Phylogeography of Ara militaris (Military Macaw): Implications for Conservation

Round 1

Reviewer 1 Report

Dear authors
The ms is well-written and the conclusions are based on a large, geographically consistent, data set. I enjoyed the reading, and I think this represents a fine contribution to this species. I found some points listed below, but my main criticism is the lack of boldness of the authors in doing taxonomic conclusions. Their data is robust, clear, and well-collected, and it's time to define the number of species in Ara militaris. I think that elevating mexicanus to species status and synonymizing bolivianus with militaris will increase the value of the paper and will provide a robust tool for the conservation of both taxa. Please do a little effort to define this important question with these data sets.
Line 70-71 - it is not an alarming rate (so far). Please rephrase and give the correct tone for it.
Line 75 - Ara macao is not listed as critically endangered. Rephrase it. And it is Scarlet Macaw, not Macaws.
Line 77 - Please include a ref. here.
Line 96 - please rephrase as it is incorrect as currently written.
Line 188 - Ara severus
Line 237 - Ara severus - correct through the text, please
Line 399 - Ara chloropterus - authors, please attention to the scientific names. I will not correct them from this point.
Lines 553-554 - Ara macao and Cyanoliseus patagonus are not threatened.

Please include the number of the collecting permits and other permits, if existent (ethical approval etc.)

none.

Author Response

La respuesta se agrega en un archivo PDF

Author Response File: Author Response.pdf

Reviewer 2 Report

see attahed file

Comments for author File: Comments.docx

see attahed file

Author Response

answer is added in a PDF file

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

No more comments.

Author Response

There were no further comments.

Reviewer 2 Report

I appreciate the rapid turnaround that the authors have attempted to make on my comments, but I am afraid they have either not grasped or addressed my central concern, which is that they have chosen several outgroups for their analysis, and none of these outgroups are the known closest sister taxon to the focal taxon of study.  Choosing taxa other than the known closest sister taxon can affect the reliability of phylogenetic inference, particularly when sampling is low.  Until this issue is addressed adequately, unfortuantely I cannot recommend this valuable research for publication.  Perhaps the authors would benefit from reading and incorporating the latest research in this area (e.g., DeSalle et al 2023  https://www.sciencedirect.com/science/article/abs/pii/S1055790323001069 and references therein). I simply do not see how the authors can omit the sister taxon to their focal taxon and expect to be able to infer relationships within their focal taxon accurately.  Asserting that the sister taxon and the focal taxon have independent evolutionary trajectories is irrelevant, and I fail to see how this addresses the issue.  The authors do not state that samples or sequence would be difficult to obtain, so in the absence of further justification, these should be included in the next version of this manuscript. 

Author Response

Please see the attachment.

Author Response File: Author Response.docx

Round 3

Reviewer 2 Report

I congratulate the authors on their rapid turnaround of these comments and their efforts to thoroughly and courteously address them. I appreciate the addition of the new text in red making it easy to see how the points were addressed. It is a shame the sister taxon could not be included, but the extra work to examine biases (adding an extra analysis in which extra outgroups were removed; comparison with another analysis that did include the sister taxon) provide full transparency on any limitations that could arise.  Nice work!