Dear Dr Lorch,

Thank you for submitting your manuscript entitled "Population genetic analysis of Ophidiomyces ophidiicola, the causative agent of snake fungal disease, suggests recent introductions to the USA" for consideration as a Research Article by PLOS Biology.

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Dario Ummarino, PhD

Senior Editor

PLOS Biology

dummarino@plos.org

Dear Dr Lorch,

Thank you for submitting your manuscript "Population genetic analysis of Ophidiomyces ophidiicola, the causative agent of snake fungal disease, suggests recent introductions to the USA" for consideration as a Research Article at PLOS Biology. Your manuscript has been evaluated by the PLOS Biology editors, an Academic Editor with relevant expertise, and by independent reviewers. Please accept my sincere apologies for the delayed editorial process, which was due to difficulties in securing reviewers with relevant expertise.

As you will see in the reviews attached below, all reviewers appreciate the importance and accuracy of your work, and raised minor points around methodology, reporting and discussion/interpretation of the results. In light of these reviews, we are pleased to offer you the opportunity to address the comments from the reviewers in a revised version that we anticipate should not take you very long. We will then assess your revised manuscript and your response to the reviewers' comments and we may consult the reviewers and the Academic Editor again. We also request that your please address the following data and other policy-related requests:

1) Title - we suggest minor changes for clarity and appeal: "The population genetics of the causative agent of snake fungal disease suggests recent introductions to the USA".

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Sincerely,

Dario

Dario Ummarino, PhD

Senior Editor

PLOS Biology

dummarino@plos.org

*****************************************************

REVIEWS:

Reviewer #1: In the paper "Population genetic analysis of Ophidiomyces ophidiicola, the causative agent of snake fungal disease, suggests recent introductions to the USA", the authors sequence 82 strains of the snake fungal disease Oo and perform genomic, population genetic and dating analysis to predict the timing and location of its emergence in the United States.

Overall, it is very nice study, with clear results regarding the population of Oo in north America. Correspondingly, I only have very minor suggestions for improvement.

Firstly, given the authors have generated a new reference strain, I'd like to see a BUSCO gene completeness report for that (E.g. what percent of single copy orthologs were found?). It would also be nice to give further details about any previous genome assemblies that were available, and why these were deemed unsuitable / why they generated a new one?

Secondly, for variant calling with GATK, I'd like a proper description of the pipeline, including all commands used, and in particular, a description of any hard or soft filters used. The current description of variant calling would not be sufficient to replicate this study.

Finally, I think the tree with all clades i.e. clade III (currently in supplemental) should probably be added to Figure 1 (perhaps as part A, while the other 2 parts become B and C). I'm not certain what the rationale of having it supplemental is, other than it appearing much more distant. For the Figure 1 legend, you should also describe what the branch lengths show / the length key.

Otherwise, this was an enjoyable and informative report on their work.

Reviewer #2: This is an important study on the population genetic history of an emerging fungal pathogen affecting a large and diverse group of wildlife. I think the work warrants close consideration by PLOS Biology. I really only have one significant concern, which is that the distinction between the two hypotheses seems somehow artificial. We understand the range of historical possibilities without arbitrarily designating these as two different hypotheses, although I recognize scientific writers differ in style sometimes to achieve the appearance of adherence to the relatively simplistic concepts of the "hypothetico-deductive method". The point is, I would welcome the authors to describe the historical possibilities with greater nuance and richness rather than adopt the binary either/or of the "novel pathogen hypothesis" vs "endemic pathogen hypothesis", especially since their own findings support a much more complicated pattern of introduction. Also, might it not be the case that the relatively recent detections of Oo are due to environmental change or stress, in which case the "emergence" of this disease should be causally attributed to both recent (post-colonial) introductions AND environmental changes?

I also have a few questions that the study does not address, but which might be considered in the discussion.

- Why is Clade II not now spreading in other parts of the world?

- What mechanisms might be offered to explain recombination, i.e. under what conditions might coinfection of different lineages within Clade II have occurred?

Overall, this is a well-conducted and well-written study. One qualification I would like the authors and editors to note is that I do not consider myself sufficiently qualified to evaluate the specific details of the bioinformatic pipeline.

Dear Dr Lorch,

On behalf of my colleagues and the Academic Editor, Andy Dobson, I am pleased to say that we can in principle accept your Short Reports "The population genetics of the causative agent of snake fungal disease indicate recent introductions to the USA" for publication in PLOS Biology, provided you address any remaining formatting and reporting issues. These will be detailed in an email that will follow this letter and that you will usually receive within 2-3 business days, during which time no action is required from you. Please note that we will not be able to formally accept your manuscript and schedule it for publication until you have completed any requested changes.

Please take a minute to log into Editorial Manager at http://www.editorialmanager.com/pbiology/, click the "Update My Information" link at the top of the page, and update your user information to ensure an efficient production process.

PRESS

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Thank you again for choosing PLOS Biology for publication and supporting Open Access publishing. We look forward to publishing your study. 

Sincerely, 

Dario Ummarino, PhD 

Senior Editor 

PLOS Biology

dummarino@plos.org