Aloha! I've been reading up on analysis of molecular data, but I am still not quite sure how to "best" analyze my molecular data sets of intergenic spacer (IGS) regions. The scope of my study is to identify closely relates species of a popular ornamental plant in Hawaii. I'm currently trying to analyze the utility of 6 IGS regions, but I'm not sure how to analyze it properly. I have the sequence data and have played around with various analyses and parameters in MEGA 6. However, I'm not quite sure if I'm doing it correctly, or at least if my methodology is correct.
I just wanted to gather educated opinions on whether or not there is a "CORRECT" or thorough way to do this kind of analysis. Or, in other words, I'm a little confused as to whether or not there are standard metrics to report to show whether or not a given IGS region is suitable for further testing of species discriminatory power on a much larger data set. How should I proceed?
Dear Kauahi,
You are working in the realm of barcode of life in plants. There are several criteria to qualify the power of a kind of sequence in terms of its ability to discriminate/identify species.
This is a good paper were you can see a well accepted criterion:
http://www.pnas.org/content/106/31/12794.full
On the other hand, Mega is a very good software; it can help you for the phylogenetic analyses, a good support for barcode of life. If you work with R, then you can use a package called spider, specialized in barcode of life analyses.
So far, rbcl, matk and ITS are among the best kinds of sequences to identify plant species.
Best wishes!
Humberto
Aloha Dr. Reyes-Valdes. Thank you very much for your response and the information. I did consider working with ITS, but I was worried that I might run into "problems" associated with tetraploid organisms. I haven't done deep research, but I have been told by others who work with ITS that this region can be a little tricky when dealing with polyploid species.
Aloha Kauahi, best wishes for your research. I doubt that the polyploid condition may bring any problems for this objective, but one never knows.
Buena suerte
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