Assessing Niche Dynamics and Population Connectivity in an Endangered Tree Species, Emmenopterys henryi: Implications for Conservation and Management
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe manuscript contains important results and is done at a high scientific level. Modern methods of species distribution modeling are correctly applied. The manuscript is interesting in methodology, and also provides new information about a plant species of сoncervation concern. I really liked your manuscript, so I took it seriously and carefully to help you make it even better. I think that it can be published with additional corrections.
Please respond to the submitted comments below or reasonably reject.
1. Ln. 239-240. Which is the basis for selecting Utilizing thresholds ranging from 0.5 to 0.75 and 0.75 to 1.0 to delineate moderately and highly suitable ranges for our focal species. Different thresholds are used to convert continuous probabilities calculated, e.g. in Maxent, into discrete predictions (Liu, C. Selecting thresholds for the prediction of species occurrence with presence-only data / C. Liu, M. White, G. White, M. White, M. White, G. Liu. Liu, M. White, G. Newell // J. Biogeogr. Biogeogr. - 2013. - Vol. 40. - P. 778-78). It is stated that one of the widely used approaches, i.e. fixed threshold approach, is the worst one, which is therefore not recommended.
2. I recommend that the authors prepare an ODMAP protocol, which describes in detail all the modeling procedures. This point will help a lot in the subsequent reproducibility of the study. For more details, please see Zurell, D. Franklin, J., König, C., Bouchet, P.J., Dormann, C.F., Elith, J., Fandos, G., Feng, X., Guillera-Arroita, G., Guisan, A., et al. 2020. A standard protocol for reporting species distribution models // Ecography. V. 43. P. 1261–1277. https://doi.org/10.1111/ecog.04960
Author Response
Comments and Suggestions for Authors
The manuscript contains important results and is done at a high scientific level. Modern methods of species distribution modeling are correctly applied. The manuscript is interesting in methodology, and also provides new information about a plant species of сoncervation concern. I really liked your manuscript, so I took it seriously and carefully to help you make it even better. I think that it can be published with additional corrections.
Response: Thanks for your comments.
Please respond to the submitted comments below or reasonably reject.
- Ln. 239-240. Which is the basis for selecting Utilizing thresholds ranging from 0.5 to 0.75 and 0.75 to 1.0 to delineate moderately and highly suitable ranges for our focal species. Different thresholds are used to convert continuous probabilities calculated, e.g. in Maxent, into discrete predictions (Liu, C. Selecting thresholds for the prediction of species occurrence with presence-only data / C. Liu, M. White, G. White, M. White, M. White, G. Liu. Liu, M. White, G. Newell // J. Biogeogr. Biogeogr. - 2013. - Vol. 40. - P. 778-78). It is stated that one of the widely used approaches, i.e. fixed threshold approach, is the worst one, which is therefore not recommended.
Response: We appreciate your thoughtful comments. Indeed, it is acknowledged that varying threshold selections, aimed at converting the continuous range dynamics of a species under alternative climates, may yield different outcomes in terms of potential habitats, although the fixed threshold method is prevalent when predicting range shifts under anticipated climatic changes. However, even using fixed threshold, the total predicted habitats are stable. In the present study, we used the fixed threshold method to delineate the moderately and highly suitable ranges when comparing the potential ranges between the distinct intraspecific lineages. Recognizing the concern you have raised, we have supplemented our analysis by calculating the aggregate potential ranges both at the lineage and species levels, with a threshold exceeding 0.5 (detailed in Supplementary Table S4). Furthermore, in assessing population connectivity, we incorporated the initial projections from ENMs without applying specialized fixed thresholds for the construction of resistance layers.
- I recommend that the authors prepare an ODMAP protocol, which describes in detail all the modeling procedures. This point will help a lot in the subsequent reproducibility of the study. For more details, please see Zurell, D. Franklin, J., König, C., Bouchet, P.J., Dormann, C.F., Elith, J., Fandos, G., Feng, X., Guillera-Arroita, G., Guisan, A., et al. 2020. A standard protocol for reporting species distribution models // Ecography. V. 43. P. 1261–1277. https://doi.org/10.1111/ecog.04960
Response: Thanks for your suggestion. In the present study, we primarily relied on R packages to evaluate the range and niche dynamics of our focal species. The pertinent R scripts, manuals, and associated literature can be easily accessed online or through relevant libraries. We made minimal modifications to the existing scripts, manuals, and commands referenced in the literature to suit our specific needs. Additionally, the genetic connectivity analysis pipeline and its accompanying manual are available at http://www.sdmtoolbox.org/, providing a comprehensive resource for interested researchers.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for Authors
Introduction:
Overall, your introduction is well-written and informative. Addressing these points can help provide a more focused and coherent transition from the background to the specific objectives of your study.
Clarify the research gap: While you provide a strong background on the importance of genetic diversity, metapopulation structure, and ecological niche models (ENMs) in the context of climate change, it would be helpful to explicitly state the research gap or knowledge deficiency that your study aims to address. What specific aspects of niche dynamics and population connectivity within E. henryi have not been adequately explored in previous research?
Explicitly mention the shortcomings: You mention the importance of incorporating insights from population structure and phylogenetic relationships into ENMs but don't explicitly mention any shortcomings or limitations in existing research. Addressing these limitations can help readers understand why your study is necessary and what specific contributions it will make.
Focus on E. henryi: While you touch upon the importance of habitat connectivity and population connectivity in general, you could emphasize why studying E. henryi, in particular, is crucial. What makes this species unique or especially vulnerable to the impacts of climate change? This would help justify the focus of your research.
Clear transition to the study's objectives: Towards the end of the introduction, you briefly mention the focus of your study on evaluating niche dynamics and population connectivity within E. henryi's distinct intraspecific lineages. It would be helpful to provide a clear and concise transition that introduces your specific research objectives. For example, you could explicitly state that your study aims to address these gaps by assessing range and niche dynamics and exploring patterns of population connectivity within and between the two intraspecific lineages of E. henryi.
Formatting: There seems to be a numbering issue in your text. For example, the sentence "A previous study focusing on the demographic history of E. henryi had shed light on..." appears out of sequence. Ensure that the numbering and formatting align with the conventions of your paper.
Materials and Methods
Clarity and Organization: Overall, the section is well-organized and clear. However, it might benefit from subheadings within each subsection to make it easier for readers to navigate through the different steps of your methods.
Division of Occurrences: You explain how you allocated species occurrences to their respective intraspecific lineages based on phylogenetic tree results. It would be helpful to briefly mention the criteria or rationale used for this allocation, as this decision can have a significant impact on your analysis.
Line 142-143 on pseudo-absence generation:
This subject has been discussed in many publication and different approaches have been proposed. While, authors have done a good job in assigning equal weight to the presence and absence data, the pseduo-absence creation needs to be discussed. Look at the caveats mentioned in these papers that discuss pseudo-absence generation. A short paragraph would be enough:
1- Narouei-Khandan, Hossein Ali. Ensemble models to assess the risk of exotic plant pathogens in a changing climate. Diss. Lincoln University, 2014.
2- Iturbide, Maialen, et al. "A framework for species distribution modelling with improved pseudo-absence generation." Ecological Modelling 312 (2015): 166-174.
Population Connectivity Analysis:
It would be beneficial to briefly discuss the importance of shared haplotypes and resistance layers in this context.
It also might be helpful to briefly summarize the significance of niche overlap and dynamics in the context of your study.
Results: Are well presented.
Discussion:
Your "Discussion" section effectively summarizes the key findings of your study and provides valuable insights into the implications for conservation and the broader ecological context. You discuss the potential consequences of niche divergence between the lineages, suggesting that if these trends continue, they may lead to the emergence of new species. This speculation is intriguing and highlights the evolutionary significance of your findings. Some points that may improve this section are:
Discuss the caveats of ENMs or SDMs. And the potential effect of low number of presence data on model performance.
Population Connectivity: Your discussion of population connectivity patterns within and between lineages is informative. However, you might briefly mention the potential impact of climate change on these patterns, even though your study primarily focused on current climates.
Comments for author File: Comments.pdf
Author Response
Comments and Suggestions for Authors
Introduction:
Overall, your introduction is well-written and informative. Addressing these points can help provide a more focused and coherent transition from the background to the specific objectives of your study.
Response: Thanks for your comments.
Clarify the research gap: While you provide a strong background on the importance of genetic diversity, metapopulation structure, and ecological niche models (ENMs) in the context of climate change, it would be helpful to explicitly state the research gap or knowledge deficiency that your study aims to address. What specific aspects of niche dynamics and population connectivity within E. henryi have not been adequately explored in previous research?
Response: Thanks for your comments. We have amended accordingly, please see our latest MS highlighted in light blue in Lines 88-94.
Explicitly mention the shortcomings: You mention the importance of incorporating insights from population structure and phylogenetic relationships into ENMs but don't explicitly mention any shortcomings or limitations in existing research. Addressing these limitations can help readers understand why your study is necessary and what specific contributions it will make.
Response: We are grateful for your valuable suggestions, it’s critical for our MS. We have made the necessary changes, please see our latest MS highlighted in light blue in Lines 42-45.
Focus on E. henryi: While you touch upon the importance of habitat connectivity and population connectivity in general, you could emphasize why studying E. henryi, in particular, is crucial. What makes this species unique or especially vulnerable to the impacts of climate change? This would help justify the focus of your research.
Response: Thanks for your comment. In our initial MS, we have indeed emphasized the significance of our focal species. Specifically, the sentence within Lines 77-79 clarified that Emmenopterys belongs to a monotypic genus, highlighting its uniqueness. Furthermore, the sentences spanning Lines 74-76 and 81-83 shed light on the endangered status of our focal species, underscoring the critical need for conservation efforts.
Clear transition to the study's objectives: Towards the end of the introduction, you briefly mention the focus of your study on evaluating niche dynamics and population connectivity within E. henryi's distinct intraspecific lineages. It would be helpful to provide a clear and concise transition that introduces your specific research objectives. For example, you could explicitly state that your study aims to address these gaps by assessing range and niche dynamics and exploring patterns of population connectivity within and between the two intraspecific lineages of E. henryi.
Response: Thanks for your suggestions. We have amended our MS accordingly, please see our latest MS highlighted in light blue in Lines 95-97.
Formatting: There seems to be a numbering issue in your text. For example, the sentence "A previous study focusing on the demographic history of E. henryi had shed light on..." appears out of sequence. Ensure that the numbering and formatting align with the conventions of your paper.
Response: We are grateful for your comments. In response, we have carefully rewritten this sentence and placed it within the preceding paragraph for improved clarity and coherence. Please refer to our revised manuscript, where the updated text is clearly marked in light blue, specifically within Lines 88-94.
Materials and Methods
Clarity and Organization: Overall, the section is well-organized and clear. However, it might benefit from subheadings within each subsection to make it easier for readers to navigate through the different steps of your methods.
Response: Thanks for your comments. While we have indeed incorporated several subheadings in our initial manuscript, we are concerned that an excessive use of subheadings, given the scope and limitations of the data and analytical techniques presented in this study, might hinder readability.
Division of Occurrences: You explain how you allocated species occurrences to their respective intraspecific lineages based on phylogenetic tree results. It would be helpful to briefly mention the criteria or rationale used for this allocation, as this decision can have a significant impact on your analysis.
Response: In our analysis, we incorporated a total of 38 occurrences of E. henryi, which correspond to 38 populations retrieved from Zhang et al. (2016). To ensure clarity regarding the delineation of these populations, we have carefully revised the relevant sentence in our latest MS, please see the sentence highlighted in light blue in Lines 112-115.
Zhang, Y.-H.; Wang, I.J.; Comes, H.P.; Peng, H.; Qiu, Y.-X. Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae). Scientific Reports 2016, 6, 24041, doi:10.1038/srep24041.
Line 142-143 on pseudo-absence generation:
This subject has been discussed in many publication and different approaches have been proposed. While, authors have done a good job in assigning equal weight to the presence and absence data, the pseduo-absence creation needs to be discussed. Look at the caveats mentioned in these papers that discuss pseudo-absence generation. A short paragraph would be enough:
1- Narouei-Khandan, Hossein Ali. Ensemble models to assess the risk of exotic plant pathogens in a changing climate. Diss. Lincoln University, 2014.
2- Iturbide, Maialen, et al. "A framework for species distribution modelling with improved pseudo-absence generation." Ecological Modelling 312 (2015): 166-174.
Response: Thanks for your comments. Indeed, the methods utilized for generating pseudo-absences have significant impact on model performance of ENMs. We have carefully revised our MS and incorporated the necessary changes, please see our latest MS highlighted in light blue in Lines 147-152.
Population Connectivity Analysis:
It would be beneficial to briefly discuss the importance of shared haplotypes and resistance layers in this context.
Response: Thanks for your comments. We have amended our MS accordingly, please see our latest MS highlighted in light blue in Lines 217-223.
It also might be helpful to briefly summarize the significance of niche overlap and dynamics in the context of your study.
Response: Thanks for your comments. We have amended our MS accordingly, please see our latest MS highlighted in light blue in Lines 204-208.
Results: Are well presented.
Response: Thanks for your comments.
Discussion:
Your "Discussion" section effectively summarizes the key findings of your study and provides valuable insights into the implications for conservation and the broader ecological context. You discuss the potential consequences of niche divergence between the lineages, suggesting that if these trends continue, they may lead to the emergence of new species. This speculation is intriguing and highlights the evolutionary significance of your findings. Some points that may improve this section are:
Response: Thanks for your comments.
Discuss the caveats of ENMs or SDMs. And the potential effect of low number of presence data on model performance.
Response: Thanks for your comments. We have addressed the caveats of ENMs in the instruction section. Please see our revised MS highlighted in light blue in Lines 42-45. Additionally, we have also considered the potential impact of limited presence data on the performance of ENMs and made the necessary adjustments. These updates can be found in our latest MS, specifically highlighted in light blue in Lines 394-400.
Population Connectivity: Your discussion of population connectivity patterns within and between lineages is informative. However, you might briefly mention the potential impact of climate change on these patterns, even though your study primarily focused on current climates.
Response: Thanks for your comments. In our initial MS, we have indeed tackled the important issue of how population connectivity patterns are anticipated to shift under alternative climates. For your reference, please see the relevant sentence highlighted in Lines 427-429 of our revised MS. We believe this addition strengthens our argument and provides valuable insight into this complex topic.
Author Response File: Author Response.pdf
