I would like to perform RAD-seq on one zooplankton with a body-size between 0.5-1cm. However, the DNA extracted from each individual by chelex can not work for library preparation. So I am considering pooling several individuals together to extract DNA, but I am not sure if it will affect the later population genomic analysis.
Or maybe I should think about some other NGS methods such as UCE?
Hope for your help, thank you!!!
Hard to say without knowing what sort of yields you are getting from your extracts. What is your concentration/ total yield looking like?
It will depend on what is the concentration range you are getting and what is your target.
There are ways to concentrate the DNA extract like speedvac, please try if this helps. And to prepare the ddRAD library you do not actually need a lot of DNA, it is advisable to use 200ng but I have successfully sequenced using as alow as 1ng of DNA.
If you pool the individuals you won't be able to do any individual-based analysis.
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