We routinely use RADseq and UCE on Hymenoptera but also several other groups of insects (bark beetles, moths, carabid beetles). Each have different applications, the first may be powerful within genera and in species complexes. UCE can be efficient at that level also but are very convenient to decipher relationships at deeper level (between genera, families). It's difficult if not impossible to combine both into one analysis, because the sequenced sites globally do not overlap. RADseq is ideal for small genome (

Dear Yean-Yves Rasplus,

Thanks for your prompt and wonderful answer on the question. Also, we do appreciate your kind comments and offers of helps.

Best,

cd

Hello Chao-Dong,

I agree with what Jean-Yves said about the differences between RAD-seq and UCE. With that said I would just like to add that there is no point in using all four of these methods since GBS and RAD-seq are different variants of the same method of reducing the representation of the genome using restriction enzymes. Some of these methods can be used for even larger genome. For example, my lab uses ddRAD for organisms with genome sizes of up to 3Gb and can still pool 96 or more individuals per lane with high coverage. Below is a paper that briefly goes through these methods along with other similar popular methods.

https://www.researchgate.net/publication/266914823_Demystifying_the_RAD_fad

In the same both UCE and AHE typically can answer very similar questions and there is no real point in running both of these for the same study.

The idea on combining a restriction-site based method and a probe based method has been gaining some attention in the recent literature, although the focus has been more on which one is base for particular question and for resolving phylogenies at certain time scales. Below is a recent post that talks about some of these papers and gives citations that are useful. The over all conclusion is that these methods often arrive at the same question and by comparing the different methods we have learned more about how to analyze data better especially with regards to setting parameters for quality filtering.

http://www.molecularecologist.com/2016/03/radseq-vs-uces-round-3/

Hope this helps.

Best Regards. 

Article Demystifying the RAD fad

How many individuals do you need to do DNA extraction for RADseq? When doing the test experiments, we put 5-15 ones together to extract DNA. The sequencing company reported serious DNA degradations. Any comments/suggestions?

cd

Usually with RADseq you do not pool individuals for extraction. You usually extract each individual and barcode after digestion in order to pool them for sequencing, this way you have information on each individual. Many protocols suggest digesting 100-1000ng of DNA but we have had success with less than 40ng before. DNA degradation is a big problem, if you do not have at least some intact genomic DNA than it is really hard to use any of the methods you mentioned. If you have a gel picture of your DNA feel free to post it, it may help with telling you if the DNA is too degraded.

Best Regards 

Dear Max, we are dealing with small parasitoid wasps, which are normally 1-3 mm long. I'll request the gel from the company.

Best,

cd

Here is a preprint of a paper doing nextRAD on psyllid insects which are also a few mm long. http://biorxiv.org/content/biorxiv/early/2016/04/06/046540.full.pdf

Dear all,

We are doing RADseq on Trichogramma unique individuals, these "beasts" are ca 0.3 mm long !!!. To do so we use Qiagen individual extraction followed by WGA and it works very well. We tested the reliability of WGA and we did not detect any problems. To do so we let a male (M1) and a female (F1) tricho mating. We obtained multiple female descents (F2s) that we isolated (no mating) and let them produced males (M3s). We pooled all these males (n=ca 2000, in a kind of natural genome amplification) and compare the results with WGA of  M1 and F1. However, for some reasons we had poor results using WGA for UCE capture, in average we lost one third of the loci captured on WGA individuals.

Best

JY