Pleistocene Glacial Refugia in the Don River Basin: Witness from the Endangered Depressed River Mussel

Round 1

Reviewer 1 Report

The ms (Diversity-2417522) reported the genetic diversity and differentiation of a mussel species (Pseudanodonta complanata) using nucleotide sequence analysis of the mitochondrial COI and ND1 gene fragments. The study found population in the Don River basin had higher genetic diversity, isolated divergent lineage, and significant differentiation with populations in other basins. The authors supposed that their results provided proofs for the existence of Pleistocene glacial refugia in the south of the Russian Plain. General, The study was interesting and provided important information on the conservation management of the mussel, an endangered species. However, I do not find direct correlation between their results and the conception of Pleistocene glacial refugia. The authors can find my detailed comments for all sections below. Furthermore, I am not a native English speaker, so my comments will mainly not involve it.

 

Main concerns:

The authors found the genetic diversity and divergent lineage of population in the Don River basin were obviously different with other populations. And the authors thought their results were similar with research of another closely related species (duck mussel). Furthermore, the research of duck mussel had described the presence of localized and divergent lineages in several glacial refugees. So the authors supposed that their results also indicated the Don River basin may be a composition of the Pleistocene glacial refugia. However, I think the supposition absent direct data or results to support. On the contrary, results in the haplotype network and genetic differentiation indicated a long-term isolation of population in the Don River basin. The authors also agreed they could not draw the conclusion that European populations of P. complanata originated from the Don River Basin. I suggest the authors soften the topic of glacial refugia and focus on management or conservation unit of the species.

 

The second concerns is about ND1 gene fragments. The study included the fragment from 19 individuals. And I can not find new insights from the results of the fragment. So I doubt necessity of the fragment in this study. Maybe the authors can submit sequences of the fragment to Genbank and delete results of the fragment from the ms.

 

Minor concerns:

Lines 2-3: the title need to revise if the author agree the main comment.

Lines 16-21: there are four sentences to introduce study background in the Abstract. I suggest to simplify background and to add conclusion on the conservation management of the mussel in the Abstract.

Lines 34-35: add a reference for the sentence.

Lines 35-37: the concept of glacial refugia at lines 260-261 can be moved here.

Lines 37-38: I can not catch the meaning of “accumulation of genetic diversity”.Genetic diversity increases through accumulation of drifting and mutation? And there also need some references.

Lines 39-40: “individuals in these refugia”? By the way, language of the ms need improve by some native speaker or editing service.

Lines 45-48: this paragraph can combine with next paragraph. And the sentence “mussels provide important ecosystem services that ...”is ambiguous.

Line 52: unify name usage of “duck mussel Anodonta anatina”through next text. Such as line 229, two names of this species appeared simultaneously. Same situation in usages of “P. complanata” and “ depressed river mussel”.

Lines 58-60: “the question on its actual population dynamic”. So did the authors study the dynamic? I suggest “the question on its conservation” or similar issues.

Line 65: “Molecular data are keystone information to ...”

Lines 67-69: give some reasons for the failure because the authors also used molecular markers from mitochondrial DNA.

Lines 69-70: delete the sentence.

Lines 74-75: I can not understand the sentence.

Figure 1: note sampling basins and groups in the map and full names for abbreviations in the legend. Additional, it is better to note sampling sites of sequences from GenBank using different symbols.

Line 110: “ddH₂O”?

Line 133: “nucleotide diversity (Pi) ” or “nucleotide diversity (π) in table 1”?

Line 136: “Fu’s F” not “ Fu' Fs”in table 1.

Line 142: “Fst’s” not “FSTs”.

Line 145: “TCS” not “TSC”

Line 149: “n=105”.

Table 1: note “panEUR lineage”.

Lines 172-181: simplify the results, which was profitless for the conclusion.

Lines 208 and 212: “figure 2A” and “figure 2B”.

The Discussion need revise around the topic “conservation management”, especially for “management unit”, if the authors agree the main concern.

Author Response

Dear Reviewer,

We are grateful for your positive assessment of our manuscript and significant comments and suggestions. Please find our point-by-point response in the attachment.

Sincerely yours,

Ilya V. Vikhrev et al.

Author Response File: Author Response.docx

Reviewer 2 Report

The manuscript entitled "Pleistocene glacial refugia in the Don River basin: witness from the endangered depressed river mussel" by Vikhrev et al., is highly interesting and I believe it would be of great interest to the readership of "Diversity." The study explores the genetic diversity and differentiation of the endangered freshwater bivalve, Pseudanodonta complanata, shedding light on its population genetics and demography, which is currently limited in available data.

 

The authors present a comprehensive introduction that effectively contextualizes the research within the broader field of European freshwater biota and the importance of understanding species refugia in elucidating current intraspecific diversity and differentiation. This introduction is well-supported by relevant and important references. The materials and methods section is thorough, providing a clear description of the approach employed in studying the genetic diversity and differentiation of P. complanata. The results section is presented in a clear and concise manner, allowing for easy comprehension of the findings. The identification of a localized and highly divergent lineage in the Don River basin, along with a widespread but low diversified lineage distributed from the Volga River basin to the Oise River in France, provides valuable insights into the genetic structure of P. complanata populations. The discussion is well-drafted and comprehensive, effectively linking the obtained results to the broader implications for understanding Pleistocene glacial refugia in the south of the Russian Plain. The authors successfully highlight the significance of their findings, particularly in confirming the existence of refugia in the Don River basin. Additionally, they address the implications of their study in the conservation and management of P. complanata populations, emphasizing the conservation priority of this endangered species. In summary, I believe this manuscript represents a valuable contribution to the field of evolutionary biology, specifically in understanding the genetic diversity and differentiation of Pseudanodonta complanata in relation to Pleistocene glacial refugia. The manuscript is well-written, and the research conducted is robust and scientifically sound. Therefore, I recommend its publication in "Diversity."

Author Response

Dear Reviewer,

We are very much grateful to you for your high positive assessment of our paper and kind words about our study.

Sincerely yours,
Ilya V. Vikhrev et al.

Reviewer 3 Report

The manuscript by Ilya V. Vikhrev et al., entitled: Pleistocene glacial refugia in the Don River basin: witness from 2 the endangered depressed river mussel, presents an interesting, well-structured and interpreted study on genetic diversity and genetic differentiation of P. complanata.

The authors developed an important study and presented it very well, but I think it would be necessary to add a Conclusions section in which they can resume in a few sentences the most important findings.

 Only minor editing of the English language is required

Author Response

Dear Reviewer,

We are grateful for your positive assessment of our study and for your suggestion about resuming our findings in the conclusion. We agree with your recommendation and added the Conclusion section.

Sincerely yours,
Ilya V. Vikhrev et al.

Round 2

Reviewer 1 Report

I reviewed the revised version of the diversity 2417522 and supposed that the manuscript has been improved, although several points that I commented for the last versions were not followed without any reasons or explanations. In this time, I will simplify my comments.

Lines 39: add a definition for refugia, or change “refugia” into “area”.

Lines 49-53: what means “ecosystem services” and “ecosystem functioning”? In my understanding, “role of ecosystem” to human is the service, and to nature(species/ community/ecosystem) is the function.

Lines 52 and 55: the authors put scientific name and common name of a species when it mentioned in the text for a first time. Both names are used as synonyms through the rest of the text. Sometimes, both names appeared simultaneously, such as lines 238, 253-255, and 288-289, which are easy to mislead the readers.

Line 71: what means “actual population diversity and differentiation”?

Lines 75-76: the sentence is inaccurate and should be like “weak genetic differentiation among P. complanata populations across the UK”. furthermore, do you find the differentiation in your data? Why the differentiation revealed by AFLP should be pointed here?

Line 141: “Fst’s”? “FST’s” was used through the rest of the text.

Lines 158 and 160: maybe past tense is appropriate to describe results, such as “varies”. bu the way, I still suggest that language of the ms need improve, such as lines 263 “comfirm”, 265 “indicates”.

Lines 160-167: these are not results. Delete it or move into the Discussion.

Line 173: “TCS”?

Line 308: “mussel”?

Author Response

Dear Reviewer,

We are very much grateful to you for clarifying the comments. We found them reliable and accepted all of them. Please find our point-by-point responses in the attachment and in the edited version of the manuscript.

Sincerely yours,
Ilya V. Vikhrev et al.

Author Response File: Author Response.pdf