Referee 3's review:

The study by James et al., according to the abstract, "explores the utility of DArT in evolutionary studies of non-model organisms" and is a "demonstrably valuable addition to the set of existing molecular approaches used to infer biological phenomena" using the company's microarray genotyping technology.

General Comments
Unfortunately, because of the loose presentation of the scientific questions and the experimental data, it is extremely difficult to gauge whether or not they actually succeeded at accomplishing any of their claims. I would recommend that the study be extensively edited and the following issues addressed-

1. What is DArT?
2. What is the problem/question that they seek to address?
3. What are the existing technologies that are currently available to address the problem/question?
4. What are the advantages and disadvantages of DArT, and these should be presented in a consistent, quantitative manner.

Additionally, the content of the study is extremely uneven, at some points the authors go into exhaustive detail, whereas at others they gloss over important points; for example the treatment of plant phylogenetics is overly detailed and not put into context for the reader- indeed this material seems much too specific and filled with jargon for the general reader. In contrast, the comparison to existing genotyping technologies is inconsistent, at times they compare DArT to gel based techniques and sequencing, but without quantitation.
Finally, the manuscript is quite long and rambling given the amount of information it contains.

Specific comments
The lack of p. #s is irritating
Introduction: why are DNA microarrays limited to model organisms? There would appear to be many non-model genomes that have been sequenced. Why has DArT been previously restricted to Angiosperms? Last sentence is out of place.
Methods: what is a discovery array and a genotyping array, should be specific. Is this technology tied to the DArT software? Is it opensource? Can other array acquisition and analysis platforms be used? Define the "other parameters" used in the analysis. Provide reference for fuzzy k-means clustering. Explain the impact of ploidy differences on scoring efficiency in plain language.
Results: Describe the independent assay confirmation so the reader knows what comparison was performed.
Paragraph beginning PCO and PCoA analysis... this section needs a table summarizing the results.
Discussion: The section beginning, "Because the aim of this study was to pilot..., a range of methodologies were compared to inform similar future studies". The content that follows contains several additions observations that are better-suited for the results section. In addition the comparison is far from systematic, making it difficult to judge the relative merits of DArT vs. other methods. This is particularly evident in the paragraph that begins, "Practical advantages of DArT in Evolutionary Research".
All of the figures appear incomplete. Axes need to be labeled and descriptive legends included.

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N.B. These are the comments made by the referee when reviewing an earlier version of this paper. Prior to publication the manuscript has been revised in light of these comments and to address other editorial requirements.