On 2015 Jul 21, Eric Johnson commented:

The authors may have left an incorrect impression about the cost of carrying out RAD-Seq library preparation when they write, "we use a double restriction enzyme (RE) digest (i.e., a restriction digest with two enzymes simultaneously) that results in at least five-fold reduction in library production cost–complete ddRADseq libraries cost ~$5 per sample, while the necessary enzymatic steps following the initial restriction digest and ligation in random shearing RAD libraries alone introduce a cost of ~$25 per library (NEB, Ipswich, MA)."

RAD-Seq genotyping when performed on a population involves a pooling step of combining 12-48 individuals before shearing. Thus, the $25 cost for shearing is typically $1 or less for each individual in a pool. A single-sample ddRAD library would usually include a Pippen Prep size-selection step, driving the cost towards $50. ddRAD is a fine method and can stand on its own without needing poorly constructed comparisons.

The article may also leave readers with the impression that RAD-Seq cannot be carried out with less than 100 ng DNA, when the authors write "Furthermore, the elimination of several high-DNA-loss steps permits construction of ddRAD libraries from 100 ng or less of starting DNA." Rad-Seq does just fine with 50 ng, so the elimination of the steps is not what permits libraries to be made with 100 ng or less.

On 2015 Jul 21, Eric Johnson commented:

The authors may have left an incorrect impression about the cost of carrying out RAD-Seq library preparation when they write, "we use a double restriction enzyme (RE) digest (i.e., a restriction digest with two enzymes simultaneously) that results in at least five-fold reduction in library production cost–complete ddRADseq libraries cost ~$5 per sample, while the necessary enzymatic steps following the initial restriction digest and ligation in random shearing RAD libraries alone introduce a cost of ~$25 per library (NEB, Ipswich, MA)."

RAD-Seq genotyping when performed on a population involves a pooling step of combining 12-48 individuals before shearing. Thus, the $25 cost for shearing is typically $1 or less for each individual in a pool. A single-sample ddRAD library would usually include a Pippen Prep size-selection step, driving the cost towards $50. ddRAD is a fine method and can stand on its own without needing poorly constructed comparisons.

The article may also leave readers with the impression that RAD-Seq cannot be carried out with less than 100 ng DNA, when the authors write "Furthermore, the elimination of several high-DNA-loss steps permits construction of ddRAD libraries from 100 ng or less of starting DNA." Rad-Seq does just fine with 50 ng, so the elimination of the steps is not what permits libraries to be made with 100 ng or less.