Paper: Climatic and Geographic Influences on Cumacea Genetics in the Northern North Atlantic #925
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@TahiriNadia @JustGag thanks for the submission. Can you make the updates requested to run the checks? |
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Hi @ameyxd and @rowanc1 I don't know why I found the following issue; the DOI is functional.
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@cbcunc any idea related to DOI? |
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Hello, @TahiriNadia! I am the reviewer for your paper. Could you please provide me with the compiled PDF in this PR?
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Dear @TahiriNadia et al.,
Thank you for your submission to the SciPy conference proceedings. I have reviewed your paper, and I commend you for the thorough research and detailed analysis presented. Below, I provide feedback and suggestions for improvement based on the review criteria provided.
Written Quality
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Clarity and Coherence:
- The language is clear and the narrative is coherent. However, a few sentences are lengthy and could be split for better readability. For example, in the abstract, "These initial findings necessitate further exploration to elucidate the intricate relationships between Cumacean genetics and their environment." could be revised to "These findings necessitate further exploration to understand the relationships between Cumacean genetics and their environment."
- Some sections, particularly in the "Materials and Methods" and "Results" sections, use complex sentence structures that might be simplified for clarity.
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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."
Technical Content
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Scientific Soundness:
- The scientific content is robust and well-referenced. However, some claims would benefit from additional support or clarification. For instance, the assertion that "Cumacean diversity also exhibited variation across habitat types" could be strengthened by directly referencing specific data or figures.
- 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.
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Computational Content:
- The computational methods, including the use of
aPhyloGeosoftware, are thoroughly explained. Including a supplementary section or appendix with the complete code used for the analyses could enhance verifiability.
- The computational methods, including the use of
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.
Verifiability
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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.
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Workflow Description:
- The workflow description is comprehensive. A flowchart or diagram summarizing the workflow could help readers better understand the sequence of steps involved.
Other Requirements
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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.
- Maintain consistency in citation style. For example, use either
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Figures and Tables:
- Figures have clear captions, but some text within the figures is small and difficult to read. Increase the font size for better readability.
- Ensure all figures are properly referenced in the text and discussed in detail.
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Code Snippets:
- Code snippets are well-formatted. Ensure that all code snippets are indented consistently and follow PEP8 guidelines.
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.
Summary Feedback
Overall, this paper is a valuable contribution to the field of marine biology and environmental science. It effectively combines genetic and environmental data to explore the adaptation of Cumacea to their habitats. The methodology is robust, and the findings are well-supported by the data. A few minor revisions could enhance clarity and accessibility for a broader audience.
Cheers,
Kevin Lacaille
papers/Gagnon_Kebe_Tahiri/main.tex
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| However, studies have highlighted the complexity of the relationships between genetics and the environment, which many factors, such as genotype-environment interaction and natural selection, can influence. This complexity can make it challenging to identify unambiguous causal relationships between these two parameters \citep{balkenhol_identifying_2009}. Other studies mention that it is difficult to distinguish between the direct and indirect effects of the environment on genetics \citep{manel_perspectives_2010, balkenhol_landscape_2019}. Studies of the impact of the environment on the genetics of organisms may be limited by the methods available to measure genetic and environmental characteristics, as well as by logistical constraints related to data collection \citep{manel_perspectives_2010, shafer_widespread_2013}. To our knowledge, this last point may contribute to the fact that research on the environment and genetics of Cumacea is little explored, even though they remain essential for understanding how these deep-sea invertebrates adapt to fluctuating environmental conditions. | ||
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| As stipulated in the hypothesis of Darwin, individuals best adapted to their environment are likely to survive, reproduce, and evolve. The objective of this study is to deepen and strengthen the natural selection hypothesis by examining whether there are one or more locations within the DNA sequence of Cumacea, specifically in the mitochondrial 16S rRNA gene, that could correlate not only the segments of the sequence (i.e., windows) but also the Cumacea to their environment. |
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Consider adding a brief summary at the end highlighting the gap this study fills.
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Thank you for your comment. We added a paragraph at the end of the "Related work" section highlighting the gap this study fills.
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| As stipulated in the hypothesis of Darwin, individuals best adapted to their environment are likely to survive, reproduce, and evolve. The objective of this study is to deepen and strengthen the natural selection hypothesis by examining whether there are one or more locations within the DNA sequence of Cumacea, specifically in the mitochondrial 16S rRNA gene, that could correlate not only the segments of the sequence (i.e., windows) but also the Cumacea to their environment. | ||
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| \section{Materials and Methods}\label{materials-methods} |
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Consider adding a flowchart or diagram of the methodology.
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While detailed, some subsections could benefit from further simplification or breaking down into smaller, more digestible parts.
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While detailed, some subsections could benefit from further simplification or breaking down into smaller, more digestible parts.
Thank you for your comment. We have broken down most of the "Materials and Methods" section into smaller parts to make it easier to read.
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Consider adding a flowchart or diagram of the methodology.
Thank you for this insightful remark. We have included a flowchart in the Materials and Methods section that summarizes the workflow.
papers/Gagnon_Kebe_Tahiri/main.tex
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| Unlike the benthic invertebrates inhabiting the rocky intertidal environments of the Northwest and Northeast Atlantic, the evolutionary history and dynamics of deep-sea benthic invertebrates in the North Atlantic are less understood \citep{jennings_phylogeographic_2014}. Although many studies reveal intriguing patterns of genetic distribution among deep-sea benthic invertebrates (e.g., \citep{wilson_historical_1998, havermans_genetic_2013}), understanding the origin and demography of deep Atlantic biota is fundamental for comprehending their relationship with ongoing climate change, which should be considered a factor in the range expansion of deep-sea fauna \citep{jennings_phylogeographic_2014}. | ||
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| In response to the current climate emergency, this study aims to undertake an in-depth analysis of the influence of extreme climatic parameters and environmental peculiarities on Cumacea (crustaceans: Peracarida). Specifically, we seek to determine whether there is a correlation between the genetic information of mitochondrial 16S rRNA gene regions (i.e., windows) of Cumacea species sampled and the characteristics of their habitats. Our approach includes a comparative study to validate different phylogeographic models by comparing them with environmental factors found inside and outside the waters of the North Atlantic seas around Iceland. Additionally, we will update a Python package (currently in beta), called aPhyloGeo, to simplify these complex analyses. |
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Some domain-specific jargon (e.g., phylogeographic terms) could benefit from brief explanations.
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Provide a brief explanation of what aPhyloGeo does and why it's suitable for this analysis.
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Provide a brief explanation of what
aPhyloGeodoes and why it's suitable for this analysis.
Thank you for your comment. We have provided a brief explanation of what aPhyloGeo does and why it's suitable for our analyses.
papers/Gagnon_Kebe_Tahiri/main.tex
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| \begin{abstract} | ||
| Cumacea crustaceans serve as vital indicators of benthic health in marine ecosystems. This study investigates the influence of environmental parameters on their genetic makeup in the North Atlantic, focusing on Icelandic waters. We analyze mitochondrial 16S rRNA gene sequences from 62 Cumacea specimens collected across varying depths. Using aPhyloGeo software, we correlate these sequences with environmental data encompassing temperature, oxygen concentration, depth, and other relevant factors. | ||
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| Our analyses reveal significant spatial variation in environmental parameters, particularly depth, temperature, and dissolved oxygen. Cumacean diversity also exhibited variation across habitat types. Interestingly, specific genetic sequences displayed correlations with wind speed and oxygen levels, suggesting potential local adaptations to these fluctuating environmental conditions. |
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Can you quantify "significant"? Consider adding p-values or effect sizes, etc.
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Thank you for your comment. As we cannot quantify our results, we removed the word “significant” from the article.
papers/Gagnon_Kebe_Tahiri/main.tex
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| Our analyses reveal significant spatial variation in environmental parameters, particularly depth, temperature, and dissolved oxygen. Cumacean diversity also exhibited variation across habitat types. Interestingly, specific genetic sequences displayed correlations with wind speed and oxygen levels, suggesting potential local adaptations to these fluctuating environmental conditions. | ||
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| These initial findings necessitate further exploration to elucidate the intricate relationships between Cumacean genetics and their environment. This study lays the groundwork for establishing correlations between specific mitochondrial gene regions and environmental variables. If substantiated, these findings would support the hypothesis of natural selection driving local adaptation of Cumacea to environmental gradients in the face of climate change. The aPhyloGeo Python package is freely and publicly available on \href{https://github.com/tahiri-lab/aPhyloGeo}{GitHub}, and it is also available on \href{https://pypi.org/project/aphylogeo/}{PyPi}, to facilitate complex analyses. |
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This first sentence is passive. Consider rephrasing actively: "These initial findings highlight the need for further exploration..."
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Thank you for your comment. We have changed the sentence in the article according to your recommendation.
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| This paper is organized as follows: Section \autoref{related-works} reviews related work on the biodiversity and biogeography of deep-sea benthic invertebrates. Section \autoref{materials-methods} details the materials and methods used in this study, including sampling procedures, genetic analyses, and environmental data collection. Section \autoref{metrics} discusses the metrics used to evaluate phylogeographic models and the impact of environmental factors. Section \autoref{results} presents the results of our analyses. Finally, Section \autoref{conclusion} summarizes our findings and discusses their implications for future research and conservation efforts. | ||
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| \section{Related Works}\label{related-works} |
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Some sections in "Related Works" could be shortened or summarized to maintain focus on the primary research question.
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Thank you for your comment. We have shortened most of the sentences in the third and fourth paragraphs of the "Related work" section.
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| Our phylogeography study utilizes the Robinson-Foulds, normalized Robinson-Foulds, Euclidean, and Least-Squares distances to quantify topological differences between phylogenetic trees and assess dissimilarities between genetic sequences and environmental characteristics, providing a comprehensive analysis of evolutionary dynamics in Cumacea populations. | ||
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| \section{Results}\label{results} |
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The interpretation of figures could be expanded to provide more context and implications of the findings.
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The results are comprehensive but could be more concise. Focus on key findings and their implications. For example, the detailed explanation of figures could be summarized, with in-depth analysis provided in supplementary materials.
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The interpretation of figures could be expanded to provide more context and implications of the findings.
Thank you for your pertinent comment. We have expanded the interpretation of the figures to give more context and implications to our findings.
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The results are comprehensive but could be more concise. Focus on key findings and their implications. For example, the detailed explanation of figures could be summarized, with in-depth analysis provided in supplementary materials.
Thank you for this pertinent comment. We have summarized the results to focus on the key findings and their implications. We have also included an in-depth analysis of our results in the “supplementary” section on this GitHub link (https://github.com/tahiri-lab/Cumacea_aPhyloGeo).
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| All these results will need to be further investigated and analyzed in order to provide a more complete understanding of these results, and thus enable us to draw solid conclusions. | ||
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| \section{Conclusion}\label{conclusion} |
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The conclusion effectively summarizes the findings but could emphasize the broader implications more. For example, discuss how these findings could inform conservation strategies or future research directions. Consider adding a sentence or two about potential limitations of the study and how future research could address them.
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We thank you for these pertinent comments. We have added explanations and clarifications in the penultimate paragraph of the "Conclusion" on how our results could improve conservation strategies and the direction of future studies on the subject. We also discuss this in the last paragraph of the "Related work" section.
In addition, we have also added a fourth paragraph to the "Conclusion" concerning the limitations of our study and how future studies should address them.
papers/Gagnon_Kebe_Tahiri/main.tex
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| \section{Introduction}\label{introduction} | ||
| The vast North Atlantic and subarctic regions, particularly the Icelandic area and its surrounding waters, present significant ecological interest \citep{schnurr_composition_2014, uhlir_adding_2021}. The seas around Iceland exhibit a remarkable diversity of water bodies originating from various sources \citep{brix_iceage_2014}. These unique oceanographic and hydrographic characteristics shape benthic habitats through multiple parameters such as depth gradients, water mass indicators, and specific habitat configurations \citep{meisner_benthic_2014, uhlir_adding_2021}. Consequently, research in these areas enhances our understanding of deep-sea ecosystems and the patterns of biodiversity within them \citep{rogers2007corals, meisner_prefacebiodiversity_2018}. | ||
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| The biological and environmental baseline data collected by the IceAGE project and its predecessors BIOFAR and BIOICE, which studied the biodiversity of the Faroe Islands and Iceland, are invaluable resources. They provide essential information for addressing two significant issues facing present and future generations: the impacts of climate change and seabed mining. For decades, the North Atlantic region around Iceland has been recognized as a crucial area for regulating global thermohaline circulation \citep{meisner_prefacebiodiversity_2018}. The Greenland, Iceland, and Norwegian (GIN) seas, along with the high-latitude North Atlantic, play a crucial role in modern deep-sea ventilation. The surface waters of these regions are critical source areas for global deep-sea renewal and are vital to the thermohaline circulation \citep{johannessen_relationship_1994}. One of the most significant changes observed is the formation of cold, deep water. With the loss of Arctic sea ice, the deep-sea formation process has slowed, likely impacting the dynamics and chemistry in the regions studied during the IceAGE expedition \citep{meisner_prefacebiodiversity_2018}. |
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The introduction provides a comprehensive background. However, the paragraph starting with "The biological and environmental baseline data..." could be shortened by summarizing the projects mentioned.
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Thank you for your comment. We have shortened the paragraph you mentioned (the second paragraph of the "Introduction" section) by summarizing the projects mentioned.
| \subsection{Description of the data} | ||
| The study area is located in a northern region of the North Atlantic, including the Icelandic Sea, the Denmark Strait, and the Norwegian Sea. The specimens examined in this study were gathered during the IceAGE project (Icelandic marine Animals: Genetic and Ecology; Cruise ship M85/3 in 2011; \cite{brix_iceage_2014}), which investigated the deep continental slopes and abyssal waters around Iceland \citep{meisner_prefacebiodiversity_2018}. The sampling period for the specimens included in this study was from August 30 to September 22, 2011, and they were collected at depths ranging from 316 to 2568 m. Information about the sampling plan, sample processing, the steps of DNA extraction, PCR amplification, sequencing, and the extracted and aligned DNA sequences are available in the article by \citep{uhlir_adding_2021}. | ||
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| \subsection{Data pre-processing} |
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Consider breaking down lengthy paragraphs into bullet points or numbered steps for clarity. For instance, this subsection "Data pre-processing" could list steps in the data reduction process more clearly.
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Thank you for your thoughtful comments. We have included bullet points in most of the paragraphs listing the attributes selected in this study. We have also added numbering to the section dealing with data processing (beginning of the "Data pre-processing" section).
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Hi @kevinlacaille , Thank you for your comments and suggestions. |
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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 |
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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 |
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@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: |
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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". |
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@JustGag , @TahiriNadia , et al., Thank you for the updates. Please tag me back in when the paper is ready for a re-review! Cheers, |
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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. 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. |
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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. |
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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). |
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@JustGag will you please stop pushing more commits now? We are closing the branches to merge everything for publishing the proceedings. |
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Hi,
I thought that September 23rd would be the date for the final signature of the acts by the publishers? So I still had time to edit our publication.
Do I still have time between now and the end of the evening?
Thank you very much.
Justin
…________________________________
De : Sanhita Joshi ***@***.***>
Envoyé : 19 septembre 2024 20:36
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)
@JustGag<https://github.com/JustGag> will you please stop pushing more commits now? We are closing the branches to merge everything for publishing the proceedings.
—
Reply to this email directly, view it on GitHub<#925 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BFW5PNL34ARA4B4NL6ZDA2LZXNUX7AVCNFSM6AAAAABITSMO6CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNRSGQ4DKMJYGE>.
You are receiving this because you were mentioned.Message ID: ***@***.***>
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I have one last commit to push.
Thank you very much for your understanding
…________________________________
De : Sanhita Joshi ***@***.***>
Envoyé : 19 septembre 2024 20:36
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)
@JustGag<https://github.com/JustGag> will you please stop pushing more commits now? We are closing the branches to merge everything for publishing the proceedings.
—
Reply to this email directly, view it on GitHub<#925 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BFW5PNL34ARA4B4NL6ZDA2LZXNUX7AVCNFSM6AAAAABITSMO6CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNRSGQ4DKMJYGE>.
You are receiving this because you were mentioned.Message ID: ***@***.***>
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Hi,
I commit my last push.
Thank you very much for your understanding.
Justin
…________________________________
De : Sanhita Joshi ***@***.***>
Envoyé : 19 septembre 2024 20:36
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)
@JustGag<https://github.com/JustGag> will you please stop pushing more commits now? We are closing the branches to merge everything for publishing the proceedings.
—
Reply to this email directly, view it on GitHub<#925 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BFW5PNL34ARA4B4NL6ZDA2LZXNUX7AVCNFSM6AAAAABITSMO6CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNRSGQ4DKMJYGE>.
You are receiving this because you were mentioned.Message ID: ***@***.***>
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Hi,
Could you please confirm receipt of the e-mails I sent yesterday?
Thank you very much and have a nice day.
Justin
…________________________________
De : Sanhita Joshi ***@***.***>
Envoyé : 19 septembre 2024 20:36
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)
@JustGag<https://github.com/JustGag> will you please stop pushing more commits now? We are closing the branches to merge everything for publishing the proceedings.
—
Reply to this email directly, view it on GitHub<#925 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BFW5PNL34ARA4B4NL6ZDA2LZXNUX7AVCNFSM6AAAAABITSMO6CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNRSGQ4DKMJYGE>.
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@TahiriNadia @JustGag Please cease creating commits to this paper as previously requested. The deadline for author revisions was September 2 as shown in the timeline. The paper has already been reviewed. We need your cooperation in order to publish. |
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Hi,
We will stop creating commits to our paper.
Thank you and have a nice day.
Justin
…________________________________
De : Chris Calloway ***@***.***>
Envoyé : 23 septembre 2024 20:19
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)
@TahiriNadia<https://github.com/TahiriNadia> @JustGag<https://github.com/JustGag> Please cease creating commits to this paper as previously requested. The deadline for author revisions was September 2 as shown in the timeline<https://github.com/scipy-conference/scipy_proceedings?tab=readme-ov-file#timeline-for-2024>. The paper has already been reviewed. We need your cooperation in order to publish.
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Hi @cbcunc, I hope you're well. After noticing some typos, I wanted to ask if it would be possible to make some changes to improve the robustness of our paper? We've already implemented the changes on our side, so it would be a matter of including them in the conference paper. Thank you for your understanding. Justin |
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 apaperlabel and GitHub Actions will be run to check and build your paper.See the project readme for more information.
Editor: Sanhita Joshi @sanhitamj
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