I am finding out R value for different species through MEGA by comparing to other similar species.
I am confused about the transition/transversion (R) value. It should be higher or lower? How many sequences should I select? The sequences should be of same species or also of different species?
I need your expert guidance please.
Tell me what your project is: what are your all of the species you are comparing and what molecular data are you using (what markers?)
You will need to read a textbook about molecular evolution. This will teach you about the Transitions/Tranversion ratio and other useful parameters for constructing trees in MEGA or any other phylogeny software.
Li and Grauer. Fundamentals of molecular evolution. Sinauer.
Ziheng Yang. 2014. Molecular Evolution: A Statistical Approach.
Sidhar Kumar. Molecular Phylogeny Reconstruction Chapter Molecular Phylogeny Reconstruction
Aloha Sohail, I can say a few words here. First point: transition mutations are generated at higher frequency than transversions.
Transitions (tn) are substitutions of purine for purines or pyrimidines for pyrimidines, transversions (tv) are purines for pyrimidines and vice versa, these are more rare in coding sequences, tn tend to have a diminished phenotypic impact relative to tv, along the lines of the way that the third position substitutions in a reading frame are more common, and tend to be evolutionarily, and phenotypically, neutral, in this case due to third position wobble of course. Thus 1st and 2nd position substitutions are scored as more important (rare) in phylogenetic data, again akin to tv/tn ratio.
Patrice Showers Corneli I am working on DNA barcoding of fish species. I want to construct phylogenetic trees for different fish species.
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