Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE CHARACTERISTICS AND ROLES OF ANTIMICROBIAL PEPTIDES AS POTENTIAL TREATMENT FOR ANTIBIOTIC-RESISTANT PATHOGENS: A REVIEW
Review round: 1
Reviewer: 1

Output:
Basic reporting: In the review article submitted by Baharin and co-workers under the title “The characteristics and roles of antimicrobial peptides as potential treatment for antibiotic-resistant pathogens: A review”, the authors discuss the characteristics, advantages and disadvantages of antimicrobial peptides for their potential in treating antibiotic-resistant pathogens. The topic is important and of great interest to a good section of researchers in the medical/pharmaceutical field.

-	Multiple recent review articles have been published addressing a similar topic, the authors need to highlight what is new and different from what has been recently reviewed in the literature as in the following examples:
o	Dijksteel GS, Ulrich MMW, Middelkoop E, Boekema BKHL. Review: Lessons Learned From Clinical Trials Using Antimicrobial Peptides (AMPs). Front Microbiol. 2021 Feb 22;12:616979. doi: 10.3389/fmicb.2021.616979. PMID: 33692766; PMCID: PMC7937881.

o	Ryu M, Park J, Yeom JH, Joo M, Lee K. Rediscovery of antimicrobial peptides as therapeutic agents. J Microbiol. 2021 Feb;59(2):113-123. doi: 10.1007/s12275-021-0649-z. Epub 2021 Feb 1. PMID: 33527313.

-	The authors talked extensively about the dilemma of antibiotics; this can be shortened as this is not the focus of the review. Instead, the authors can highlight the impact of antibiotics resistance on mortality, prognosis, rise in the cost of care, etc.) by providing data with documented references.
Experimental design: -In the methodology, please indicate if the assessment of the included articles was performed by multiple individuals for the same article(s) or each individual was assigned alone to certain articles to be assessed, especially that the number of the authors is unusually large.
Validity of the findings: -	The comparison in table 1 is somehow oversimplifying the differences generalizing the features of some AMPs overall antibiotics based on findings in a very limited number of studies.
Additional comments: -	The sentences in the review in many instances tend to be very long; three lines and even longer, the authors can consider shortening some of them for more clarity.
-	In the abstract, the authors abruptly mentioned sepsis treatment by novel AMPs, why it was singled out away from other types of infections?
-	Data in figure 1 is outdated and needs to be updated.
-	The quality of both figures 2 and 3 needs to be improved and their source needs to acknowledge if they are not the original work of the authors. If the latter is the case, then they need to cite in the legend how they were generated.
-	Only two references are from 2020, more recent findings need to be included.
Minor comments:
Line 87: resistance should be resistant
Line 87: Staphylococci should not be italicized
Line 202: CAMA should be mentioned in full first before being abbreviated
The titles of the subsections are uniformly written regarding the capitalization of the words in the title
Line 307: Staphylococcus aureus should be abbreviated
Line 307: “Typhoid bacillus” is this the name of a bacterial species?


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE CHARACTERISTICS AND ROLES OF ANTIMICROBIAL PEPTIDES AS POTENTIAL TREATMENT FOR ANTIBIOTIC-RESISTANT PATHOGENS: A REVIEW
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript by Baharin et al. offers an overview of the current multi-drug resistant bacterial infection crisis and how antimicrobial peptide could be used as a promising therapeutic strategy. The manuscript is divided into subsections that help the reader to follow the authors’ ideas. Nevertheless, I have minor and major concerns about the manuscript. It is not evident how this review article differs from hundreds of other review articles regarding AMPs in the context of resistant bacterial infections. Moreover, in the end of the Introduction, the authors claim that the paper provides an overview on the synthetic and long-lasting AMPs analogues. However, this was not accomplished in any part of the manuscript, as the authors described (with lack of details) many naturally occurring AMPs, instead of focusing on optimized AMPs and their improved characteristics over their parent peptides. Some figures should be reorganized. Please find below a list of comments that should be addressed:

Line 49 and 51: The authors start with “Today, the number of deaths…” However, they cite a reference from 2018. The authors should consider updating this for a more recent reference.

Please use either “anti-microbial peptides” or “antimicrobial peptides”. Both forms appear in the main text.

Line 57: The authors affirm “They are host defense peptides…” Please rephrase, not all AMP are HDPs. For instance, synthetic computationally designed peptides and peptidomimetics with improved therapeutic potential are not HDPs.

Line 57 – 59. The authors mention only membrane-associated mechanisms of action. It would be interesting to add a short sentence explaining that some AMPs can also translocate across bacterial membranes to act on intracellular targets, including ribosomes. Non-lytic AMPs may include, buforin II, indolicidin, drosocin, among others.

A native English speaker should revise the manuscript. There are some minor issues.

In some sections of the manuscript, there are repetitive statements. For instance “the overuse and inappropriate prescribing of antibiotics has led to the emergence of more resistant bacteria and toxicity problems”. Although this information is relevant, the authors should carefully check the entire manuscript to modulate the use of repetitive sentences.

This work is focused on AMPs against bacterial infections. It was quite strange for me to see that the terms “germs” and “germs infections” were overused in the manuscript. These terms are too broad in my view and the authors should consider being more specific (e.g., bacterial, fungi, virus, etc.).

Lines 130 – 131: “The less developed body’s immune defence may then increase infection risk in a case of infectious germ transmission”. Very confusing sentence, please rephrase.

Lines 133 to 136 lack literature citations. Please add.

Figure 1: Why this particular database? When I clicked to check the database it appears: server not found. Considering that the authors were very clear on how they used Google Scholar, Pubmed, etc, to find the most relevant articles for their review, I also encourage them to better organize the data in this figure. Initially, the graph must be edited. For instance, the y axis says “percentage”. But percentage of what? AMP sequences? What is “percentage of diversity” in this case? It is not clear. Moreover, this analysis should be highly improved by comparing different databases, including APD, YAMPD, CAMP among others. I could not find the citation (Mahlapuu et al., 2019) described in the figure 1 caption in the references list. Please double-check.

Avoid expressions like “good antibacterial activity (line 139)”, “good” is too relative.

In the topic  “The Archival and the Diversity of AMPs” the authors focused only on naturally occurring AMPs. It should be in the topic title. Actually, the authors affirm in the end of the Introduction “This paper provides an overview on the synthetic and long-lasting AMPs analogues”, but little is really described and discussed about synthetic peptides... Therefore, at some points, the manuscript lacks focus considering the authors’ goals.

Line 193 – 195: Same as comment 1.

Figure 2 must be completely redesigned. The quality is poor. There is not description of the PDB IDs used in the figure. Why did the authors bind to an ion? Why did the authors not specify disulfide bonds? Moreover, this figure can be highly improved if the authors add more AMP structural scaffolds (e.g., cyclotides and other head-to-tail or side-to-side chain cyclic peptides, stapled peptides, among others.)

Line 201: What did the authors mean by rolling indolicidin? I understand that some chemical modifications may favor helical structure in indolicidin-like peptides. However, this is a well-known AMP that cause non-lytic effects on bacterial and presents random coil arrangements… There are many other well-known AMPs that adopt α-helix that would be better examples.

Line 202. The same as above… Defensin is a mix of helix, loops and beta-sheet. Not the best example for α-helical AMPs. The authors should rethink their examples in this entire section.

Line 204. Some studies have reported short β-sheet forming AMPs that do not present disulfide bonds (please check: 10.1002/adfm.201202850, 10.1021/acsinfecdis.9b00073, 10.1016/j.biomaterials.2013.10.053).

Line 206. Same of line 2. It would be better if the authors opened a subsection for mixed structures (e.g, defensins).

Line 216: “Besides, many peptides form their active structure only after” please, replace “form” by “adopt”. Moreover, the authors use as example, indolicidin. Indeed, this AMP changes its structural profile to a “boat-like” structural orientation to translocate bacterial membrane and act on DNA. However, it is not clear in the present manuscript that such structural transition occurs. For someone that it not an expert in AMPs the best examples, by far, would be random coil AMPs in solution that, when in contact with bacterial surfaces, adopt α-helical structures to perform their membrane-associated or intracellular mechanisms of action.

In general the “AMP structure” section should be highly improved. What about cyclic peptides? Different structural scaffolds? And, once again, considering the last sentence of the introduction, I believe the authors should provide the readers with more examples for optimized AMPs, not only naturally occurring ones.

Figure 3 looks much better. A more detailed caption should be organized for this one, describing (very briefly) the mechanisms.

“The Bacterial Resistance Mechanisms towards Antibiotics and the Way AMPs can help” How is this topic different from hundreds of other review articles regarding AMPs? Moreover, some of the statements are controversial. There are studies indicating that bacterial can resist to AMP treatment at sub-lethal doses. Most changes occur in the bacteria surface, efflux pumps production, among others (10.1038/s41598-017-04181-y). Finally, bacterial biofilms have attracted great attention in the last five years. Why did the authors decide not to mention this resistance mechanism, which is currently responsible for >70% of all bacterial infections in humans?

“Advantages of AMPs”: the authors mention AMP synergism with antibiotics as an advantage. Please highlight that such strategy is highly controversial.  We are still to fully understand the determinants for AMP/antibiotics synergism and, because of that, some results are positive, some are not, some are effective in vitro, but not in vivo and vice-versa. Therefore, maybe the authors should not emphasize this as an advantage.

“Interestingly, AMPs have no/less side effects for the user, as their use causes zero to only very minimal toxicity to the body when compared with other antibiotics”. This sentence is very confusing, please rephrase.  Moreover, the authors give only on example of a peptide “citrus-amp1” with non-toxic effects. Please, add more examples.

“AMPs, which have a low synthetic cost, are small molecules that are” please review this statement carefully. Low synthesis cost compare to what? Chemically modified AMPs (D-amino acids, for instance) can be quite expensive. Moreover, they are more expensive to produce then most antimicrobials already available in the market and, this characteristic has been highlighted as a bottleneck in AMP-based therapies. Finally, small molecules are usually describe with up to 200 Da, which is not the case here (AMPs).

The explanation about the anti-cancer activities of AMPs is not complete…. The authors should also mention that the phospholipids asymmetry in cancer cells provides them with more negatively charged residues in their upper leaflet, thus favoring electrostatic attraction of cationic AMPs.

Lines 365 – 367: “Moreover, the cost of production of AMPs is very high when compared with the production costs of conventional antibiotics” The authors should carefully review the manuscript, as they are often controversial.

The relevance of Table 1 is questionable. Antibiotics and AMPs are highly different classes of antimicrobials. If we check carefully, most studies not even consider their correlation in number of mols for biological experiments. I do believe that AMPs represent a promising strategy, but it is not like they will completely replace antibiotics in a short-term. A more interesting comparison here, would be between naturally occurring and optimized AMPs (which should be the focus of this manuscript according with its title and last sentence of the Introduction).
Experimental design: The manuscript by Baharin et al. offers an overview of the current multi-drug resistant bacterial infection crisis and how antimicrobial peptide could be used as a promising therapeutic strategy. The manuscript is divided into subsections that help the reader to follow the authors’ ideas. Nevertheless, I have minor and major concerns about the manuscript. It is not evident how this review article differs from hundreds of other review articles regarding AMPs in the context of resistant bacterial infections. Moreover, in the end of the Introduction, the authors claim that the paper provides an overview on the synthetic and long-lasting AMPs analogues. However, this was not accomplished in any part of the manuscript, as the authors described (with lack of details) many naturally occurring AMPs, instead of focusing on optimized AMPs and their improved characteristics over their parent peptides. Some figures should be reorganized. Please find below a list of comments that should be addressed:

Line 49 and 51: The authors start with “Today, the number of deaths…” However, they cite a reference from 2018. The authors should consider updating this for a more recent reference.

Please use either “anti-microbial peptides” or “antimicrobial peptides”. Both forms appear in the main text.

Line 57: The authors affirm “They are host defense peptides…” Please rephrase, not all AMP are HDPs. For instance, synthetic computationally designed peptides and peptidomimetics with improved therapeutic potential are not HDPs.

Line 57 – 59. The authors mention only membrane-associated mechanisms of action. It would be interesting to add a short sentence explaining that some AMPs can also translocate across bacterial membranes to act on intracellular targets, including ribosomes. Non-lytic AMPs may include, buforin II, indolicidin, drosocin, among others.

A native English speaker should revise the manuscript. There are some minor issues.

In some sections of the manuscript, there are repetitive statements. For instance “the overuse and inappropriate prescribing of antibiotics has led to the emergence of more resistant bacteria and toxicity problems”. Although this information is relevant, the authors should carefully check the entire manuscript to modulate the use of repetitive sentences.

This work is focused on AMPs against bacterial infections. It was quite strange for me to see that the terms “germs” and “germs infections” were overused in the manuscript. These terms are too broad in my view and the authors should consider being more specific (e.g., bacterial, fungi, virus, etc.).

Lines 130 – 131: “The less developed body’s immune defence may then increase infection risk in a case of infectious germ transmission”. Very confusing sentence, please rephrase.

Lines 133 to 136 lack literature citations. Please add.

Figure 1: Why this particular database? When I clicked to check the database it appears: server not found. Considering that the authors were very clear on how they used Google Scholar, Pubmed, etc, to find the most relevant articles for their review, I also encourage them to better organize the data in this figure. Initially, the graph must be edited. For instance, the y axis says “percentage”. But percentage of what? AMP sequences? What is “percentage of diversity” in this case? It is not clear. Moreover, this analysis should be highly improved by comparing different databases, including APD, YAMPD, CAMP among others. I could not find the citation (Mahlapuu et al., 2019) described in the figure 1 caption in the references list. Please double-check.

Avoid expressions like “good antibacterial activity (line 139)”, “good” is too relative.

In the topic  “The Archival and the Diversity of AMPs” the authors focused only on naturally occurring AMPs. It should be in the topic title. Actually, the authors affirm in the end of the Introduction “This paper provides an overview on the synthetic and long-lasting AMPs analogues”, but little is really described and discussed about synthetic peptides... Therefore, at some points, the manuscript lacks focus considering the authors’ goals.

Line 193 – 195: Same as comment 1.

Figure 2 must be completely redesigned. The quality is poor. There is not description of the PDB IDs used in the figure. Why did the authors bind to an ion? Why did the authors not specify disulfide bonds? Moreover, this figure can be highly improved if the authors add more AMP structural scaffolds (e.g., cyclotides and other head-to-tail or side-to-side chain cyclic peptides, stapled peptides, among others.)

Line 201: What did the authors mean by rolling indolicidin? I understand that some chemical modifications may favor helical structure in indolicidin-like peptides. However, this is a well-known AMP that cause non-lytic effects on bacterial and presents random coil arrangements… There are many other well-known AMPs that adopt α-helix that would be better examples.

Line 202. The same as above… Defensin is a mix of helix, loops and beta-sheet. Not the best example for α-helical AMPs. The authors should rethink their examples in this entire section.

Line 204. Some studies have reported short β-sheet forming AMPs that do not present disulfide bonds (please check: 10.1002/adfm.201202850, 10.1021/acsinfecdis.9b00073, 10.1016/j.biomaterials.2013.10.053).

Line 206. Same of line 2. It would be better if the authors opened a subsection for mixed structures (e.g, defensins).

Line 216: “Besides, many peptides form their active structure only after” please, replace “form” by “adopt”. Moreover, the authors use as example, indolicidin. Indeed, this AMP changes its structural profile to a “boat-like” structural orientation to translocate bacterial membrane and act on DNA. However, it is not clear in the present manuscript that such structural transition occurs. For someone that it not an expert in AMPs the best examples, by far, would be random coil AMPs in solution that, when in contact with bacterial surfaces, adopt α-helical structures to perform their membrane-associated or intracellular mechanisms of action.

In general the “AMP structure” section should be highly improved. What about cyclic peptides? Different structural scaffolds? And, once again, considering the last sentence of the introduction, I believe the authors should provide the readers with more examples for optimized AMPs, not only naturally occurring ones.

Figure 3 looks much better. A more detailed caption should be organized for this one, describing (very briefly) the mechanisms.

“The Bacterial Resistance Mechanisms towards Antibiotics and the Way AMPs can help” How is this topic different from hundreds of other review articles regarding AMPs? Moreover, some of the statements are controversial. There are studies indicating that bacterial can resist to AMP treatment at sub-lethal doses. Most changes occur in the bacteria surface, efflux pumps production, among others (10.1038/s41598-017-04181-y). Finally, bacterial biofilms have attracted great attention in the last five years. Why did the authors decide not to mention this resistance mechanism, which is currently responsible for >70% of all bacterial infections in humans?

“Advantages of AMPs”: the authors mention AMP synergism with antibiotics as an advantage. Please highlight that such strategy is highly controversial.  We are still to fully understand the determinants for AMP/antibiotics synergism and, because of that, some results are positive, some are not, some are effective in vitro, but not in vivo and vice-versa. Therefore, maybe the authors should not emphasize this as an advantage.

“Interestingly, AMPs have no/less side effects for the user, as their use causes zero to only very minimal toxicity to the body when compared with other antibiotics”. This sentence is very confusing, please rephrase.  Moreover, the authors give only on example of a peptide “citrus-amp1” with non-toxic effects. Please, add more examples.

“AMPs, which have a low synthetic cost, are small molecules that are” please review this statement carefully. Low synthesis cost compare to what? Chemically modified AMPs (D-amino acids, for instance) can be quite expensive. Moreover, they are more expensive to produce then most antimicrobials already available in the market and, this characteristic has been highlighted as a bottleneck in AMP-based therapies. Finally, small molecules are usually describe with up to 200 Da, which is not the case here (AMPs).

The explanation about the anti-cancer activities of AMPs is not complete…. The authors should also mention that the phospholipids asymmetry in cancer cells provides them with more negatively charged residues in their upper leaflet, thus favoring electrostatic attraction of cationic AMPs.

Lines 365 – 367: “Moreover, the cost of production of AMPs is very high when compared with the production costs of conventional antibiotics” The authors should carefully review the manuscript, as they are often controversial.

The relevance of Table 1 is questionable. Antibiotics and AMPs are highly different classes of antimicrobials. If we check carefully, most studies not even consider their correlation in number of mols for biological experiments. I do believe that AMPs represent a promising strategy, but it is not like they will completely replace antibiotics in a short-term. A more interesting comparison here, would be between naturally occurring and optimized AMPs (which should be the focus of this manuscript according with its title and last sentence of the Introduction).
Validity of the findings: The manuscript by Baharin et al. offers an overview of the current multi-drug resistant bacterial infection crisis and how antimicrobial peptide could be used as a promising therapeutic strategy. The manuscript is divided into subsections that help the reader to follow the authors’ ideas. Nevertheless, I have minor and major concerns about the manuscript. It is not evident how this review article differs from hundreds of other review articles regarding AMPs in the context of resistant bacterial infections. Moreover, in the end of the Introduction, the authors claim that the paper provides an overview on the synthetic and long-lasting AMPs analogues. However, this was not accomplished in any part of the manuscript, as the authors described (with lack of details) many naturally occurring AMPs, instead of focusing on optimized AMPs and their improved characteristics over their parent peptides. Some figures should be reorganized. Please find below a list of comments that should be addressed:

Line 49 and 51: The authors start with “Today, the number of deaths…” However, they cite a reference from 2018. The authors should consider updating this for a more recent reference.

Please use either “anti-microbial peptides” or “antimicrobial peptides”. Both forms appear in the main text.

Line 57: The authors affirm “They are host defense peptides…” Please rephrase, not all AMP are HDPs. For instance, synthetic computationally designed peptides and peptidomimetics with improved therapeutic potential are not HDPs.

Line 57 – 59. The authors mention only membrane-associated mechanisms of action. It would be interesting to add a short sentence explaining that some AMPs can also translocate across bacterial membranes to act on intracellular targets, including ribosomes. Non-lytic AMPs may include, buforin II, indolicidin, drosocin, among others.

A native English speaker should revise the manuscript. There are some minor issues.

In some sections of the manuscript, there are repetitive statements. For instance “the overuse and inappropriate prescribing of antibiotics has led to the emergence of more resistant bacteria and toxicity problems”. Although this information is relevant, the authors should carefully check the entire manuscript to modulate the use of repetitive sentences.

This work is focused on AMPs against bacterial infections. It was quite strange for me to see that the terms “germs” and “germs infections” were overused in the manuscript. These terms are too broad in my view and the authors should consider being more specific (e.g., bacterial, fungi, virus, etc.).

Lines 130 – 131: “The less developed body’s immune defence may then increase infection risk in a case of infectious germ transmission”. Very confusing sentence, please rephrase.

Lines 133 to 136 lack literature citations. Please add.

Figure 1: Why this particular database? When I clicked to check the database it appears: server not found. Considering that the authors were very clear on how they used Google Scholar, Pubmed, etc, to find the most relevant articles for their review, I also encourage them to better organize the data in this figure. Initially, the graph must be edited. For instance, the y axis says “percentage”. But percentage of what? AMP sequences? What is “percentage of diversity” in this case? It is not clear. Moreover, this analysis should be highly improved by comparing different databases, including APD, YAMPD, CAMP among others. I could not find the citation (Mahlapuu et al., 2019) described in the figure 1 caption in the references list. Please double-check.

Avoid expressions like “good antibacterial activity (line 139)”, “good” is too relative.

In the topic  “The Archival and the Diversity of AMPs” the authors focused only on naturally occurring AMPs. It should be in the topic title. Actually, the authors affirm in the end of the Introduction “This paper provides an overview on the synthetic and long-lasting AMPs analogues”, but little is really described and discussed about synthetic peptides... Therefore, at some points, the manuscript lacks focus considering the authors’ goals.

Line 193 – 195: Same as comment 1.

Figure 2 must be completely redesigned. The quality is poor. There is not description of the PDB IDs used in the figure. Why did the authors bind to an ion? Why did the authors not specify disulfide bonds? Moreover, this figure can be highly improved if the authors add more AMP structural scaffolds (e.g., cyclotides and other head-to-tail or side-to-side chain cyclic peptides, stapled peptides, among others.)

Line 201: What did the authors mean by rolling indolicidin? I understand that some chemical modifications may favor helical structure in indolicidin-like peptides. However, this is a well-known AMP that cause non-lytic effects on bacterial and presents random coil arrangements… There are many other well-known AMPs that adopt α-helix that would be better examples.

Line 202. The same as above… Defensin is a mix of helix, loops and beta-sheet. Not the best example for α-helical AMPs. The authors should rethink their examples in this entire section.

Line 204. Some studies have reported short β-sheet forming AMPs that do not present disulfide bonds (please check: 10.1002/adfm.201202850, 10.1021/acsinfecdis.9b00073, 10.1016/j.biomaterials.2013.10.053).

Line 206. Same of line 2. It would be better if the authors opened a subsection for mixed structures (e.g, defensins).

Line 216: “Besides, many peptides form their active structure only after” please, replace “form” by “adopt”. Moreover, the authors use as example, indolicidin. Indeed, this AMP changes its structural profile to a “boat-like” structural orientation to translocate bacterial membrane and act on DNA. However, it is not clear in the present manuscript that such structural transition occurs. For someone that it not an expert in AMPs the best examples, by far, would be random coil AMPs in solution that, when in contact with bacterial surfaces, adopt α-helical structures to perform their membrane-associated or intracellular mechanisms of action.

In general the “AMP structure” section should be highly improved. What about cyclic peptides? Different structural scaffolds? And, once again, considering the last sentence of the introduction, I believe the authors should provide the readers with more examples for optimized AMPs, not only naturally occurring ones.

Figure 3 looks much better. A more detailed caption should be organized for this one, describing (very briefly) the mechanisms.

“The Bacterial Resistance Mechanisms towards Antibiotics and the Way AMPs can help” How is this topic different from hundreds of other review articles regarding AMPs? Moreover, some of the statements are controversial. There are studies indicating that bacterial can resist to AMP treatment at sub-lethal doses. Most changes occur in the bacteria surface, efflux pumps production, among others (10.1038/s41598-017-04181-y). Finally, bacterial biofilms have attracted great attention in the last five years. Why did the authors decide not to mention this resistance mechanism, which is currently responsible for >70% of all bacterial infections in humans?

“Advantages of AMPs”: the authors mention AMP synergism with antibiotics as an advantage. Please highlight that such strategy is highly controversial.  We are still to fully understand the determinants for AMP/antibiotics synergism and, because of that, some results are positive, some are not, some are effective in vitro, but not in vivo and vice-versa. Therefore, maybe the authors should not emphasize this as an advantage.

“Interestingly, AMPs have no/less side effects for the user, as their use causes zero to only very minimal toxicity to the body when compared with other antibiotics”. This sentence is very confusing, please rephrase.  Moreover, the authors give only on example of a peptide “citrus-amp1” with non-toxic effects. Please, add more examples.

“AMPs, which have a low synthetic cost, are small molecules that are” please review this statement carefully. Low synthesis cost compare to what? Chemically modified AMPs (D-amino acids, for instance) can be quite expensive. Moreover, they are more expensive to produce then most antimicrobials already available in the market and, this characteristic has been highlighted as a bottleneck in AMP-based therapies. Finally, small molecules are usually describe with up to 200 Da, which is not the case here (AMPs).

The explanation about the anti-cancer activities of AMPs is not complete…. The authors should also mention that the phospholipids asymmetry in cancer cells provides them with more negatively charged residues in their upper leaflet, thus favoring electrostatic attraction of cationic AMPs.

Lines 365 – 367: “Moreover, the cost of production of AMPs is very high when compared with the production costs of conventional antibiotics” The authors should carefully review the manuscript, as they are often controversial.

The relevance of Table 1 is questionable. Antibiotics and AMPs are highly different classes of antimicrobials. If we check carefully, most studies not even consider their correlation in number of mols for biological experiments. I do believe that AMPs represent a promising strategy, but it is not like they will completely replace antibiotics in a short-term. A more interesting comparison here, would be between naturally occurring and optimized AMPs (which should be the focus of this manuscript according with its title and last sentence of the Introduction).
Additional comments: The manuscript by Baharin et al. offers an overview of the current multi-drug resistant bacterial infection crisis and how antimicrobial peptide could be used as a promising therapeutic strategy. The manuscript is divided into subsections that help the reader to follow the authors’ ideas. Nevertheless, I have minor and major concerns about the manuscript. It is not evident how this review article differs from hundreds of other review articles regarding AMPs in the context of resistant bacterial infections. Moreover, in the end of the Introduction, the authors claim that the paper provides an overview on the synthetic and long-lasting AMPs analogues. However, this was not accomplished in any part of the manuscript, as the authors described (with lack of details) many naturally occurring AMPs, instead of focusing on optimized AMPs and their improved characteristics over their parent peptides. Some figures should be reorganized. Please find below a list of comments that should be addressed:

Line 49 and 51: The authors start with “Today, the number of deaths…” However, they cite a reference from 2018. The authors should consider updating this for a more recent reference.

Please use either “anti-microbial peptides” or “antimicrobial peptides”. Both forms appear in the main text.

Line 57: The authors affirm “They are host defense peptides…” Please rephrase, not all AMP are HDPs. For instance, synthetic computationally designed peptides and peptidomimetics with improved therapeutic potential are not HDPs.

Line 57 – 59. The authors mention only membrane-associated mechanisms of action. It would be interesting to add a short sentence explaining that some AMPs can also translocate across bacterial membranes to act on intracellular targets, including ribosomes. Non-lytic AMPs may include, buforin II, indolicidin, drosocin, among others.

A native English speaker should revise the manuscript. There are some minor issues.

In some sections of the manuscript, there are repetitive statements. For instance “the overuse and inappropriate prescribing of antibiotics has led to the emergence of more resistant bacteria and toxicity problems”. Although this information is relevant, the authors should carefully check the entire manuscript to modulate the use of repetitive sentences.

This work is focused on AMPs against bacterial infections. It was quite strange for me to see that the terms “germs” and “germs infections” were overused in the manuscript. These terms are too broad in my view and the authors should consider being more specific (e.g., bacterial, fungi, virus, etc.).

Lines 130 – 131: “The less developed body’s immune defence may then increase infection risk in a case of infectious germ transmission”. Very confusing sentence, please rephrase.

Lines 133 to 136 lack literature citations. Please add.

Figure 1: Why this particular database? When I clicked to check the database it appears: server not found. Considering that the authors were very clear on how they used Google Scholar, Pubmed, etc, to find the most relevant articles for their review, I also encourage them to better organize the data in this figure. Initially, the graph must be edited. For instance, the y axis says “percentage”. But percentage of what? AMP sequences? What is “percentage of diversity” in this case? It is not clear. Moreover, this analysis should be highly improved by comparing different databases, including APD, YAMPD, CAMP among others. I could not find the citation (Mahlapuu et al., 2019) described in the figure 1 caption in the references list. Please double-check.

Avoid expressions like “good antibacterial activity (line 139)”, “good” is too relative.

In the topic  “The Archival and the Diversity of AMPs” the authors focused only on naturally occurring AMPs. It should be in the topic title. Actually, the authors affirm in the end of the Introduction “This paper provides an overview on the synthetic and long-lasting AMPs analogues”, but little is really described and discussed about synthetic peptides... Therefore, at some points, the manuscript lacks focus considering the authors’ goals.

Line 193 – 195: Same as comment 1.

Figure 2 must be completely redesigned. The quality is poor. There is not description of the PDB IDs used in the figure. Why did the authors bind to an ion? Why did the authors not specify disulfide bonds? Moreover, this figure can be highly improved if the authors add more AMP structural scaffolds (e.g., cyclotides and other head-to-tail or side-to-side chain cyclic peptides, stapled peptides, among others.)

Line 201: What did the authors mean by rolling indolicidin? I understand that some chemical modifications may favor helical structure in indolicidin-like peptides. However, this is a well-known AMP that cause non-lytic effects on bacterial and presents random coil arrangements… There are many other well-known AMPs that adopt α-helix that would be better examples.

Line 202. The same as above… Defensin is a mix of helix, loops and beta-sheet. Not the best example for α-helical AMPs. The authors should rethink their examples in this entire section.

Line 204. Some studies have reported short β-sheet forming AMPs that do not present disulfide bonds (please check: 10.1002/adfm.201202850, 10.1021/acsinfecdis.9b00073, 10.1016/j.biomaterials.2013.10.053).

Line 206. Same of line 2. It would be better if the authors opened a subsection for mixed structures (e.g, defensins).

Line 216: “Besides, many peptides form their active structure only after” please, replace “form” by “adopt”. Moreover, the authors use as example, indolicidin. Indeed, this AMP changes its structural profile to a “boat-like” structural orientation to translocate bacterial membrane and act on DNA. However, it is not clear in the present manuscript that such structural transition occurs. For someone that it not an expert in AMPs the best examples, by far, would be random coil AMPs in solution that, when in contact with bacterial surfaces, adopt α-helical structures to perform their membrane-associated or intracellular mechanisms of action.

In general the “AMP structure” section should be highly improved. What about cyclic peptides? Different structural scaffolds? And, once again, considering the last sentence of the introduction, I believe the authors should provide the readers with more examples for optimized AMPs, not only naturally occurring ones.

Figure 3 looks much better. A more detailed caption should be organized for this one, describing (very briefly) the mechanisms.

“The Bacterial Resistance Mechanisms towards Antibiotics and the Way AMPs can help” How is this topic different from hundreds of other review articles regarding AMPs? Moreover, some of the statements are controversial. There are studies indicating that bacterial can resist to AMP treatment at sub-lethal doses. Most changes occur in the bacteria surface, efflux pumps production, among others (10.1038/s41598-017-04181-y). Finally, bacterial biofilms have attracted great attention in the last five years. Why did the authors decide not to mention this resistance mechanism, which is currently responsible for >70% of all bacterial infections in humans?

“Advantages of AMPs”: the authors mention AMP synergism with antibiotics as an advantage. Please highlight that such strategy is highly controversial.  We are still to fully understand the determinants for AMP/antibiotics synergism and, because of that, some results are positive, some are not, some are effective in vitro, but not in vivo and vice-versa. Therefore, maybe the authors should not emphasize this as an advantage.

“Interestingly, AMPs have no/less side effects for the user, as their use causes zero to only very minimal toxicity to the body when compared with other antibiotics”. This sentence is very confusing, please rephrase.  Moreover, the authors give only on example of a peptide “citrus-amp1” with non-toxic effects. Please, add more examples.

“AMPs, which have a low synthetic cost, are small molecules that are” please review this statement carefully. Low synthesis cost compare to what? Chemically modified AMPs (D-amino acids, for instance) can be quite expensive. Moreover, they are more expensive to produce then most antimicrobials already available in the market and, this characteristic has been highlighted as a bottleneck in AMP-based therapies. Finally, small molecules are usually describe with up to 200 Da, which is not the case here (AMPs).

The explanation about the anti-cancer activities of AMPs is not complete…. The authors should also mention that the phospholipids asymmetry in cancer cells provides them with more negatively charged residues in their upper leaflet, thus favoring electrostatic attraction of cationic AMPs.

Lines 365 – 367: “Moreover, the cost of production of AMPs is very high when compared with the production costs of conventional antibiotics” The authors should carefully review the manuscript, as they are often controversial.

The relevance of Table 1 is questionable. Antibiotics and AMPs are highly different classes of antimicrobials. If we check carefully, most studies not even consider their correlation in number of mols for biological experiments. I do believe that AMPs represent a promising strategy, but it is not like they will completely replace antibiotics in a short-term. A more interesting comparison here, would be between naturally occurring and optimized AMPs (which should be the focus of this manuscript according with its title and last sentence of the Introduction).


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE CHARACTERISTICS AND ROLES OF ANTIMICROBIAL PEPTIDES AS POTENTIAL TREATMENT FOR ANTIBIOTIC-RESISTANT PATHOGENS: A REVIEW
Review round: 2
Reviewer: 1

Output:
Basic reporting: The authors have addressed all my comments in a satisfactory way.
Experimental design: The authors have addressed all my comments in a satisfactory way.
Validity of the findings: The authors have addressed all my comments in a satisfactory way.
Additional comments: The authors have addressed all my comments in a satisfactory way.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: THE CHARACTERISTICS AND ROLES OF ANTIMICROBIAL PEPTIDES AS POTENTIAL TREATMENT FOR ANTIBIOTIC-RESISTANT PATHOGENS: A REVIEW
Review round: 2
Reviewer: 2

Output:
Basic reporting: Lines 69 and 70: “This review is intended for all scientists and academicians in related fields to foresee
70 AMPs as a therapeutic agent and as a reference for their future related studies.” this sentence is quite confusing. Please rephrase

The topic “The evolution of synthetic AMPs” is not straightforward and there is no “evolution” “chronology” “time line” considering the different methods applied for naturally occurring AMP optimization, thus generating synthetic variants. If the authors retrieved published that from the last 10 years, in this topic they should start with the rational design strategies applied in 2011 and how they have “evolved” up to date.

The topic “the analogy between naturally occurring AMPs and synthetic AMPs” is really necessary? There is no useful information there, apart from the fact that Table 1 is cited. I suggest just citing Table 1 in another section and removing this topic.

The manuscript still lacks a better connection between all the ideas presented. The writing was improved, but the topics are, somewhat, disconnected. For instance, one can read the “AMP structures” topic without reading the full manuscript, as the topic is loosely connected with the others. This is also very clear in the Conclusions topic, which does not address or summarize all the topics present in the manuscript. I believe the manuscript would benefit of such connections of ideas.

The figures were highly improved

There are still some English issues that must be checked.
Experimental design: Lines 69 and 70: “This review is intended for all scientists and academicians in related fields to foresee
70 AMPs as a therapeutic agent and as a reference for their future related studies.” this sentence is quite confusing. Please rephrase

The topic “The evolution of synthetic AMPs” is not straightforward and there is no “evolution” “chronology” “time line” considering the different methods applied for naturally occurring AMP optimization, thus generating synthetic variants. If the authors retrieved published that from the last 10 years, in this topic they should start with the rational design strategies applied in 2011 and how they have “evolved” up to date.

The topic “the analogy between naturally occurring AMPs and synthetic AMPs” is really necessary? There is no useful information there, apart from the fact that Table 1 is cited. I suggest just citing Table 1 in another section and removing this topic.

The manuscript still lacks a better connection between all the ideas presented. The writing was improved, but the topics are, somewhat, disconnected. For instance, one can read the “AMP structures” topic without reading the full manuscript, as the topic is loosely connected with the others. This is also very clear in the Conclusions topic, which does not address or summarize all the topics present in the manuscript. I believe the manuscript would benefit of such connections of ideas.

The figures were highly improved

There are still some English issues that must be checked.
Validity of the findings: Lines 69 and 70: “This review is intended for all scientists and academicians in related fields to foresee
70 AMPs as a therapeutic agent and as a reference for their future related studies.” this sentence is quite confusing. Please rephrase

The topic “The evolution of synthetic AMPs” is not straightforward and there is no “evolution” “chronology” “time line” considering the different methods applied for naturally occurring AMP optimization, thus generating synthetic variants. If the authors retrieved published that from the last 10 years, in this topic they should start with the rational design strategies applied in 2011 and how they have “evolved” up to date.

The topic “the analogy between naturally occurring AMPs and synthetic AMPs” is really necessary? There is no useful information there, apart from the fact that Table 1 is cited. I suggest just citing Table 1 in another section and removing this topic.

The manuscript still lacks a better connection between all the ideas presented. The writing was improved, but the topics are, somewhat, disconnected. For instance, one can read the “AMP structures” topic without reading the full manuscript, as the topic is loosely connected with the others. This is also very clear in the Conclusions topic, which does not address or summarize all the topics present in the manuscript. I believe the manuscript would benefit of such connections of ideas.

The figures were highly improved

There are still some English issues that must be checked.
Additional comments: Lines 69 and 70: “This review is intended for all scientists and academicians in related fields to foresee
70 AMPs as a therapeutic agent and as a reference for their future related studies.” this sentence is quite confusing. Please rephrase

The topic “The evolution of synthetic AMPs” is not straightforward and there is no “evolution” “chronology” “time line” considering the different methods applied for naturally occurring AMP optimization, thus generating synthetic variants. If the authors retrieved published that from the last 10 years, in this topic they should start with the rational design strategies applied in 2011 and how they have “evolved” up to date.

The topic “the analogy between naturally occurring AMPs and synthetic AMPs” is really necessary? There is no useful information there, apart from the fact that Table 1 is cited. I suggest just citing Table 1 in another section and removing this topic.

The manuscript still lacks a better connection between all the ideas presented. The writing was improved, but the topics are, somewhat, disconnected. For instance, one can read the “AMP structures” topic without reading the full manuscript, as the topic is loosely connected with the others. This is also very clear in the Conclusions topic, which does not address or summarize all the topics present in the manuscript. I believe the manuscript would benefit of such connections of ideas.

The figures were highly improved

There are still some English issues that must be checked.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: NO RELEVANT DIFFERENCES IN CONDITIONED PAIN MODULATION EFFECTS BETWEEN PARALLEL AND SEQUENTIAL TEST DESIGN. A CROSS-SECTIONAL OBSERVATIONAL STUDY
Review round: 1
Reviewer: 1

Output:
Basic reporting: Basic Reporting
Abstract:
1.	Line 34-35, “either during (parallel design) or after (sequential design) the test stimulus” – do you mean either during or after the conditioning stimulus? This might be confusing for individuals who are not familiar with CPM.
2.	The methods section of the abstract is currently lacking statistical analyses. This may be due to a limited word count, but if it allows, I recommend the authors add statistical analyses that used in the present study.

Introduction:
3.	Line 65, please provide examples of mechanical and thermal test stimuli.
4.	Line 67, please be more specific with the test and conditioning stimuli. For example, CPM consist of two test stimuli, and conditioning stimuli can be applied consecutively or simultaneously with the second test stimulus but not with the first test stimuli.
5.	Line 71-72, the last sentence of this paragraph seems unnecessary.
6.	Paragraph 3-5, I think it would be of benefit to make them into one single paragraph rather than having multiple paragraphs.
7.	Line 85, please explain further what are the “conflicting results”.
8.	Line 95-96, this paragraph seems unnecessary. I suggest deleting it or combining with the previous paragraph.
9.	Line 100-101, study aim 2) is somewhat confusing. Please address it more clearly.

Results:
10.	In Figure 2, one of “Experiment 2” has to be “Experiment 3”.
11.	In Table 2, what do you mean by “baseline measurements in Experiment 3 are the same for both designs”? It was mentioned that both a sequential and parallel design were performed in each experiment. Please explain why there is only one baseline PPT value for Experiment 3.
12.	Please double-check and match all the values (e.g. β, 95% CI values) in the manuscript with those values in the tables to avoid any confusion.
13.	Please address the results of the order effect (Table 3) in the results part. Although it is briefly explained in Table 3 and discussion, it might be helpful for reader to further understand what those results represent.

References:
14.	Please double-check the reference list (e.g. reference #83-84, #92-95).
Experimental design: Methods:
15.	Were participants familiarized with the procedures on the first testing day or on a separate day? Please provide it in the familiarization part of the methods.
16.	Line 134, please provide how long did participants rest between parallel and sequential design for Experimental 3. Since Experimental 3 was performed in a single day whereas other two experiments were performed on two consecutive days, is it problematic to compare these three experiments for the first study aim?
17.	Line 152, were participants also refrained from exercise? If not, is there any possibility that exercise could influence the CPM effect (e.g. exercise-induced hypoalgesia).
18.	Was PPT measured first and then followed by thermal stimuli? It is mentioned that there was 10 minutes between test stimuli, however, the order of test stimuli is not stated.
19.	Line 286-288, please further explain what “regression coefficients adjusted for the effect of order of measurements (first or second measurement)” reflects or means (e.g. why does it have to be adjusted and what does it tell us?).
Validity of the findings: Discussion & Conclusion:
20.	Line 417-425, this paragraph includes useful information, however, this paragraph appears to be unrelated to your main research questions.
21.	Line 426-434, please provide rationale for why both absolute and relative values were reported in the present study (e.g. is it recommended to report both absolute and relative values? If so, why is it recommended?).
22.	Higher relative CPM effects (PPT) in the parallel design were observed at cervical spine and lower leg, but not at forearm. It might be useful to address and explain these findings.
23.	As CPM effect was examined only at 3 sites (i.e., CS, forearm, lower leg), this should not be generalized. Once again, the authors did not observe higher relative CPM effects in the parallel design at forearm. This may indicate that the influence of design on CPM effects may differ between limbs or sites. I think it would be of benefit to address this point in discussion.
Additional comments: Research questions of this study are interesting. However, the manuscript was not easy to follow. As an overall comment, I would strongly encourage the authors to improve the readability of the paper (also for those readers who may not be familiar with the CPM literature).


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: NO RELEVANT DIFFERENCES IN CONDITIONED PAIN MODULATION EFFECTS BETWEEN PARALLEL AND SEQUENTIAL TEST DESIGN. A CROSS-SECTIONAL OBSERVATIONAL STUDY
Review round: 1
Reviewer: 2

Output:
Basic reporting: The manuscript is well-written with clear English language throughout. A significant body of literature has been acknowledged and discussed throughout. It is evident that the authors have a deep understanding of the existing literature and gaps in the research area. Referencing, structure and tables are appropriate.
Experimental design: The research questions are relevant to the area of research and are appropriate to address the knowledge gap identified. These questions are designed to deliver important, relevant data within the field. Due to the study design (i.e. multiple aims across multiple experiments), I have provided the authors with a suggestion for improving the clarity of these aims. The methodology is very good, with exceptional detail provided within the manuscript. It is clear that this was a well-controlled experiment.
Validity of the findings: Raw data is provided, and the analysis methods are sound. The conclusions are supported by the data and are discussed relative to the research questions and existing literature.
Additional comments: Overall this is an interesting study that targets an important area of pain research. The authors should be commended for the design and control of the study, the thorough analysis conducted and the overall quality of the written manuscript. It is clear the authors have a deep understanding of the research area. I have two suggestions that I hope will add additional strength to the manuscript, and have detailed some specific revisions to be made.

General comments

If possible, please include effects sizes for your comparisons.

The description of how each of the study aims were addressed across the different experiments is sufficiently detailed but may appear confusing to some readers. Presentation of this information in figure format would be welcome; please consider this.

Lines 70-71 – Please consider expanding upon this point, to provide detail on/summarise the discrepancies within the literature so it is clear for the reader. This would add further support for the study rationale and some of the discussion points following the results.

Specific comments

Line 38 – ...as “the” conditioning stimulus?

Line 61 – please add a space between the last word and references

Line 68 – add a space between the period and beginning of the next sentence

Line 85 – remove hyphen

Lines 92 and 94 - please add a space between the last word and reference

Line 95-96 – This paragraph is one sentence long. Please merge with the previous paragraph.

Line 402 = “advise”


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: NO RELEVANT DIFFERENCES IN CONDITIONED PAIN MODULATION EFFECTS BETWEEN PARALLEL AND SEQUENTIAL TEST DESIGN. A CROSS-SECTIONAL OBSERVATIONAL STUDY
Review round: 2
Reviewer: 1

Output:
Basic reporting: no comment
Experimental design: no comment
Validity of the findings: no comment
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: NO RELEVANT DIFFERENCES IN CONDITIONED PAIN MODULATION EFFECTS BETWEEN PARALLEL AND SEQUENTIAL TEST DESIGN. A CROSS-SECTIONAL OBSERVATIONAL STUDY
Review round: 2
Reviewer: 2

Output:
Basic reporting: No additional comment
Experimental design: No additional comment
Validity of the findings: No additional comment
Additional comments: No additional comment


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: OCCUPANCY OF WILD SOUTHERN PIG-TAILED MACAQUES IN INTACT AND DEGRADED FORESTS IN PENINSULAR MALAYSIA
Review round: 1
Reviewer: 1

Output:
Basic reporting: The authors present a generally sound paper, with strong methods and results sections. The figures and tables are of high quality, and the raw data are shared. The structure is now always coherent, please find more specific comments in the general comments section.
Experimental design: The authors used a clear experimental design that is well presented and with strong links to published literature, mainly from the same research group. Some of the methods are referred too much to previous papers, while some more information are required so that the reader do not have to find other papers to get important information. For example, I would add the resolution and the source of the raster you used to obtain NDVI in this paper. That is an important information that otherwise the reader would have to find in Rayan & Linkie, 2015. I suggest checking the methods to see if some of these important information that refer to previously published papers might be added.
The research aims are clearly stated, although they are descriptive and no predictions are presented. The authors should include specific research questions and hypotheses following the general structure of the journal.
Validity of the findings: The authors did a good job in presenting the data clearly, and I have no issues with their data analysis. What I found weak is the data interpretation, as the authors are missing to discuss some important implications of their findings. The structure of the discussion is also not always clear as the authors do not present clear research questions and hypotheses. The discussion is too specific on the studied species and context. The authors often discuss arguments that are not expanded in the discussion and introduced in the introduction. For example, line 371-373, you do not explain why you did that analysis, you do not introduce the topic, and you do not expand on your claim. That is valid also for other findings that you do discuss but you do not have in your introduction (you are mainly missing to introduce clear hypotheses and that is reflected in your discussion). Please find more specific comments in the general comments section.
Additional comments: I have two major concerns that I suggest to be solved before considered this paper for publication.
1) The introduction in not well structured. You need a funnel structure and not going into your specific context in the 4th line. It is now difficult to follow. I suggest restructuring your introduction having a more coherent narrative. For example, lines 74-108 are very broad and should be presented earlier. You do not have clear research questions and hypotheses.
2) I think the authors here are missing to expand the discussion on why they found higher probabilities of detection in the small forest adjacent to the oil palm plantations than in the relatively undisturbed forests. They just list some possible reasons (lines 174-180) but do not expand on that, and that weakens your paper. A reader may think that, if you do not have differences between selectively logged and undisturbed forests in BTFC, and the detection in PFC is even higher than in BTFC, the conclusion is that Macaca nemestrina prefers disturbed habitats adjacent to plantations. It is true that you found a decrease in the detection between 2013 and 2017 in PFC and that it is related to the increase in forest clearing, but the explanation why PFC has higher detection rates is not expanded. I suggest included some more clarification.
I have two arguments that I think should be expanded, but I guess the authors should think a bit more about expanding their current arguments as well as they now read very speculative and unsupported.
a) The first argument I would add is about elevation. PFR is more a lowland rainforest while the BTFC is more mid altitude. If you check Goodman and Ganzhorn (2004), they suggest that the average intermediate elevation point for primates in Asia is around 450 m a.s.l., and Macaca nemestina prefers lowland habitats (check also Yanuar et al. 2009). You can also check a work from Campera et al. (2020) who made an extensive argument on the importance of elevation on animal abundance.
Goodman SM, Ganzhorn JU (2004) Elevational ranges of lemurs in the humid forests of Madagascar. International Journal of Primatology 25: 331–350.
Yanuar A, Chivers DJ, Sugardjito J, Martyr DJ, Holden JT (2009) The Population Distribution of Pig-tailed Macaque (Macaca nemestrina) and Long-tailed Macaque (Macaca fascicularis) in West Central Sumatra, Indonesia. Asian Primates Journal 1: 2–11.
Campera, M., Santini, L., Balestri, M., Nekaris, K. A. I., & Donati, G. (2020). Elevation gradients of lemur abundance emphasise the importance of Madagascar’s lowland rainforest for the conservation of endemic taxa. Mammal Review, 1, 25–37.
b) The other argument I suggest to expand is that there are several species that actually prefer disturbed habitats, especially a matrix of forest and plantations. This argument is almost absent while that is very important as your data goes in that direction. Also, since you are inevitability discussing the impact of palm oil plantations, I suggest also to include discussion over this topic, integrating for example the following paper:
Parsons et al. (2020). The viability and desirability of replacing palm oil. Nature Sustainability


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: OCCUPANCY OF WILD SOUTHERN PIG-TAILED MACAQUES IN INTACT AND DEGRADED FORESTS IN PENINSULAR MALAYSIA
Review round: 1
Reviewer: 2

Output:
Basic reporting: This paper in general is well-written, clear, and concise. However, there are some grammatical mistakes (primarily missing articles) throughout that should be addressed. I highlighted some of these in the general comments below.
Experimental design: It is not immediately clear from the abstract or the introduction why these two different data sets and analyses were included in this paper. Besides the use of camera traps on the same species, all other aspects (time period, sampling period, number of cameras, camera configuration, covariates, etc.) are different between the two sites making direct comparison difficult. It appears that the two sites differ in terms of the amount of degradation (though PFR is perhaps similar to TFR). Right now, the two analyses are very disjunct – making a clear story that connects the two and explains why they are both important for reaching the conclusions of the paper will really strengthen this study.
Generally, the knowledge gap and methods are clearly defined and detailed. However, I have noted a few comments below where extra clarification could be useful primarily in the methods and discussion.
Validity of the findings: This study is not currently replicable as covariate information is not included. It would be great to include this as well as the associated R code, if possible.

The conclusions are well-stated; however, there are a few additional questions highlighted in the general comments below that could warrant addressing or further discussion.
Additional comments: Here are some line-by-line comments:

L33: provide the first insights
L40: should this be no effect of selective logging on prob of ext? this variable wasn’t included on occupancy
L42-44: How does having the same age and sex structure suggest that selectively logged forest are important habitats?
L103: indicative of the ability for a species
L124: remove ‘totally’
L127: remove ‘about’
L157: Can standard deviation be added (as an error measure) on all of the averages for number of days that cameras are active?
L169-179: This information on camera trap settings and the reasoning behind why ground cameras are more appropriate than arboreal cameras for this species should be included in the paper instead of the figure legend. This could also be an interesting point to make in the discussion.
L188: why were different sampling occasion lengths used for each data set? What do you mean by ‘chosen to ensure a good model fit’?
L191: were all cameras functioning in PFR?
L201: remove ‘correctly’
L217: this section is unclear – what values can a site take for forest degradation – or is it a categorical covariate? If so, the category it falls within is based on what has happened in that site in the 5 years before camera trapping began? Does this category change over the study or each site is put into a category for the whole study?
Did colonization or extinction change over time? Was this tested? It seems that depending on when the clear cutting or selective logging happened this could affect these model parameters.
Were any of the covariates include in the same model correlated? It seems there could be a correlation between elevation and distance measures.
L247: why was distance to the nearest human settlement used instead of distance to the forest edge like in the analysis for PFR? It is not clear why different covariates were used for each analysis.
L271-272: this is results not methods
Why were different covariates used for each analyses – this makes comparison between the two study sites difficult.
L277: what is meant by limitations in data availability? TEAM data is all freely available.
L304: AICc?
L320: through?
L324: six-fold?
L339-340: this is discussion, not results – remove
L365: time and space?
L366: as compared to sites with no tree felling?
L368: this is confusing – selective logging is not tested as a covariate against extinction – the category of forest degradation was – so maybe instead you could say that there was no difference in extinction prob between selective logged sites and sites with no tree felling? (unless forest degradation was actually 3 separate covariates one for each category – but this is unclear in the methods)
L373: what are these certain conditions? It would be good to have more discussion about the age/sex structure.
L374: how are these values comparable when the sampling occasions are different? Even if the sites with fewer days is higher, doesn’t mean they are comparable.
L380: could this also be because ground cameras were used not arboreal cameras – if the species is likely to have increased movement on the ground in degraded forests?
L454: this study doesn’t address severe human encroachment – I would rephrase stresses the high sensitivity to clear cutting.
L455-460: delete this – this current study shows that areas that are selectively logged are also viable for this species

Figure 1: why do you the scale bars not start at 0? It seems in Royal Belum State Park and Temengor Forest Reserve some of the cameras are very close together – are these all more than 1 km apart? Does this spatial configuration of cameras, which differs from PFR, affect the estimates from the models?
Figure 2: What do you meant by smoothed site occupancy estimates? Aren’t these model averaged estimates?
Figure 3: Is it possible to show how many sites are selectively logged as well as clear cut? It seems that maybe there are few sites which is why there is such large error bars?
Table S2: Why are the estimates 0 for all the sampling months? For BTFC, it looks like sampling month Jan to Aug was not estimable?


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: LOCAL ANCESTRY PREDICTION WITH PYLAE
Review round: 1
Reviewer: 1

Output:
Basic reporting: In “Local ancestry prediction with PyLAE” Smetanin et al present a new method, PyLAE, for inferring local ancestry. Local ancestry programs are often complicated and PyLAE’s straightforward methodology (Bayesian posterior probabilities followed by Viterbi processing) makes it a potentially useful tool. The manuscript is generally well-written and easy to understand however I have some concerns about how well the algorithm is validated, and how other analyses presented in the manuscript serve to illustrate PyLAE’s utility. These concerns are outlined in more detail in “Validity of Findings” and “General Comments” below.
The authors point out that there is “always room to develop a user-friendly, fast, accurate” approaches for local ancestry (line 40), and I agree; very few programs are well-suited to every research question and new programs that are well-validated may fill a previously unoccupied niches, supplant existing programs, or improve accessibility of local ancestry methods to more researchers. With that in mind, I still believe that the authors should provide more motivation for developing a new local ancestry program or provide additional information in the Introduction or elsewhere on how PyLAE represents an improvement over other local ancestry inference programs, or what knowledge gaps may be filled with PyLAE. Inclusion of this information could provide a stronger ecntral purpose for the manuscript, as some of the manuscript’s different sections in Results seem to don’t seem to tie together well, even if the results presented within each section may be independently interesting if explored in more depth.
The figures and tables presented in the manuscript are relevant to the results discussed in the manuscript and appear to be of good quality, however I have concerns with the colors of Figures 1-3 and I have few suggestions to improve the interpretability of figure 4. These comments can be found in the “General Comments” below.
Experimental design: Although the algorithm for PyLAE is generally well-explained in the methods section, experiments to validate PyLAE are generally lacking. The only experiment that attempts to validate PyLAE’s accuracy is a correlation test between PyLAE’s local ancestry inference and global ancestry inference determined by ADMXITURE (presented in Figure 5). This experiment is a good start to validate PyLAE’s output, but it is insufficient on its own to validate the program. I make specific suggestions on PyLAE validation in “General Comments” below.
Validity of the findings: The manuscript lacks a single central finding though there are potentially interesting findings on the inflation of admixture proportions presented in the “Investigation of the reference dataset” (lines 208-289), and another potentially interesting finding about power to investigate selection on different molecular pathways with and without local ancestry information presented in “Application of Local Ancestry”. From the title and abstract, I would anticipate that most findings from the manuscript would be found in the “Performance of the PyLAE algorithm” section, but just one figure (Figure 5) is found in this section (specific suggestions to improve this section are recorded in “General Comments”). As such, the summary finding that PyLAE is “an easy-to-use and fast tool to perform ancestry decomposition” (lines 369-370) is not well-supported.
I note that the section “Application of Local Ancestry” provides a potentially useful illustration of an analysis which can be improved with local ancestry information and is an appropriate section for a manuscript that introduces a new program, but this section demonstrates the potential utility of PyLAE without addressing its accuracy. Since the authors had not previously compared PyLAE to existing local ancestry programs in depth or otherwise demonstrated its accuracy beyond simple correlation with global ancestry proportions, it is difficult to interpret the findings presented in this section.
Additional comments: Major Points:
1.	As mentioned above, the manuscript seems to struggle tying the different analyses presented in the manuscript into one cohesive message. Each of the three different sections in Results presents findings that could be of potential interest to readers if explored in more detail but the authors should clarify more explicitly how the result is relevant to the central message of the manuscript.
2.	I strongly suggest revision of the abstract to include the full scope of what is presented in the manuscript. As it is currently written, the abstract suggests that the manuscript’s focus will be nearly exclusively on the implementation of PyLAE. Instead, though PyLAE remains a substantial portion of the methods section, it is a minor topic in the results section. Additionally, certain properties of PyLAE mentioned in the abstract are not mentioned in the text (i.e., efficiency, speed, presentation of results, number of populations).
3.	If the subject of the manuscript is to introduce PyLAE as a program (as the title and abstract imply), I recommend the authors present analyses that demonstrate PyLAE’s sensitivity and specificity. I further recommend that the authors address the following questions in the manuscript:
•	How concordant are PyLAE results with results from other local ancestry programs?
•	Using simulation, how accurately does PyLAE capture ancestry switches? Are breakpoints introduced by recombination between different ancestries accurately captured? Does accuracy change with segment size?
•	How does PyLAE’s accuracy change with more or fewer ancestral populations?
•	What is PyLAE’s runtime (include information about the processor)and how much memory does it require?
•	How well does PyLAE scale (in memory and runtime) with more samples, more variants, or more ancestral populations?
4.	Figure 4. Please provide an in-depth caption to describe what is represented in the heatmap. I suggest at a bare minimum that color scale be provided with some information about how values depicted in the scale are generated. Readers may additionally appreciate some form of grouping along each axis to help demarcate different super-populations (e.g., boxes around populations that belong to the same super-population).
5.	Figure 3. I suggest a more informative label for the x axis, maybe something like “value for largest admixture component”. Additionally, shapes and colors are not consistent between the figure legend and points in the figure. For example, the legend indicates that blue diamonds represent individuals from European populations, but there are no blue diamonds in the figure. Instead, blue points in the figure are circles and diamonds in the figure are teal, neither of which are in the legend. This makes it difficult to interpret the figure and evaluate what is written in the text about the figure.
6.	Lines 117-119. Although the number of snps in the dataset used in the manuscript suggests that linkage disequilibrium between snps may not be a substantial problem for these analyses, accounting for linkage disequilibrium between sites is critical to avoid likelihood mis-specification for researchers interested in using PyLAE. Please elaborate on the relationship between marker density and linkage disequlibrium, and if possible, provide a range of marker densities that would be acceptable. Specifically, since this work was performed in humans, what is an acceptable range of marker densities or how much LD can be tolerated? Also, what does it mean for a distance between two points to be “above LD” (lines 118-119; 132)? Does this refer to sites being in approximate linkage equilibrium?
Minor Points:
7.	Figures 1 and 2. The captions of both Figures 1 and 2 mention brown as a color in the plot, but I do not see a color that appears brown in the figure. I suspect that the brown mentioned in the caption corresponds to what appears to be orange on my screen. Please double check that all population colors are labeled appropriately.
8.	Lines 239-241. Do these sentences refer to the Toscani individuals?
9.	Lines 269-270. Could this frequent misclassification be the result of the supervised ADMIXTURE run not being appropriate to separate individuals in these West African populations from each other?
10.	Lines 133-138. Font sizes appear to be inconsistent in this area.
11.	Lines 193-195. This appears to be a duplicate sentence.
12.	Lines 302-303. There appears to be an error correctly inserting the name of a figure. I believe that it should be referring to Figure 5, but this is a typo that must be fixed.
13.	Lines 358-368. This paragraph seems somewhat out of place. It is definitely worthwhile to discuss how the putative ancestral populations used for analyses presented in the manuscript may have influenced the results, and to point out why the particular set of ancestral populations is appropriate compared to reasonable alternatives, however this paragraph feels more like instructions for how to use a different set of ancestral populations, and seems more appropriate for a software user-manual.
14.	Abbreviations: “1kG” is used only once, but “1000 Genomes” is written many times.
15.	GitHub repository: It would be helpful to provide some test data with the software so that users can ensure that their installation is working as intended.
16.	I noticed on the github page that it is possible to start with data in plink format (.bed/.bim/.fam). If this is the case, how will local ancestry for a site be determined when snps are not phased?


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: LOCAL ANCESTRY PREDICTION WITH PYLAE
Review round: 1
Reviewer: 2

Output:
Basic reporting: The writing and logic is generally strong and clear. The topic is well-introduced and references, figures and data are appropriate.

One suggestion: A lot of discussion in the manuscript involves the differences between the “haploid mode” and “diploid mode” of the approach and it is not explained why this is so significant. It would be useful to discuss how previous approaches have dealt with the issue and/or why it is a particular problem for PyLAE.
Experimental design: The problem is clearly stated and the methodology is well-described. The PyLAE method makes sense as a solution to the problem of identifying admixture through the genome.
However, the methods used to validate PyLAE are not very convincing. The authors compare the aggregated PyLAE results (destroying the local information) to admixture vectors from Admixture (Figure 5) but this is not really a test of the accuracy of the local results because the local character of the results do not come into play here.

I appreciate that validating the local ancestry inference is challenging as we have no direct measure to compare against. However, there are multiple other approaches available for local ancestry prediction discussed in the introduction to this article and a direct comparison with PyLAE would be informative. Agreement between methods using different approaches supports all of them and disagreements would also be informative.

The authors repeatedly and believably claim PyLAE’s as a major advantage of the method but this is not demonstrated anywhere.
Validity of the findings: Aside from issues mentioned above, all conclusions are supported.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: LOCAL ANCESTRY PREDICTION WITH PYLAE
Review round: 2
Reviewer: 1

Output:
Basic reporting: The revision of “Local Ancestry Prediction with PyLAE” makes it a much-improved manuscript. The authors provided point-by-point responses to most reviewer comments and have added additional information and analyses to the manuscript that were suggested by the reviewers. I commend the authors for their revisions, however after reading through the revised manuscript, I have several new comments which are detailed in the “Experimental Design” and “General Comments” sections below.
Experimental design: With the additional information provided on the difference between PyLAE’s haploid mode and diploid mode, I have some additional concerns on the validity of findings. Specifically, it appears that the difference between haploid mode and diploid mode lies primarily in how the admixture coefficients that will be used as priors are generated. In haploid mode, after phasing an individual, the prior is generated from supervised ADMIXTURE where the input data consists of homozygotic genotypes for each of the positions of the phased individual’s haplotype. I caution that such manipulation likely exaggerates differences between populations and artificially inflates (or deflates) admixture coefficients.
The addition of a comparison between PyLAE and RFMix strengthens the manuscript and the concordance of aggregated local ancestry estimates suggests that PyLAE performs well. However, the authors still do not present an adequate analysis of how well PyLAE performs locally, which is an essential element of a local ancestry algorithm. The correlation of aggregate local ancestry proportions between PyLAE and RFMix suggests that the two algorithms find the same amount of ancestry of each population, but not necessarily that they find the same ancestry at the same locations. I suggest the authors include some analysis about how concordant RFMix and PyLAE are at local scales (e.g., similarity of local ancestry inference across moving windows, determining what proportion of the local ancestry inference in concordant vs discordant).
As a final note, I mention that concordance between RFMix and ADMIXTURE is important as these are well-vetted and commonly used tools for local and global ancestry inference, but PyLAE’s concordance with these tools merely demonstrates that its estimates achieve the same standard as these commonly used tools. A more appropriate test of PyLAE’s accuracy would be to test it on simulated genotype data where there is known ancestry at each position of the genome.
Validity of the findings: Given some limitations due to issues mentioned in “Experimental Design” that may change the interpretation of some results, findings and conclusions seem consistent with results.
Additional comments: 1.	In responding to a comment about testing PyLAE’s accuracy, the authors performed an analysis that compares aggregated ancestry information generated with PyLAE and RFMix with ancestry proportions inferred with ADMIXTURE. The analysis demonstrates that PyLAE is largely concordant with RFMIX under a range of different window sizes and readers may be interested in this information. I request that the authors include the results from the analysis in the revised manuscript, potentially as a supplemental figure.
2.	As part of their response, the authors include information about the speed on PyLAE but did not include this information in the revised manuscript. Readers interested in using PyLAE for their own research would likely be interested in having this information, and I request that the authors include it in the resubmission, or even on the software’s GitHub page.
3.	Labels on figure axes throughout the manuscript are quite small and are difficult to read, even when the figure is the size of an entire page.
4.	Line 438: The term “locations of regions along the genome” may be misunderstood to refer to actual positions (base pair coordinates) along the genome. I suggest using an alternate term like “population origins of regions of the genome.”


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: LOCAL ANCESTRY PREDICTION WITH PYLAE
Review round: 2
Reviewer: 2

Output:
Basic reporting: No new comments.
Experimental design: No new comments.
Validity of the findings: The addition of a comparison between RFMix and PyLAE strengthens the support for the claims made in the manuscript, as do other revisions. However, as in the initial submission, the only method used to assess prediction accuracy is to compare the aggregated local ancestry predictions to global predictions from Admixture. As PyLAE is designed for local prediction, the predicted local ancestry structure is itself of interest, not just the aggregated results. In the RFMix paper, for example, accuracy is assessed using the agreement between prediction and simulated results at each SNP.

The idea behind PyLAE appears sound, but it is difficult to assess and compare to other methods with no data presented on the local predictions. If the authors do not want to use simulations, it would be helpful to directly compare local predictions between RFMix and PyLAE, perhaps showing how each method predicts ancestry along some example genomes and/or producing quantitative measures of overall local agreement.
Additional comments: No additional comments


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: GROWTH AND FEEDING ECOLOGY OF CONIFORM CONODONTS
Review round: 1
Reviewer: 1

Output:
Basic reporting: For: PeerJ
There are no significant problems with the science of this submission as the article is self-contained with relevant results to the hypotheses. It is very well-written in a professional English throughout the manuscript and well-organized. The literature references are sufficient and up-to-date. The minor problems are the following:
1.	 Generally, the citation format could be more consistent. Sometimes it is written “and” and sometimes “&”. E.g. Murdock and Smith, 2021 (line 83) but Szaniawski & Bengtson 1998 (line 100)

2.	 line 84: publication year of reference is incorrect.

3.	There is a confusion in the manuscript referring to the citation of Murdock & Smith 2021. In the reference list are two references from Murdock & and Smith 2021, (Murdock & Smith 2021a) and (Murdock & Smith 2021b). This should be marked the same way throughout the manuscript.

4.	line 477: “exaptation” spelling error

5.	lines 488-492 and lines 500-504. There is a repetition of almost the same sentences.

“The Sr/Ca ratio, proposed as a proxy for the trophic position, changed only minimally throughout the ontogeny in both species and in opposite directions: it decreased, as predicted based on comparisons with Ozarkodina confluens (Shirley et al., 2018), in Pr. muelleri, 491 but increased by ca 1% per 1 µm in Pa. equicostatus. These results indicate that neither species changed their trophic niche substantially during their life”
and
“The Sr/Ca ratio changed only minimally throughout the ontogeny in both species and in opposite directions: it decreased, as predicted based on comparisons with Ozarkodina confluens (Shirley et al., 2018), in Pr. muelleri, but increased in 503 Pa. equicostatus. These results indicate that either species did not change their trophic niche substantially during their life”
I suggest some rephrasing.
Experimental design: The research question is well defined, relevant and meaningful. This research fills an important knowledge gap. No previous studies on conodonts examined the trophic levels and the lifestyles of conodonts by using Sr/Ca ratios. Furthermore there are only very limited studies on growth rates in primitive coniform conodonts. The technical standards used in this study are state-of-the-art with the newest techniques available, e.g. backscatter electron (BSE) imaging, energy-dispersive X-Ray spectroscopy (EDX) and synchrotron radiation X-ray tomographic microscopy (SRXTM).

1.	Lines237-238: The authors attempted to fit von Bertalanffy and logistic growth models using the package growth rates, but these models could not be fitted to the data. There should be an additional sentence or add on to find the explanation in the discussion (e.g. (see discussion)).
Validity of the findings: The results of this study are significant because the using Sr/Ca ratios for paleodiets in aquatic systems is a novelty and makes an important contribution to the field. The conclusions are well stated and linked to the original research questions. The minor problems are the following:
1.	line 324: The claim that most conodonts lived less than a year without any citation is mainly based on assumptions that lamellae in conodont crown tissues represent regular daily episodes of depositions. To my knowledge there is not enough evidence supporting this claim. With no similar living present representatives of conodonts, it is highly speculative to impose circadian rhythms from mammals and reptiles on conodonts. Maybe one or two sentences on which basis the implementation was made would help the reader to better understand.

2.	lines 327-328: To my knowledge there is no data or evidence available concerning the reproduction in conodonts. Thus the claim that condonts reproduced multiple times during a season is highly speculative. Maybe more information to support your sentence is needed.
Additional comments: The main issues of this study are the small amount of investigated specimens (2). Whether the elements are representative for the whole animal or even the entire population can be neglected for the Sr/Ca ratio studies and the investigations on the growth rates. But the damage surface of the element can be highly individual and it has to be questions if the lack of crown tissue damage in two elements are enough evidence to suggest the trophic ecology of coniform conodonts in early
Palaeozoic ecosystems in general. However, the authors support their findings to a certain degree with independent Sr/Ca studies.
The interpretation of the Sr/Ca ratio data needs more detail. De Villiers (1994; 1999) documented and increase of the Sr/Ca values with water depth, there is a minute depth gradient (in modern oceans). Furthermore, the Sr/Ca values differ latitudinal and longitudinal (in modern oceans). Your interpretation is mainly based as if the conodonts were living always on the same spot. I am missing in the discussion the possibility of conodonts changing the water depth during their live or that they migrated. How would this influence the Sr/Ca values? Different Sr/Ca values in different parts of the paleo-waters should be more elaborated in the Discussion.

In summary, this study should be published but only after the minor revisions mentioned before.


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: GROWTH AND FEEDING ECOLOGY OF CONIFORM CONODONTS
Review round: 1
Reviewer: 2

Output:
Basic reporting: I think this is a really interesting contribution to our understanding of the feeding ecology of conodonts, specifically addressed to the conodont group bearing coniform elements that is usually hardly investigated. A few suggestions are reported below.
Experimental design: I appreciated the clarity of the exposure.
The only two minor comments that you might consider having the authors address would be the need to specify for non-conodont people what euconodonts are (line 113) and perhaps discuss/reply to those who have recently questioned geochemical stability of bioapatite, i.e. Shohel et al. (2020, R. Soc. Open Sci. just using coniform elements of Dapsilodus obliquicostatus) or Ferretti et al. (2021, Palaeo3).
Validity of the findings: My only concern is that all data derive from the study of two only elements, one for each genus. Maybe the authors should discuss how confident their result may be.
Additional comments: A few minor comments regard the need of:
- line 84: 2021 instead of 202;
- line 86: replace assigned with a synonym (assigned used also in previous line);
- add commas before year of publication (e.g., lines 100, 120, 123, 198., ...);
- remove commas before et al. (e.g., lines 127, 184, 201, ...);
- remove and at the end of line 139;
- line 165: late and not Upper Cambrian;
- be consistent in using numbers in arabic (e.g., line 255: 4-7 growth increments) or written in full (four-seven in explanation of figure 7).


Instruction: You are one of the reviewers, your task is to write a review for the article. You will be given the title of the article, the number of the round in which the article is located, and your order among the reviewers.

Input:
Title: GROWTH AND FEEDING ECOLOGY OF CONIFORM CONODONTS
Review round: 1
Reviewer: 3

Output:
Basic reporting: The manuscript was well written and well organized.
Experimental design: The research goal has been well achieved.
Validity of the findings: All these data, as well as the method, are tremendous important for our understanding of the evolutionary of conodonts. Thus I strongly support its publication in the journal.
Additional comments: Dear editor and author,
This interesting article addresses the growth and feeding ecology of conodonts using histological and geochemical methods. In general, the manuscript was well written and well organized. The research goal has been well achieved. All these data, as well as the method, are tremendous important for our understanding of the evolutionary of conodonts. Thus I strongly support its publication in the journal.
However, there are also some problems, especially see my comments on conodont life spans, which should be carefully considered before its publication. My comments and suggestions are as follow.
With best regards,
Yanlong Chen
------------------
Northwest University, China; email: yanlong.chen@nwu.edu.cn
------------
Line 57:  may add reference: Joachimski et al., 2002, 2009
Line 129: may add reference: Chen et al., 2016
Line 144: the “formula (Ca5Na0.14(PO4)0.016F0.73(H2O)0.85)” is problematic. It should be changed as “Ca5Na0.14(CO3)0.16(PO4)3.01(H2O)0.85F0.73”, and a reference may added: Joachimski, M. M., Breisig, S., Buggisch, W., Talent, J. A., Mawson, R., & Gereke, M., Morrow J.R., Day J., Weddige K., 2009. Devonian climate and reef evolution: insights from oxygen isotopes in apatite. Earth & Planetary Science Letters, 284, 599–609.
Line 519:  In the “Conclusions” part. The life span of 27 and 58 days is not well discussed and supported in the “Discussion” part. To my knowledge, it is still debate whether each lamina is the result of a daily, weekly, seasonal or annual secretion (e.g. Muller & Nogami 1971; Zhang et al. 1997; Dzik 2008). Though it is very similar to enamel of mammals, but there is no evidence to support that conodont lamina is daily, as there is large difference between conodonts and mammals. Even if it is day, I am wondering if it is possible that the number of lamellae stopped increase in a potential stage when the animal is till alive? As the numbers of cross-striations of human teeth stopped increase after its eruption from gum, so the number of cross-striations does equal to the life span of the man.