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Dear Dr. Juárez-Ramírez ,
you satisfied all the reviewer's concerns. So, I am pleased to inform you that your paper "Past and present genetic structure of the tropical rainforest palm Astrocaryum mexicanum: Effects of anthropogenic fragmentation" is accepted for publication in the PeerJ. Congratulations!
Thank you for submitting your work to PeerJ.
Sincerely,
Gabriele Casazza
[# PeerJ Staff Note - this decision was reviewed and approved by Richard Schuster, a PeerJ Section Editor covering this Section #]
Dear Authors,
Thank you for taking all the suggestions of the reviewers into consideration. There are only two very small corrections to be made before article can be accepted. Please make these last two changes so that the article is completely fine.
In this third review, I noticed that the authors incorporated all the suggestions into an improved manuscript. However, I noticed two very small details, that need corrections.
1) I would like to apologyse for this correction, as it was my mistake. The text was correct before.
Lines 108-109. "... a feature that is shared with A. mexicanum (though secondary
dispersal by rodents may be important in the latter (Brewer, 2001). In this study...
Please alter to your original version:
"... a feature that is shared with A. mexicanum (though secondary
dispersal by rodents may be important in the latter (Brewer, 2001)). In this study...
2) The following reference should have a correction in both the article's and Journal's title, as the correct Journal title is "Plants":
Ramos S, Gomes M, Meneses C, Dequigiovanni G, Vasconcelos J, Lopes R, Magno A, Freire R,
de Jesus T, Veasey E. 2022. Natural populations of Astrocaryum aculeatum Meyer in
Amazonia. Genetic Diversity and Conservation 11: 2957
https://doi.org/10.3390/plants11212957
The correct citation is the following:
Ramos S, Gomes M, Meneses C, Dequigiovanni G, Vasconcelos J, Lopes R, Magno A, Freire R,
de Jesus T, Veasey E. 2022. Natural populations of Astrocaryum aculeatum Meyer in
Amazonia: Genetic diversity and conservation. Plants 11: 2957. https://doi.org/10.3390/plants11212957
I noticed that the authors provided a good review on the references and in the manuscript. And I congratulate them for this important study.
No further comments are needed.
No further comments are needed.
No comments.
Dear Authors,
Unfortunately, I still have to go back for a small revision. Not all the changes requested by the reviewers have been made. Please go through the text carefully and make all the necessary changes. Please, respond point by point to the comments of the reviewer.
This is my second review of this manuscript. In my first review I suggested minor review. The authors have incorporated most of the suggestions in the manuscript, but still, there are other corrections needed. Therefore, I will ask the authors to provide another minor review, to improve the manuscript. The suggestions are described in the following text. The lines cited refer to the reviewed pdf file sent in this last review.
Lines 99, 104, 108, 110: Simplicio et al. (2023), etc. The ‘et al.’ is in italics in these four references, but the ‘et al.’ in the other references in the manuscript is not. Please make the reference citation uniform, according to the Journal´s instructions.
Line 100: Please substitute ‘brazilian’ by ‘Brazilian’
Line 109: Please substitute “…. (Brewer, 2001)). In..” by “…. (Brewer, 2001). In..”
Lines 180-181: The authors deleted the word ‘nowadays’, as I mentioned in my previous review. And modified this sentence:
By 2004 (Guevara et al., 2004), ca. 1,551.22 km2 of rainforest remains, forming a complex fragmented landscape.
I suggest altering ‘remains’ for ‘remained’, since the reference for this data is 21 years old.
Line 197: Please delete this line, as it is repeated in line 200.
Lines 278-283: This sentence is too long. Also, I asked the authors to improve the grammar of this sentence, and this was not done. They have corrected the ‘biological reserve’ (it was written as biological preserve”), which is fine. But still, the grammar of this sentence is not fine, I cannot understand the meaning of this sentence. Especially this part: “…chosen because as part of the biological reserve is undoubtedly the best conserved population, we simulated ...”. Please review this sentence, and preferably, divide it into two sentences.
Lines 381-383: This is one short paragraph that should be united with the previous paragraph, related to it.
Lines 390-391: Instead of ‘higher probability of (or to) disappear’, I suggest altering to ‘higher probability of disappearing’. My suggestion in the previous review was to use ‘to’ instead of ‘of’. But reading it again, I noticed that the correct grammar in this sentence is ‘higher probability of disappearing’.
Lines 436, 438, 440. The references cited in these lines do not have the stop sign between the et al and the year. They are written as: Gonzales et al (2019), and they should be written as: Gonzales et al. (2019), according to all the other references in the manuscript. Two other references are just the same. This observation was made in my previous review.
Also, the ‘et al.’ in these references are in italics, while the other references in the manuscript are not. Please make the reference citations uniform throughout the manuscript.
Lines 443-444: Again, the authors in this sentence are written with the ‘et al.’ in italics.
Line 471: The first line spacing needs to be adjusted.
Table 2. I suggest that the authors abbreviate the word ‘Continuos’’, written in vertical, such as: “Contin.”. By doing this, the height of the line of “Lyell” will not be larger/ different than the other lines in the table.
I also noticed two small corrections in item c. Please correct in the third column, the name “Cola de Pescado”. It is written as “Pescado” only. And there is a “Bambu” in the third line without the accent, different from the other items, written as “Bambú”.
And I agree with the other referees, that the colors are not needed. At least in this version, only item c has different colors. I do not believe the colors are necessary for the reader to understand the table.
Also, the authors wrote in their letter to the editor that they have followed the recommendation of sending this table to Supplementary material. But it is still in the main text in the reviewed pdf file. I imagine that there should be only two tables in the manuscript after this alteration.
The experimental design is adequate for this study.
Results of this study are fine and interesting.
No further comments are needed.
Dear Authors, One of the reviewers asks for some remaining minor changes. Most of them are typo or language corrections. The reviewer also asks you to update the references.
Please, respond to these points. Once again, thank you for submitting your manuscript to PeerJ and we look forward to receiving your revision.
Sincerely,
Gabriele Casazza
[# 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 #]
[# PeerJ Staff Note: The review process has identified that the English language must be improved. PeerJ can provide language editing services if you wish - please contact us at [email protected] for pricing (be sure to provide your manuscript number and title). Your revision deadline is always extended while you undergo language editing. #]
I have read the revised version of this manuscript and I found that authors satisfactorily addressed my comments relating to the structure/figures/tables.
The work conduct robust analysis and the samplign design is adequate.
The interpretations and conclusions are solid
I have no further comments on this revised manuscript, the authors have addressed all my concerns.
This is an interesting study analyzing whether fragmentation of the lowland rainforest of Los Tuxtlas natural reserve, in Mexico, has altered the genetic structure of understory palm Astrocaryum mexicanum. The authors studied populations from undisturbed forest and forest fragments. The questions that this study addressed, according to the manuscript, were: has habitat fragmentation reduced gene flow and within-population genetic variation (allele loss)? Has this process, in turn, increased population genetic differentiation of populations in fragments? The manuscript is well written, methodology is adequate to answer the above questions, and results are interesting. But still, there are some improvements that I could suggest increasing the quality of the manuscript.
One observation that caught my attention is that most cited references are not so recent. From the 71 references cited, only six were higher than 2016, cited from 2016 to 2023. However, I looked for other studies on A. mexicanum and noticed that there aren’t new published studies on the genetic diversity and structure of this palm tree, therefore, this study is very useful, bringing more information on the species. But I believe the authors could update some of their references, searching for more recent articles related to new population genetic studies of palm trees or other plants subjected to similar studies. Of course, not taking the merit from older and relevant references in the field. For example, there are other studies with Astrocaryum species studied with microsatellite markers that might be interesting to be cited as comparisons. I believe that the following article could be useful for comparison with the present study, which is:
Ramos et al. (2016) Spatial genetic structure, genetic diversity and pollen dispersal in a harvested population of Astrocaryum aculeatum in the Brazilian Amazon. BMC Genetics 17(1):63. Doi: 10.1186/s12863-016-0371-8.
A more recent article could be useful as well:
Ramos et al. (2022) Natural populations of Astrocaryum aculeatum Meyer in Amazonia: genetic diversity and conservation. Plants 11(21): 2957. Doi: 10.3390/plants11212957.
Other articles with palm trees and genetic diversity assessed with SSR markers that seem to be related to this study are:
Fuchs et al. (2023) Genetic diversity and phylogeographic patterns of the dioecious palm Chamaedorea tepejilote (Arecaceae) in Costa Rica: the role of mountain ranges and possible refugia. AOB Plants, v. 15(1): Doi: 10.1093/aobpla/plac060
Simplicio et al. (2023) Genetic diversity and geographic expansion in Syagrus coronata (Mart) Becc. (Arecaceae), a highly exploited palm endemic to the Brazilian semiarid region: suggestion for conservation policies. Tropical Plant Biology 16 (4): 276-286. Doi: 10.1007/s12042-023-09346-w
These are only suggestions for the authors to consider. If the authors feel that they do not fit in the manuscript, it is OK for me. They are only suggestions.
The experimental design was adequate for this study. I noticed that some improvements have already been made following previous reviewer’s suggestions. Therefore, I have nothing to add in this respect.
The findings of this study are important not only for Astrocaryum mexicanum populations but also for other palm tree species in similar situations, subject to anthropogenic actions and forests fragmentation. Again, several suggestions from previous reviewers were given and included in the manuscript that helped to improve the manuscript.
I have some additional suggestions for the authors, aiming at improving the manuscript in general, such as:
Abstract:
Instead of: “Fragments were not genetically distinct to continuous forest populations.”, I suggest altering to: “Fragments were not genetically distinct from continuous forest populations.”
Line 98: Please alter to “have detected negative effects”, instead of “have detected a negative effects”.
Figure 1 title: please include a dot between (ca. 100 m a.s.l.) and Picture, such as:
“….elevation (ca. 100 m a.s.l.). Picture by J. Núñez-Farfán.”
Figure 2. I suggest that the authors simplify the title a little bit and include the explanation for the letters included in each category in the title of Figure 2, such as:
Figure 2. Hypothetical genetic divergence expected among populations of adults (A, B) and seedlings (C, D) of Astrocaryum mexicanum in the rainforest of Los Tuxtlas. Only the shaded category (seedlings in fragments) …..
However, I find it difficult to notice any differences between Figures 2A and 2B, except for the authors mentioning their origin, and from 2C and 2D, except for the shade in 2D. I also agree with a previous reviewer that this figure is not needed, although the authors believe it should stay. I do respect the author’s opinion, but I must mention that I agree with the previous reviewer. A better idea would be to include this Figure as a supplementary material Figure.
Lines 152-154: In this part of the sentence: “…which may not be able to cross the fragmentation matrix for reproductive thus affecting population outcrossing rate and reproductive success, and reducing animal fruit (seed) dispersal.”
By using ‘for reproductive’… it seems to be lacking a word…such as reproductive success….It seems better to write: “…to cross the fragmentation matrix for reproduction thus….”. Or something more adequate. Please review this sentence.
Lines 165-167: Nowadays, ca. 1,551.22 km2 of rainforest remains, forming a complex fragmented landscape (Guevara et al., 2004). The structural characteristics of this forest were analyzed by Piñero et al., (1977).
Obs: “nowadays” is not the correct word for this sentence, since the reference is 20 years old (2024 -> 2004). Aren´t there any new references for the remaining rainforest area? I imagine that there should be new data referring to this subject.
Also, please correct the cited reference: Piñero et al. (1977) (without the comma)
Lines 183-184: Please exclude this sub-item (Microsatellite development), with only one small sentence. I suggest that the authors include this information in the next sub-item (Microsatellite amplification and genotyping), such as:
We developed 8 new microsatellite markers for A. mexicanum in this study as fully described in the supplementary information. Polymerase Chain Reaction (PCR) of all samples using the primers developed were made using an AxygenTM Maxygene® thermal cycler, .....
Lines 264-265: “…. chosen because as part of the biological preserve is undoubtedly the best conserved population,…”
Please check this part of the sentence. It seems strange to me. Is it biological reserve? Or biological preservation? The grammar of the sentence also seems to be incorrect.
Lines 279-280: The results should be given in the past tense, as in the other sentences.
Ex: The mean number of alleles per locus for seedlings was 5.26 (C. I.95% ± 0.409), and for adults 5.05 …..
Figure 5. Lack of population genetic subdivision as depicted by STRUCTURE v2.3.3, for seedlings of Astrocaryum mexicanum sampled in eight sites, three in undisturbed forest, and five in isolated fragments, for seedlings. Each….
Obs: ‘for seedings’ is repeated twice in the same sentence. I suggest deleting the last one from the sentence.
Lines 349-350: “…but differences in the number of migrants between sites are very large, with values ranging from 6.05 to 89.29 migrants. “
Obs: I did not notice this data, of the number of migrants between sites in the results section. Shouldn´t it be described in a table or in the text?
Lines 368-389: “ …a result similar a pattern found in another study in the tropical tree Koompassia malaccensis.”
It should be written as: “a result similar to a pattern found….”
Line 373: “….have a higher probability of disappear”
Isn´t it better to write: “….have a higher probability to disappear” ?
Lines 381-383: The paragraph on lines 381-383 is small and should be united with the previous paragraph, in my opinion.
Line 430: Please correct a small error: “… it seems thata their likelihood”
References cited in the text: Some references have a comma between the authors and the year and others do not have a comma, such as those in lines 363, 385, 396-397, etc. This journal requires a comma between the authors and the comma, therefore, this should be reviewed throughout the manuscript.
Also, the references should be written in italics.
Lines 419 and 429: Please include a dot after “et al”, such as “et al.” in the references Gonzalez et al (2019) and Schlaepfer et al (2018), and others along the manuscript. Also, some “et al.” are in italics and others are without it. I understand that all references should be in italics, such as: Gonzales et al. (2019).
I noticed from the answers to a previous reviewer that the Genotype data is available at https://figshare.com/s/e79857ab0b3111de8328. But is this information anywhere in the manuscript? Maybe I did not notice it. I believe it is important to provide this information in the manuscript.
Dear Dr. Núñez-Farfán,
The reviewers found his manuscript interesting and generally worthy of publication. However, they underline some weaknesses that need to be addressed before acceptance. In particular, they suggest that some parts of the manuscript should be clarified and specified better. Moreover, they also suggest that the discussion needs better organization and that some parts of it are too speculative. So, I encourage you to improve the manuscript according to the tips of the reviewer. Please, respond point-to-point to the comments of reviewers to speed up the process of revision. Once again, thank you for submitting your manuscript to PeerJ and we look forward to receiving your revision.
Sincerely,
Gabriele Casazza
[# PeerJ Staff Note: Please ensure that all review and editorial comments are addressed in a response letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. #]
The subject of the work “Past and present genetic structure of the tropical rainforest palm Astrocaryum mexicanum: Effects of anthropogenic fragmentation” could be appreciated by the readers of Peer J. However, the work shows some points that must be improved to get the necessary quality for reaching the required level for publication.
The introduction needs more details and must include information from lines 172 – 192 because that information is necessary there (move from Materials & Methods). I suggest to the authors the complete rewrite of the Introduction in a clear and concise way that includes all the information regarding A. mexicanum and the analyzed process necessary for discussing the results.
All referenced literature is relevant while not all Figures are relevant. I suggest that Figure 2 could be removed even though if it is a cute figure that does not contribute to explaining the hypothesis because it is clearly established in the text. In case the authors decide to keep it, they must include the explanation for the letters included at the corner of each category. Also, Table 2 must erase and its information could be included in Table 3.
Regarding the English language, I can not evaluate it because it is not my mother tongue.
The aim of the study is determine the genetic structure of both old adults and saplings of A. mexicanum from population located in continuous undisturbed forest (three populations) and in forest fragments (five populations), using a set of eight newly developed specific microsatellites while the hypothesis is that fragmentation restricts gene flow in A. mexicanum, so seedling populations in fragments will be genetically different between sites, and less so (but still significantly) from the adults of the same site. In contrast, adults of both type of habitats will reflect the historical genetic structure of the region since they were born before the fragmentation process. Adults and seedlings from undisturbed forest sites, and adults from fragments, are expected to have comparable genetic variation (or any differences will be due to unaccounted historical factors). Seedlings from fragment sites will be different from any other group (including seedlings from other sites) because they are likely the product of altered mating patterns due to fragmentation. The aim and the hypothesis are well-defined. The focus of the study is relevant owing to the serious anthropogenic fragmentation of tropical forests at the current time.
The authors describe the process for developing loci SSR for A. mexicanum which is really valuable however all this information disturbs the focus of the manuscript. I suggest that this information could be included as Supplementary information and in addition, the authors must indicate if the getting of libraries is their own work owing to in lines 234-235 they establish “An enriched microsatellite library for A. mexicanum was developed at The Savannah River Ecology Laboratory, University of Georgia”.
In lines 255 – 258, the authors describe “Using the program Arlequin v. 3.5.1.2. (Excoffier & Lischer 2010), we obtained the following genetic variation measures for the adults and seedlings of each population: number of alleles (A), observed and expected heterozygosity (HO and HE), Hardy-Weinberg equilibrium per locus, linkage disequilibrium between pairs of loci (D), and local inbreeding coefficient (FIS)” which is wrong because not all these parameters are genetic variation measures. I suggest that the authors should review the definition of these parameters and explain what information each of them gives
The study is actual and very interesting owing to the actual condition of tropical forests. Nevertheless, I suggest the authors reevaluate the discussion taking into account that this is the first approach to the analysis of the impact of anthropogenic fragmentation of the populations of A. mexicanum and more generational times are needed for more accurate and robust conclusions. Also, the authors must reduce the discussion from a point of view of natural selection, for example, lines 411- 413 and next, because they analyze neutral loci. In the same way, the authors go beyond the time framework of their analysis, for example, lines 434-453 where discuss the result from the historical time framework from nuSSR data while the precise way for this kind of analysis is from cpSSR data. In this way, I suggest removing this analysis.
There is no additional comments.
The article is well written, contains a solid theoretical basis, and a good bibliographical review on the subject. The structure of the manuscript is correct and the results are concise based on the stated objectives. The work shows relevant results on the knowledge of long-lived species and the consequences of the fragmentation of the habitat on the generic structure, very interesting, in addition to the fact that the design involves adult individuals and progeny, with which the history before the fragmentation and after this.
The work is within the scope of PeerJ, the research questions are well formulated, and the design allows them to be answered splendidly. Genetic analyzes and statistics allow us to respond very well to the proposed objectives.
The findings of the work are very important both from the ecological and biological conservation point of view, which can also provide the basis for future research in similar systems, and put them to the test with other species.
No additional comments, the work is very interesting and give interesting results for the biological conservation in plants with high dependence of pollinators.
The manuscript needs to include more comprehensive references, for e.g. there are several meta-analyses on the effects of habitat fragmentation on plants genetic diversity, which would be ideally to include. Also there are many tables and figures, some of them can be moved to supplemental. There is no mention of the availability of the genotype data.
The experimental design is adequate, however more information needs to be provided on the sampling (fragments age and size) and on how the populations within the continuos forest were delimited and identified (the three of them near to the forest edge, which may also experience fragmentation effects).
Some methods are not mentioned until the results (e.g. statistical tests), which should be mentioned in methods first.
The results are very interesting.The discussion needs a better organization to present more clearlythe implications for conservation. These implications are mentioned in lines 384-386 very briefly, but there are more aspects that can be expanded in light of what is already known of the species and the new information generated here.
Specific comments:
Ln24-26: This first line is difficult to read, rewrite.
Ln32-34: Instead of stating the genetic diversity metrics used, it would be more interesting to known, the specific objectives, questions, or expectations of the study.
Ln34: Habitats? Fragmented and not fragmented? It’s best, to state it as it is, habitat can be confusing.
Ln66-68: The references need to be more comprehensive, for instance, there are at least three meta-analyses on habitat fragmentation effects on genetic diversity in plants that could be included (e.g., Aguilar et al. 2006 Ecology letters, 9(8), 968-980.; Gonzalez et al., 2020 Conservation Biology, 34(3), 711-720).
Ln135-139: improve the wording of this last sentence.
Ln154-156: In the map, the undisturbed A. mexicanum populations (C1-C3) look within the border of the main forest fragment, such that these populations may also experience fragmentation effects (edge effects). Why are there no sampled populations in the center of the forest? How were these populations defined in terms of their spatial extent? Does A. mexicanum is spatially aggregated or not? Please give more details about the sampling. Also, provide information regarding the age and size of the fragments.
Ln182-192: I think this information is more useful in the introduction as it is easier to understand the expectations that are stated.
Ln260: The AMOVA was made by grouping by fragmentation status and age? Otherwise, it is not clear why to perform an AMOVA. Also, genetic diversity parameters between cohorts and conditions can be compared statistically to make the inferences stronger. This was done, but in methods is not described.
Ln263-265: This sentence is incomplete… the verb is missing.
Ln304: What about the linkage-disequilibrium test?
Ln307-208: it is not mentioned this statistical test in the methods.
Ln309: Are differences significant?
Ln313: again mention all the statistical tests performed in methods first.
Ln313-317: Move these results after line 305, before reporting the diversity. Also, the LD test is not mentioned in methods.
Is there any information on population size/ density at each sampled site? This information can be used to interpret genetic diversity.
Ln387: Most genetic….. separate in a different paragraph. As this starts a different idea
Ln400-401: improve the wording of the sentence “The lack of differentiation among sites does not support this hypothesis, but…” It is not clear to which hypothesis you are referring too.
Ln1451: Move this sentence with the previous paragraph. This sentence should not be a paragraph on its own.
There are too many figures and tables, consider moving some of them to supplemental.
Fig 1. consider putting the photo in color.
Fig 2. Suggestion better to state: Continuous forest and Fragmented forest
Fig 4. Improve the figure, and increase the width-size of the bars as it is difficult to see the white bars. Add y-caption
Fig 7 move to supplemental
Table 4 move to supplemental
Table 5 move to supplemental. Also, the green and blue dashing of table c refers to what?
Information on Table 2 and 3 can be merged into a single table
I think the AMOVA can include the partition as well by age and habitat, and not separate adults and seedlings.
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