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Dear authors, I am pleased to congratulate you on the acceptance of this manuscript for publication. I hope that you will continue your research in this direction to protect biodiversity in Thailand and the world at large.
[# PeerJ Staff Note - this decision was reviewed and approved by Jennifer Vonk, a PeerJ Section Editor covering this Section #]
I ask you to make some minor additions to the manuscript so that it can be published.
[# PeerJ Staff Note: It is PeerJ policy that additional references suggested during the peer-review process should *only* be included if the authors are in agreement that they are relevant and useful #]
The authors addressed my concerns and the other reviewers and it is now in good shape.
The authors better described the design and it is now acceptable.
The findings were good in DRAFT V1.0 and still stand.
The manuscript is well revised and worth publication.
The manuscript is well revised and worth publication.
The manuscript is well revised and worth publication.
The authors addressed all comments/suggestions that I had based on a previous version of the paper. I only have a few additional comments to this revised version (provided directly on the pdf of the paper). The manuscript is currently highly improved.
No comment
The manuscript reports on data on genetic diversity of a turtle species from Northern Thailand that can be important for its conservation and management.
Dear authors, I ask you to carefully correct all the comments of the reviewers and especially seriously revise the Discussion of the article. Table 2 should be formatted in accordance with international publishing standards or it should be removed, leaving only a few of the most important indicators from it in the text.
This is a brief but insightful paper; the topic is very specific, but the authors make it clear that it is intended to look at a very unique species in a very specific habitat.
The paper is reasonably well written, the data collected and the manuscript outline addresses and follows the requirements of this journal.
I would ask that the authors devote a little more insight as to why they used AMOVA and explain the application of Analysis of MOlecular VAriance and why that is a method to detect population differentiation utilizing molecular markers and its relevance to this study.
Appropriate animal protocols were followed.
The finds reflect the data collected and appear reasonable ad reproducible.
There were several novel and several routine analyses performed all seem appropriate.
There is a suggestion that current cultural (religious) ceremonies are putting pressure on this species, it is important to offer an alternative to the current practice.
Well written and interesting, albeit very specific to a species of turtle in a very finite area, not as broadly applicable, perhaps could add something as using this as a model for other specifies assessments and give some short examples.
The Manuscript as per the basci reporting is a nice peice of work but needs some formatting regarding grammatical errors. The abstract needs some upgradation and it is a scientific practice not to use reference in abstract.
Line 53-55: Please simplify the sentence " .... confirmed the distribution range of M. khoratensis in northeastern Thailand and its distribution is limited to the Chi river basin and upper Mun river basin to the Mekong river in Thailand."
Line 59: Please check the sentence and avoid using duplicated scientific names.
Line 86 : Please be consistent with the upper case or lower case which ever is applicable throughout the manuscript.
The experimental design is upto the mark but as the species is not required conservation then why this study is needed must be added to the manuscript.
Line 95-99: Please check the sentence case and upper case.
Line 111-113: Grammatical corrections needed.
Line 139 : The author needs to double check the primer annealing temperature and explain the need of taking a more than 30bp reverse primer and which is having a high melting temperature whether the forward primer is a standard one. Will it not creating some imbalance while amplifying?
Line 147: Either write "in the supplemetary file' or simply delete it.
Line 148: Please be consistent with the subheading.
Line 153: Previously the author stated that the product size for Cytb is 1200bp and here they obtained 753bp why there is discrepancy? the author needs to explain in details. for ND4 same as previous.
Line 228-229: This is the concluding remarks which has to be written at the end.
In the discussion part the author needs to give more insights on the population differentiation and more about the bottleneck what was intended in the introduction part. Also, the Amova analysis shows no possible genetic differentiation but it showing high within population differentiation almost 100%, so author needs to address this in a descriptive manner and also author didnot described figure 3 in the discussion part.
Also, Why did the author concatenated the two genes and there was also some part of tRNA present there so what was that and author didnot discuss about that.
Also, if possible selection pressure analysis can be a great addition to understand the radiation of this species.
The submitted manuscript aims to test for population structure and identify the population trend of Malayemys khoratensis of the Isan Region in Thailand. The authors run a small suite of analyses on two mitochondrial genes to target their aims of population-level assessments of these turtles in Thailand. The manuscript is written well, with the exception of some sentences that could use clarification or rewording (I have made edits and comments for suggestions in the MS Word file).
Unfortunately, after downloading all files, I did not see any Figure legends and thus was not able to assess the full content of some of the figures (such as the map). I also had some inquiries for the authors on there analyses and interpretations. I am confused at how they have negative variation percentages from their AMOVA. This could indeed be due to a lack of population structure (which is what seems to be the case, and the authors mention this), but I think the negative values need to be addressed in the paper. I also think the authors need to be careful with their BSP interpretations, as it looks like any change in population structure is in a part of the plot with large error bars. I think recommending changes in conservation status needs to be done with more molecular data and analyses, to avoid the risk of resources being used on a species that, seemingly, is not in decline (though I cannot say this for certain).
For these reasons, I am choosing major revisions as a decision, as I believe this study is important and needed for assessing the populations of this species, but the discussion of results need to be edited and some more details are needed in the manuscript.
I think the authors have done a great job with their study, and I hope my comments and suggestions are helpful in further improving this already-interesting and well-performed study.
Experimental design is appropriate. I think the mentioning of including more data would be great for the discussion, as I understand that molecular datasets can become very expensive. I have some questions about the methods that are in the file I have attached.
The experimental design of this study is appropriate for the research aims, but I believe the interpretation of results needs to be revisited as there does not seem to be any drastic changes in population size over time. I find it interesting that the Mekong Basin has the higher diversity, but if there are many ways (human-mediated or natural movement of individuals) that turtles can get between basins, this may be a reflection of geography. I would like to see more of an explanation or hypotheses on the results of the haplotype/diversity estimates.
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I have read this paper with interest as I work and have worked on similar topics. My main comment is that the paper needs to be better focused on why it is important to study this species and this questions. There are various reasons in different sections of the paper, but none of them is clearly supported by background information on the species or the study area. Additionally, I suggest to remove one analysis, to add another one, and to check the AMOVA because I think that there may be an issue with how it has been set it up (see my comment on the Table with the AMOVA results).
I provided detailed comments and suggestions directly on the pdf of the paper. Feel free to contact me if you need additional information or have questions.
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