, that fits how the phylogenetic tree looks like ( http://www.nature.com/nrg/journal/v15/n5/fig_tab/nrg3707_F1.html like in this picture, only the upper part). I have already tried alligning sequences of insulin, cytochrom b, s16-rrna and some others but they did not fit. Now I know that a phylogenetic tree based on a single gene is very likely to show a different result than we would expect, but still, does anyone know how i could tackle this problem? The idea behind this use of blast in my paper is to find a way to show other pupils how blast can create phylogenetic trees and it would be perfect to find a gene that suits the right result.
I hope you could understand what i mean :)
Thanks a lot!!
Why do you want your phylogeny to match the figure in that paper? Is it even a good idea?
I know it sounds odd, but the idea behind this point in my paper is to find an gene e.g. teachers could use in class to show students with blast how everything is 'connected'. The focus is on the methodical-didaktic experience for the students, so they see how working with this programme can look like. Of course a phylogenetic tree based on only one gene has practically no informative value, so I know what you mean.
I get that, but I'm not sure why it must match that specific tree. Just show the one from the gene you pick for the exercise. Or, explain that the Nature figure is based on a much more complex analysis taking into account a number of features that a gene-based analysis lacks.
It may not be bad to cover a few examples and to highlight the complexity of estimating phylogeny. It could also highlight how different species have experienced different selection pressures or have responded to similar selection pressures in different ways. Different input information and methods will give different results. It would be bad to give the idea that any gene used will provide that specific result, and anything not matching that specific figure is incorrect.
Using the Ensembl gene trees might be a better approach since the trees are already created, you could just point teachers in that direction.
If you're worried about the complexity of someone not familiar with bioinformatics tools, you could create an input set of sequences to provide with the exercise. EBI has a Clustal Omega web server, and getting a tree from this is matter of a few clicks of the mouse.
Actually you convinced me, I'll talk to my teacher about that! Thanks so much :)