Paper: Climatic and Geographic Influences on Cumacea Genetics in the Northern North Atlantic

[TahiriNadia]

If you are creating this PR in order to submit a draft of your paper, please name your PR with Paper: <title>. An editor will then add a paper label and GitHub Actions will be run to check and build your paper.

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Editor: Sanhita Joshi @sanhitamj

Reviewers:

• Aris Nivorlis
• Kevin Lacaille @kevinlacaille

[github-actions[bot]]

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Directory	Preview	Checks	Updated (UTC)
papers/Gagnon_Kebe_Tahiri	🔍 Inspect	✅ 71 checks passed (3 optional)	Sep 23, 2024, 10:40 PM

[ameyxd]

@TahiriNadia @JustGag thanks for the submission. Can you make the updates requested to run the checks?

[TahiriNadia]

Hi @ameyxd and @rowanc1 I don't know why I found the following issue; the DOI is functional.

× DOI Exists: DOI not found: https://doi.org/10.1016/S0967-0645(97)00046-5 [wilson_historical_1998]

[TahiriNadia]

Hi @ameyxd and @rowanc1 I don't know why I found the following issue; the DOI is functional.

× DOI Exists: DOI not found: https://doi.org/10.1016/S0967-0645(97)00046-5 [wilson_historical_1998]

@cbcunc any idea related to DOI?

[JustGag]

Hi @kevinlacaille ,

Thank you for your comments and suggestions.

[JustGag]

Technical Content

Computational Content:

The computational methods, including the use of aPhyloGeo software, are thoroughly explained. Including a supplementary section or appendix with the complete code used for the analyses could enhance verifiability.

Reply: Thank you for your comment. We have made sure that all the code and parameters used in our analyses have been put on the aPhyloGeo library, which can be accessed via the GitHub link in the abstract.

Best regards,

Justin Gagnon

[JustGag]

Verifiability

Source Code and Data:

The paper includes references to the source code available on GitHub and PyPi, enhancing verifiability. Ensure that the links are up-to-date and that the repositories contain clear documentation for users to replicate the study.

Data sources are clearly identified, and the methodology allows for reproduction of results.

Reply: Thank you for your comment. We have ensured that the links are up-to-date and that the repositories contain clear and relevant documentation for users to reproduce our study.

Best regards,

Justin Gagnon

[kevinlacaille]

@JustGag thank you for your updates! Could you please attach the compiled PDF to this pull request?

[TahiriNadia]

@JustGag thank you for your updates! Could you please attach the compiled PDF to this pull request?

@kevinlacaille - Thank you for the positive reviews and detailed feedback. We will thoroughly review the paper multiple times to refine the writing.

For the PDF question, we currently only have the web version available: https://sites.curvenote.com/build/01906ae9-4361-7ea5-b71c-46a1bceb0204

[JustGag]

Jargon and Accessibility:

Due to the interdisciplinary nature of SciPy, highly domain-specific jargon should be avoided or explained where possible. Terms like "phylogeographic models," "mitochondrial 16S rRNA gene," and "Robinson-Foulds distance" are well-explained. However, it might be helpful to provide brief explanations or footnotes for highly specialized terms, e.g., "thermohaline circulation" or "benthic habitats."

Reply: Thank you for your comments. We have added a footnote to the article for the specific terms you suggested, such as "thermohaline circulation" and "benthic habitats".

[kevinlacaille]

@JustGag , @TahiriNadia , et al.,

Thank you for the updates. Please tag me back in when the paper is ready for a re-review!

Cheers, Kevin

[JustGag]

Novelty and Impact

Advancement of the Field:

The study presents a novel investigation into the genetic and environmental correlations in Cumacea. Emphasize the novelty more explicitly by comparing it directly with previous studies in the introduction or conclusion sections. Highlight how this research could influence future studies or practical applications in marine conservation and climate change mitigation.

Reply: We thank you for this pertinent comment. We have included a paragraph at the end of the "Related work" section explaining and highlighting this study's potential influences on future studies or practical applications in marine conservation and climate change mitigation.

[JustGag]

Other Requirements

Citations and Acronyms:

Maintain consistency in citation style. For example, use either "Figure \ref{fig}" or "Fig. \ref{fig}" uniformly throughout the text.

Acronyms are well-defined at first mention. Ensure that all technical terms are consistently defined and used throughout the paper.

Reply: Thank you for your comments. We have made sure to maintain the citation style consistent throughout the article. In addition, we have checked that all acronyms are well-defined when first used.

[JustGag]

Ensure that all methodological steps are clearly defined. The section on DNA sequence analysis should detail the specific software versions and parameters used for reproducibility.

Reply: Thank you for this comment. In the abstract, we have included the YAML file in the aPhyloGeo GitHub link. We added the main parameters to the article (Results).

[JustGag]

Written Quality

Clarity and Coherence:

Some sections, particularly in the "Materials and Methods" and "Results" sections, use complex sentence structures that might be simplified for clarity.

Reply: Thank you for your pertinent comment. We have simplified the sentence structure in the “Materials and Methods” and “Results” sections.

[JustGag]

Length

Page Limit:

TBD if the paper adheres to the page limit (8 pages). Some sections, such as the "Introduction" and "Results," could be trimmed to focus more on key findings and less on background information that might be well-known to the target audience.

Reply: Thank you for your comment. We have reduced the “Introduction” and “Results” sections to focus more on the key findings and less on background information that might be well-known to the target audience.

[JustGag]

Verifiability

Workflow Description:

The workflow description is comprehensive. A flowchart or diagram summarizing the workflow could help readers better understand the sequence of steps involved.

Reply: Thank you for this insightful remark. We have included a flowchart in the Materials and Methods section that summarizes the workflow.

[JustGag]

Other Requirements

Figures and Tables:

Ensure all figures are properly referenced in the text and discussed in detail.

Reply: Thank you for your comments. We have ensured that all figures are correctly referenced in the text and discussed in detail. However, an in-depth analysis of the results can be found in the “supplementary” section of this GitHub link (https://github.com/tahiri-lab/Cumacea_aPhyloGeo).

[TahiriNadia]

@JustGag , @TahiriNadia , et al.,

Thank you for the updates. Please tag me back in when the paper is ready for a re-review!

Cheers, Kevin

Thank you, @kevinlacaille, for your valuable feedback. @JustGag and I have implemented the suggested modifications.

[kevinlacaille]

Thank you @JustGag and @TahiriNadia! Before I re-review, could you please compile the latex and attach a PDF of the paper to the PR?

[TahiriNadia]

Thank you @JustGag and @TahiriNadia! Before I re-review, could you please compile the latex and attach a PDF of the paper to the PR?

Thank you, @kevinlacaille. This year, the format will be HTML during the preparation and review steps, and the PDF will be created only after acceptance, unlike in previous years. I asked the same question at the beginning because of the page limitations. Citation: 'The paper is written and reviewed using the interactive HTML view (i.e. myst start), the PDF is built upon acceptance only'. Source: https://github.com/scipy-conference/scipy_proceedings?tab=readme-ov-file

[sanhitamj]

Thank you @JustGag and @TahiriNadia! Before I re-review, could you please compile the latex and attach a PDF of the paper to the PR?

@kevinlacaille, @TahiriNadia you can see the (compiled) preview here. Or in the Github-Actions sections, click on the Inspect link.

[JustGag]

Language and Grammar

Grammatical Errors:

In the abstract: "The most represent cumacean are those of the Diastylidae and Leuconidae families" should be "The most represented cumaceans are those of the Diastylidae and Leuconidae families."

Lengthy Sentences:

In the abstract: "These initial results underline the need for further exploration to understand the relationships between the genetics of cumacean and their environment." could be split into "These results highlight the need for further exploration. Understanding the relationships between cumacean genetics and their environment is crucial."

Awkward Phrasing:

In the introduction: "The slowdown in the formation of cold, deep waters due to the loss of Arctic sea ice can influence their regional dynamics and chemistry" could be rephrased to "The loss of Arctic sea ice and the resulting slowdown in cold, deep water formation may influence regional dynamics and chemistry."

Reply: Thank you for your comment. We've removed this sentence from the introduction.

[JustGag]

Language and Grammar

Clarifying Terms:

In the introduction, terms like "benthic habitats" are defined well, but others, such as "thermohaline circulation," could benefit from brief explanations or a glossary to aid interdisciplinary understanding.

Reply: Thank you for your comment. We have removed the term "thermohaline circulation" from the introduction.

[JustGag]

Formatting and Consistency

Citation Style:

Ensure consistency in citation formatting. For example, in the introduction, "as well as the North Atlantic at high latitudes, play an essential role in the {thermohaline circulation}" should consistently use either full citation or abbreviation within brackets: {Thermohaline circulation}\citep{talley2013closure}.

Reply: Thank you for your comment. We have removed the term "thermohaline circulation" from the introduction.

[JustGag]

Formatting and Consistency

Figure Labeling:

Maintain consistency in figure references. For example, use "Figure \ref{fig:fig2}" uniformly throughout the text.

Reply: Thank you for your comment. We have taken care to maintain consistency in figure references.

[JustGag]

Overall Recommendations

Interdisciplinary Accessibility:

Due to SciPy's interdisciplinary nature, avoid or explain domain-specific jargon where possible. Consider adding a glossary for specialized terms like "thermohaline circulation" or "benthic habitats."

Reply: Thank you for this pertinent comment. We've added a glossary for benthic habitat as a footnote and removed the term "thermohaline circulation". You can access it by placing your mouse cursor over the number “[1]” at the top right of the term.

We have also added a footnote “[2]” for the term “phylogeographic models”.

[cbcunc]

Closing to clear pre-commit.ci check. WIll reopen immediately.

[tkoyama010]

Hmm... Still have pre-commit.ci check.

[cbcunc]

Trying again after hotfix https://github.com/scipy-conference/scipy_proceedings/pull/1018

[cbcunc]

@tkoyama010 Still there.

[tkoyama010]

@cbcunc Could you please update branch for this PR.

[cbcunc]

@cbcunc Could you please update branch for this PR.

@tkoyama010 I'm not finding this dialog or button.

[tkoyama010]

Please go to the setting tab and enable this setting.

[cbcunc]

Trying to add update button after changing settings.

[cbcunc]

@tkoyama010 Setting changed and PR closed/reopened. Failing check is still there.

[tkoyama010]

@cbcunc Could you please update branch for this PR.

@cbcunc Thanks. Please push this buttom.

[cbcunc]

@cbcunc Could you please update branch for this PR.

Again, the button is not there.

[tkoyama010]

Hmm... That's wired. What I want to do is add .pre-commit-config.yaml to this PR branch. Is it possible to add it to this branch of the file I added in #1018?

[tkoyama010]

Even if this is an error, there is no problem with merging, so we can leave it as it is.

[matthewfeickert]

Even if this is an error, there is no problem with merging, so we can leave it as it is.

I agree that this is superficial (the current .pre-commit-config.yaml on the 2024 branch doesn't do anything at the moment) and so not any concern for merging, but if Nadia wants to try to do a rebase off of 2024 that would be an easy way to test this. Should be a "trivial" rebase too in the sense that all of the paper files are new files and so it shouldn't be possible to hit any conflicts. :+1:

[cbcunc]

@tkoyama010 All it took was a new commit. Make sense as it was triggered on commit.

[JustGag]

Content and Structure

Materials and Methods:

The section is detailed but could benefit from additional clarification on methodological steps. For example, specify software versions and parameters used in DNA sequence analysis for reproducibility.

Reply: Thank you for these comments. In the abstract, we have included the YAML file in the aPhyloGeo GitHub link. We added the main parameters to the article (aPhyloGeo section).

[sanhitamj]

@JustGag tomorrow is the last day of the edits by the authors.

@kevinlacaille will you please take a look at the paper and get back with your verdict about the final draft?

[kevinlacaille]

Hi all, please let me know when updates have been completed so I can provide my final review.

[JustGag]

Formatting and Consistency

Consistent Terminology:

Ensure consistent use of "Cumacea" versus "cumacean" throughout the document. For example, use "Cumacea" when referring to the taxonomic group and "cumacean" when referring to individual species.

Reply: Thank you for your comment. We have made sure that the use of “Cumacea” versus “Cumacean” is consistent.

[JustGag]

Formatting and Consistency

Section Headings:

Ensure consistent capitalization and formatting of section headings. For example, use either "Materials and Methods" or "Materials & Methods" consistently across the document.

Reply: Thank you for your comment. We have made sure that the capitalization and formatting of section headings are consistent.

[JustGag]

Formatting and Consistency

Code Formatting:

Code snippets should consistently follow PEP8 guidelines, ensuring proper indentation and line spacing, as shown in the aPhyloGeo package code listings.

Provide comments within the code to explain key steps and logic, particularly for complex calculations.

Consider providing a brief description before each code listing to summarize its purpose and relevance to the study.

Reply: Thank you for your pertinent comments. We have ensured that the code extracts comply with the PEP8 guidelines. We have also provided comments explaining the key steps and logic of each code. Finally, we've included a brief description before each code to summarize its purpose and importance in our study.

[JustGag]

Hi @kevinlacaillehttps://github.com/kevinlacaille, I am replying that we have implemented your suggestions in the comments you filed on our GitHub page. Would it be better if I finished replying to these before you start reviewing the article?

Thank you very much

Justin Gagnon

---

De : Kevin Lacaille @.> Envoyé : 3 septembre 2024 13:50 À : scipy-conference/scipy_proceedings @.> Cc : Justin Gagnon @.>; Mention @.> Objet : Re: [scipy-conference/scipy_proceedings] Paper: Climatic and Geographic Influences on Cumacea Genetics in the Northern North Atlantic (PR #925)

Hi all, please let me know when updates have been completed so I can provide my final review.

— Reply to this email directly, view it on GitHubhttps://github.com/scipy-conference/scipy_proceedings/pull/925#issuecomment-2327100903, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BFW5PNNRUPIBLSCKEHLKH5DZUXZHBAVCNFSM6AAAAABITSMO6CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMRXGEYDAOJQGM. You are receiving this because you were mentioned.Message ID: @.***>

[kevinlacaille]

@JustGag no need to reply to the comments, just please let me know when you're done updating the paper.

Cheers, Kevin