Hi colleagues,
I try to screen some chloroplast universal primers to construct TCS network (and maybe cp haplotype phylogenetic tree and divergent time for each code) for one species. I read some papers and try to find how many variations are necessary. But, I found that the number of variations researchers used are very different (from c.10- c.40).
Is there any principle to decide how many variations is necessary?
Is it as more as possible or others?
Thank you!
There is no minimum number of variations required to use TCS or other minimum spanning network/tree algorithms. If you only had a single variable site, but it split your samples by taxonomy, geography, morphology, etc. that could be informative for interpreting your data. Certainly, the more variability you have the more structure your network will show. There are many published networks with less than 10 steps/mutation changes within chloroplast haplotype networks, especially when researchers are examining populations within a species or recent divergence among species..
Hi Yue
Yous should use synapomorphic (or apomorphic) mutations, avoiding homoplasy. Then, the greates the number of mutations you score, the greatest the chances to find informative mutations.
Hope this helps
Pablo
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