To do so, we did not download named sequences from GenBank, but used a carefully annotated and checked database with a built-in phylogeny that would allow us to obtain monophyletic clades, regardless of their names. We thus only briefly discuss names and taxonomy in our analysis. Given that both reviewers commented on this issue, we tried to clarify our aims and included a sentence at the end of the introduction, in order to clarify the point. We hope that now both reviewers, and all other potential readers, will not be misled by our approach. We do not deal with taxonomy at all, only with testing the presence of a barcoding gap. Similarly to the replies for the previous reviewer, our aim was not to start from known and named sequences and test whether species from DNA taxonomy matched them or not; our aim was to test whether a barcoding gaps existed at all. Given this rationale and the kind of data we used, no clear statement towards the two barcoding groups within Cylindrospermopsis can be made. Nearly all sequences within the database are termed Cylindrospermopsis raciborskii by the people who deposited the sequences. However the clade does not contain the type-strain (which was not in the database). So we would rather not speculate too much on the taxonomic naming of these and other barcoded groups. However, we can clearly say that what is deposited in database SILVA 111 as Cylindrospermopsis contains two species with a barcoding gap. For Planktothrix we added a sentence: “Considering the naming of Planktothrix sequences in the database, some OTUs and ABGD units seem to correspond not only to monophyletic groups but also to named species such as P. mougeotii or similarly in the case of Fischerella muscicola (Figure 3).” R6 However we wish to remain careful on these kinds of statements since we are not sure if the underlying naming of the species used is correct or not.
Given that both reviewers commented on this issue, we tried to clarify our aims and included a sentence at the end of the introduction, in order to clarify the point.