On 2014 May 06, Eric Johnson commented:

The authors make a comparison between RAD and ddRAD and present the higher read coverage at each locus as a favorable feature of ddRAD, but the comparison is not useful. The ddRAD protocol they chose yielded 26,891 ddRAD loci and a per locus depth of 111 for the 3M reads. The RAD-Seq protocol they choose yielded 206,841 loci and a per locus depth of 14 for the same amount of reads.

The protocols could have been easily changed to make the loci number even by merely changing the RAD protocol to use a less-frequently cutting enzyme such as SbfI, which is one of the more common choices in RAD projects because it creates fewer loci needing sequencing. Reducing the RAD loci number would have increased the read depth at each locus.

The only conclusion a reader should draw from this comparison is that sequencing more loci will reduce the read depth at the loci, and that an appropriate enzyme should be chosen for the number of reads planned.

On 2014 May 06, Eric Johnson commented:

The authors make a comparison between RAD and ddRAD and present the higher read coverage at each locus as a favorable feature of ddRAD, but the comparison is not useful. The ddRAD protocol they chose yielded 26,891 ddRAD loci and a per locus depth of 111 for the 3M reads. The RAD-Seq protocol they choose yielded 206,841 loci and a per locus depth of 14 for the same amount of reads.

The protocols could have been easily changed to make the loci number even by merely changing the RAD protocol to use a less-frequently cutting enzyme such as SbfI, which is one of the more common choices in RAD projects because it creates fewer loci needing sequencing. Reducing the RAD loci number would have increased the read depth at each locus.

The only conclusion a reader should draw from this comparison is that sequencing more loci will reduce the read depth at the loci, and that an appropriate enzyme should be chosen for the number of reads planned.