Basically, we used RAPD to determine the genetic variation of species from two different populations.
In which genetic variation is opposite of genetic similarity.
Numerical taxonomy and multivariate analysis system (NTSYS-pc) software Version 2.1 is commonly used to generate the dendrogram for RAPD.
The dendrogram was generated based on the similarity coefficient only. The version 2.1 does not ask me whether I want to calculate based on genetic variation or genetic similarity. So it straight away produce the dendrogram by calculating genetic similarity.
Someone told me that the dendrogram generated based on similarity coefficient is not appropriate/ VALID. Because RAPD is used to determine genetic variation only!
But I have search through many research papers, many paper generated RAPD dendrogram based on the similarity coefficient.
I think what I’m doing is correct, but I was confusing now.
I wish molecular scientists or who had experience in RAPD study need me to clarify it.
Thank you.
Kuan,
Genetic similarity is a distance between two accessions or populations with relation to genetic distance as Similarity=1-Distance. Genetic variation is usually a measure of genetic relations of individual organisms within one population (species). Geographic variation may mean genetic difference (distance) in populations from different locations as well. If you use RAPDs, Genetic similarity (GS) can be estimated based on
Jaccard similarity coefficient, using the expression GSij =a/(a+b+c), where a = number of coincidences of type (1-1), b = number of discordance of type 1-0 and c =number of discordance of type 0-1. Genetic distances (GD) is estimated by DG = 1 − GS, but where are many other ways to measure such distance, everyone has own positive and negative sides.
I am afraid that you used in NTSYS simple similarity = a+d/(a+b+c+d), where a = number of coincidences of type (1-1) d= coincidences of type (0-0), b = number of discordances of type 1-0 and c =number of discordances of type 0-1, or another simple distance.
Dear Kuan
Most references agree that RAPD represents not repeated marker and has a random pattern, and there are many markers give the best indicator like AFLP and SNP.
Good Luck
Dear Kuan,
I agree that RAPD is not so stable and reliable for genetic structure analysis. At present , the SSR and GBS based molecular marker are the mainstream to test the genetic diversity and structure.
For the dendrogram of population or individual, you have many choice to carry out with different genetic distance estimation. You could generate a genetic distance matrix firstly, then use PHYLIP or MEGA to construct the dendrogram.
Jie
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