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Additionally, individual filaments were found to undergo polarity reversals, and the maximum velocity was observed immediately following the reversal.
| null | null |
R3 Minor comments The addition of a time stamp to the supplemental movies would be useful
| null | null |
life4040819_perova
| 0 |
Additionally, individual filaments were found to undergo polarity reversals, and the maximum velocity was observed immediately following the reversal.
| null | null |
The authors demonstrate the presence of putative junctional pores by electron microscopy and other ultrastructural data that would appear to support polysaccharide secretion as the driving force for motility in this organism.
| null | null |
life4040819_perova
| 0 |
The observations and models are consistent with previously published work on motility of various cyanobacteria and provide new insights into the mechanics of motility of cyanobacteria that are interesting.
| null | null |
Response: We thank the reviewers for giving us helpful comments.
| null | null |
life4040819_perova
| 0 |
The authors’ conclusions are generally well supported and the electron microscopy provides some of the clearest images to date of the junctional pores.
| null | null |
Within the text, corrected words are highlighted.
| null | null |
life4040819_perova
| 0 |
The alternative views he previously generated are much expanded in this manuscript.
| null | null |
I must note that a careful evaluation of all facets requires expertise in a multitude of disciplines (from prebiotic chemistry and structural biology to evolutionary bioinformatics and biochemistry) and considerable time, none of which I possess.
| null | null |
life4041050_makarova
| 0 |
I have only a few comments, which might improve the manuscript.
| null | null |
He reviews some of his previous work and presents an alternative to the dominant ‘Ancient RNA world’ hypothesis.
| null | null |
life4041050_makarova
| 0 |
In light of recent research developments and argumentation (some of it reviewed), his views should be considered a welcome addition to the many ideas that populate the “origin of life” field of inquiry that counter the dominant paradigm.
| null | null |
I have however a number of quibbles that if addressed could increase the accuracy, value and impact of the manuscript.
| null | null |
life4041050_makarova
| 0 |
Therefore, my comments will be slanted by my own expertise and will only serve the author as a partial devil’s advocate effort General commentary
| null | null |
Therefore, my comments will be slanted by my own expertise and will only serve the author as a partial devil’s advocate effort General commentary
| null | null |
life4041050_makarova
| 0 |
I have only a few comments, which might improve the manuscript.
| null | null |
The article demonstrates that the iron-sulfur surface metabolism theory at high temperatures has a much better explanatory power than the RNA World theory.
| null | null |
life4041050_makarova
| 0 |
The article demonstrates that the iron-sulfur surface metabolism theory at high temperatures has a much better explanatory power than the RNA World theory.
| null | null |
I have however a number of quibbles that if addressed could increase the accuracy, value and impact of the manuscript.
| null | null |
life4041050_makarova
| 0 |
Therefore, my comments will be slanted by my own expertise and will only serve the author as a partial devil’s advocate effort General commentary
| null | null |
The alternative views he previously generated are much expanded in this manuscript.
| null | null |
life4041050_makarova
| 0 |
The alternative views he previously generated are much expanded in this manuscript.
| null | null |
The article demonstrates that the iron-sulfur surface metabolism theory at high temperatures has a much better explanatory power than the RNA World theory.
| null | null |
life4041050_makarova
| 0 |
Round 1: and Author Response The manuscript comprises an exciting account on the origin of life with emphasis on the emergence and function of RNA.
| null | null |
Therefore, my comments will be slanted by my own expertise and will only serve the author as a partial devil’s advocate effort General commentary
| null | null |
life4041050_makarova
| 0 |
Round 1: and Author Response The manuscript comprises an exciting account on the origin of life with emphasis on the emergence and function of RNA.
| null | null |
I have only a few comments, which might improve the manuscript.
| null | null |
life4041050_makarova
| 0 |
The alternative views he previously generated are much expanded in this manuscript.
| null | null |
I have however a number of quibbles that if addressed could increase the accuracy, value and impact of the manuscript.
| null | null |
life4041050_makarova
| 0 |
The article demonstrates that the iron-sulfur surface metabolism theory at high temperatures has a much better explanatory power than the RNA World theory.
| null | null |
I have however a number of quibbles that if addressed could increase the accuracy, value and impact of the manuscript.
| null | null |
life4041050_makarova
| 0 |
Therefore, my comments will be slanted by my own expertise and will only serve the author as a partial devil’s advocate effort General commentary
| null | null |
In light of recent research developments and argumentation (some of it reviewed), his views should be considered a welcome addition to the many ideas that populate the “origin of life” field of inquiry that counter the dominant paradigm.
| null | null |
life4041050_makarova
| 0 |
Summary: The manuscript is surely useful and, in principle, it presents a good contribution to the recent methodological trends (polyphasic approach) in cyanobacterial taxonomy, this conclusion should be the main result from this work.
| null | null |
Given that both reviewers commented on this issue, we tried to clarify our aims and included a sentence at the end of the introduction, in order to clarify the point.
| null | null |
life5010050_makarova
| 0 |
We thus only briefly discuss names and taxonomy in our analysis.
| null | null |
Summary: The manuscript is surely useful and, in principle, it presents a good contribution to the recent methodological trends (polyphasic approach) in cyanobacterial taxonomy, this conclusion should be the main result from this work.
| null | null |
life5010050_makarova
| 0 |
We do not deal with taxonomy at all, only with testing the presence of a barcoding gap.
| null | null |
We do not deal with taxonomy at all, only with testing the presence of a barcoding gap.
| null | null |
life5010050_makarova
| 0 |
Given that both reviewers commented on this issue, we tried to clarify our aims and included a sentence at the end of the introduction, in order to clarify the point.
| null | null |
We hope that now both reviewers, and all other potential readers, will not be misled by our approach.
| null | null |
life5010050_makarova
| 0 |
ISSN 2075-1729 www.mdpi.com/journal/life Peer-Review Record: Does a Barcoding Gap Exist in Prokaryotes?
| null | null |
ISSN 2075-1729 www.mdpi.com/journal/life Peer-Review Record: Does a Barcoding Gap Exist in Prokaryotes?
| null | null |
life5010050_makarova
| 0 |
We do not deal with taxonomy at all, only with testing the presence of a barcoding gap.
| null | null |
Summary: The manuscript is surely useful and, in principle, it presents a good contribution to the recent methodological trends (polyphasic approach) in cyanobacterial taxonomy, this conclusion should be the main result from this work.
| null | null |
life5010050_makarova
| 0 |
We do not deal with taxonomy at all, only with testing the presence of a barcoding gap.
| null | null |
We thus only briefly discuss names and taxonomy in our analysis.
| null | null |
life5010050_makarova
| 0 |
Round 1: and Author Response The authors tested novel approach to identification of species in cyanobacteria based on 16S rRNA based on identification of barcoding gaps previously used in animals.
| null | null |
Summary: The manuscript is surely useful and, in principle, it presents a good contribution to the recent methodological trends (polyphasic approach) in cyanobacterial taxonomy, this conclusion should be the main result from this work.
| null | null |
life5010050_makarova
| 0 |
Round 1: and Author Response The authors tested novel approach to identification of species in cyanobacteria based on 16S rRNA based on identification of barcoding gaps previously used in animals.
| null | null |
Round 1: and Author Response The authors tested novel approach to identification of species in cyanobacteria based on 16S rRNA based on identification of barcoding gaps previously used in animals.
| null | null |
life5010050_makarova
| 0 |
Round 1: and Author Response The authors tested novel approach to identification of species in cyanobacteria based on 16S rRNA based on identification of barcoding gaps previously used in animals.
| null | null |
ISSN 2075-1729 www.mdpi.com/journal/life Peer-Review Record: Does a Barcoding Gap Exist in Prokaryotes?
| null | null |
life5010050_makarova
| 0 |
Given that both reviewers commented on this issue, we tried to clarify our aims and included a sentence at the end of the introduction, in order to clarify the point.
| null | null |
We hope that now both reviewers, and all other potential readers, will not be misled by our approach.
| null | null |
life5010050_makarova
| 0 |
ISSN 2075-1729 www.mdpi.com/journal/life Peer-Review Record: Does a Barcoding Gap Exist in Prokaryotes?
| null | null |
We hope that now both reviewers, and all other potential readers, will not be misled by our approach.
| null | null |
life5010050_makarova
| 0 |
To do so, we did not download named sequences from GenBank, but used a carefully annotated and checked database with a built-in phylogeny that would allow us to obtain monophyletic clades, regardless of their names.
| null | null |
Given that both reviewers commented on this issue, we tried to clarify our aims and included a sentence at the end of the introduction, in order to clarify the point.
| null | null |
life5010050_makarova
| 0 |
Summary: The manuscript is surely useful and, in principle, it presents a good contribution to the recent methodological trends (polyphasic approach) in cyanobacterial taxonomy, this conclusion should be the main result from this work.
| null | null |
Given that both reviewers commented on this issue, we tried to clarify our aims and included a sentence at the end of the introduction, in order to clarify the point.
| null | null |
life5010050_makarova
| 0 |
Round 1: and Author Response The authors tested novel approach to identification of species in cyanobacteria based on 16S rRNA based on identification of barcoding gaps previously used in animals.
| null | null |
To do so, we did not download named sequences from GenBank, but used a carefully annotated and checked database with a built-in phylogeny that would allow us to obtain monophyletic clades, regardless of their names.
| null | null |
life5010050_makarova
| 0 |
ISSN 2075-1729 www.mdpi.com/journal/life Peer-Review Record: Does a Barcoding Gap Exist in Prokaryotes?
| null | null |
Round 1: and Author Response The authors tested novel approach to identification of species in cyanobacteria based on 16S rRNA based on identification of barcoding gaps previously used in animals.
| null | null |
life5010050_makarova
| 0 |
We thus only briefly discuss names and taxonomy in our analysis.
| null | null |
We thus only briefly discuss names and taxonomy in our analysis.
| null | null |
life5010050_makarova
| 0 |
Summary: The manuscript is surely useful and, in principle, it presents a good contribution to the recent methodological trends (polyphasic approach) in cyanobacterial taxonomy, this conclusion should be the main result from this work.
| null | null |
More citations of modern literature would be expectable and useful.
| null | null |
life5010050_perova
| 0 |
However, the only one universal method is quite insufficient in microorganisms, and the combination of all possible classification criteria is desirable.
| null | null |
More citations of modern literature would be expectable and useful.
| null | null |
life5010050_perova
| 0 |
My critics should inform authors about more complicated problematics of this whole group, and several principles should be respected and accepted for future cyanobacterial research.
| null | null |
It is overall well-written and innovative work, but there are few things to consider in methods and results, which should be revised, and some formal flaws.
| null | null |
life5010050_perova
| 0 |
Second Round of Evaluation Round 2: I have had the more critical remarks to the manuscript; however, I think that the presented data are useful and should be published.
| null | null |
Round 2: I accept the paper in the present form.
| null | null |
life5010050_perova
| 0 |
We do not deal with taxonomy at all, only with testing the presence of a barcoding gap.
| null | null |
ISSN 2075-1729 www.mdpi.com/journal/life Peer-Review Record: Does a Barcoding Gap Exist in Prokaryotes?
| null | null |
life5010050_perova
| 0 |
Round 1: and Author Response The authors tested novel approach to identification of species in cyanobacteria based on 16S rRNA based on identification of barcoding gaps previously used in animals.
| null | null |
We thus only briefly discuss names and taxonomy in our analysis.
| null | null |
life5010050_perova
| 0 |
Second Round of Evaluation Round 2: I have had the more critical remarks to the manuscript; however, I think that the presented data are useful and should be published.
| null | null |
We hope that now both reviewers, and all other potential readers, will not be misled by our approach.
| null | null |
life5010050_perova
| 0 |
We do not deal with taxonomy at all, only with testing the presence of a barcoding gap.
| null | null |
My critics should inform authors about more complicated problematics of this whole group, and several principles should be respected and accepted for future cyanobacterial research.
| null | null |
life5010050_perova
| 0 |
We do not deal with taxonomy at all, only with testing the presence of a barcoding gap.
| null | null |
Round 1: and Author Response The authors tested novel approach to identification of species in cyanobacteria based on 16S rRNA based on identification of barcoding gaps previously used in animals.
| null | null |
life5010050_perova
| 0 |
The molecular methods must be evidently preferred in this work, but other approaches (biochemical, ecophysiological, ecological, morphological) must be included into the final evaluation.
| null | null |
However, the only one universal method is quite insufficient in microorganisms, and the combination of all possible classification criteria is desirable.
| null | null |
life5010050_perova
| 0 |
My critics should inform authors about more complicated problematics of this whole group, and several principles should be respected and accepted for future cyanobacterial research.
| null | null |
We do not deal with taxonomy at all, only with testing the presence of a barcoding gap.
| null | null |
life5010050_perova
| 0 |
We thus only briefly discuss names and taxonomy in our analysis.
| null | null |
Summary: The manuscript is surely useful and, in principle, it presents a good contribution to the recent methodological trends (polyphasic approach) in cyanobacterial taxonomy, this conclusion should be the main result from this work.
| null | null |
life5010050_perova
| 0 |
Second Round of Evaluation Round 2: I have had the more critical remarks to the manuscript; however, I think that the presented data are useful and should be published.
| null | null |
To do so, we did not download named sequences from GenBank, but used a carefully annotated and checked database with a built-in phylogeny that would allow us to obtain monophyletic clades, regardless of their names.
| null | null |
life5010050_perova
| 0 |
The molecular methods must be evidently preferred in this work, but other approaches (biochemical, ecophysiological, ecological, morphological) must be included into the final evaluation.
| null | null |
Of course, the complex of all these methods must be corrected with the progress of science, and especially for cyanobacteria is necessary to apply the so called “polyphasic approach” for their classification.
| null | null |
life5010050_perova
| 0 |
To do so, we did not download named sequences from GenBank, but used a carefully annotated and checked database with a built-in phylogeny that would allow us to obtain monophyletic clades, regardless of their names.
| null | null |
We thus only briefly discuss names and taxonomy in our analysis.
| null | null |
life5010050_perova
| 0 |
More citations of modern literature would be expectable and useful.
| null | null |
I believe that the article with proposed changes will be useful for future research.
| null | null |
life5010050_perova
| 0 |
We hope that now both reviewers, and all other potential readers, will not be misled by our approach.
| null | null |
Thus this study intends only to verify the existence of a barcoding gaps within the 16S rRNA sequences of certain cyanobacterial groups, and by no means revise or confirm the complex cyanobacterial taxonomy.”
| null | null |
life5010050_perova
| 0 |
Round 1: and Author Response The article “Emergent Chemical Behaviour in Variable-Volume Protocells” focuses on the consequences that a changing volume may have on a set of reactions encapsulated within a semipermeable vesicle; in particular, this kind of compartment can degenerate existing bistable reactions, or promote emergent bistability from very simple reactions, which are not bistable in bulk conditions.
| null | null |
The mathematical methods used to deal with the problem are based on approximations and require the support of a huge number of simulations; on the other side, the approximations themselves constitute an interesting feature of the article and allow interesting discussions on the involved physical situations.
| null | null |
life5010181_perova
| 0 |
Produces a dynamic model for chemical evolution rather than traditional deterministic, static, systems that requires centralised information to direct evolution, such as a constant gradient.
| null | null |
Also a very thorough understanding of the limitations of the system are presented as well as proposals for even more complex instabilties that may underpin lifelike events.
| null | null |
life5010181_perova
| 0 |
The authors discuss these issues by means of differential equations and simulations.
| null | null |
Very well presented, clear and graphically illustrated experimental findings that make a clear case for the model.
| null | null |
life5010181_perova
| 0 |
The mathematical methods used to deal with the problem are based on approximations and require the support of a huge number of simulations; on the other side, the approximations themselves constitute an interesting feature of the article and allow interesting discussions on the involved physical situations.
| null | null |
Remarkably, even reaction systems that have no chemical species in common could become R2 indirectly coupled to each other through the volume they share, by means of a sort of osmotic coupling.
| null | null |
life5010181_perova
| 0 |
Round 1: and Author Response The article “Emergent Chemical Behaviour in Variable-Volume Protocells” focuses on the consequences that a changing volume may have on a set of reactions encapsulated within a semipermeable vesicle; in particular, this kind of compartment can degenerate existing bistable reactions, or promote emergent bistability from very simple reactions, which are not bistable in bulk conditions.
| null | null |
Very well presented, clear and graphically illustrated experimental findings that make a clear case for the model.
| null | null |
life5010181_perova
| 0 |
The authors discuss these issues by means of differential equations and simulations.
| null | null |
As the authors acknowledge, the article is the first step toward a more complete understanding of an interesting class of possible chemo-physical phenomena.
| null | null |
life5010181_perova
| 0 |
Round 1: and Author Response The authors present a dataset where they have characterised the relative abundance of components of the photosynthetic electron transfer chain and related this to the measured rate of electron transfer from PSII.
| null | null |
The approach and methods are robust and the ability to quantify components of the photosynthetic electron transfer chain is powerful.
| null | null |
life5010403_makarova
| 0 |
provides us with estimates of the concentrations of various proteins representing the PSII, PSI, cytb6 and Rubisco in there different cyanobacteria.
| null | null |
Second Round of Evaluation Round 2: and Author Response
| null | null |
life5010403_makarova
| 0 |
The data presented is robust and worthy of publication but should be discussed more critically with regard to published literature (outlined below) I suggest some minor suggestions that should be incorporated before publications.
| null | null |
Second Round of Evaluation Round 2: and Author Response
| null | null |
life5010403_makarova
| 0 |
Round 1: and Author Response The authors present a dataset where they have characterised the relative abundance of components of the photosynthetic electron transfer chain and related this to the measured rate of electron transfer from PSII.
| null | null |
The approach and methods are robust and the ability to quantify components of the photosynthetic electron transfer chain is powerful.
| null | null |
life5010403_makarova
| 0 |
provides us with estimates of the concentrations of various proteins representing the PSII, PSI, cytb6 and Rubisco in there different cyanobacteria.
| null | null |
This is done for a number of globally significance marine microbes of Syn and Pro lineage.
| null | null |
life5010403_makarova
| 0 |
Second Round of Evaluation Round 2: and Author Response
| null | null |
Round 1: and Author Response The authors present a dataset where they have characterised the relative abundance of components of the photosynthetic electron transfer chain and related this to the measured rate of electron transfer from PSII.
| null | null |
life5010403_makarova
| 0 |
The data presented is robust and worthy of publication but should be discussed more critically with regard to published literature (outlined below) I suggest some minor suggestions that should be incorporated before publications.
| null | null |
Round 1: and Author Response The authors present a dataset where they have characterised the relative abundance of components of the photosynthetic electron transfer chain and related this to the measured rate of electron transfer from PSII.
| null | null |
life5010403_makarova
| 0 |
Second Round of Evaluation Round 2: and Author Response
| null | null |
The approach and methods are robust and the ability to quantify components of the photosynthetic electron transfer chain is powerful.
| null | null |
life5010403_makarova
| 0 |
Second Round of Evaluation Round 2: and Author Response
| null | null |
This is done for a number of globally significance marine microbes of Syn and Pro lineage.
| null | null |
life5010403_makarova
| 0 |
Second Round of Evaluation Round 2: and Author Response
| null | null |
The data presented is robust and worthy of publication but should be discussed more critically with regard to published literature (outlined below) I suggest some minor suggestions that should be incorporated before publications.
| null | null |
life5010403_makarova
| 0 |
This is done for a number of globally significance marine microbes of Syn and Pro lineage.
| null | null |
provides us with estimates of the concentrations of various proteins representing the PSII, PSI, cytb6 and Rubisco in there different cyanobacteria.
| null | null |
life5010403_makarova
| 0 |
entitled “Functional Characterization of the FNT Family Nitrite Transporter of Marine Picocyanobacteria” is a very interesting piece of work since it shows the functional characterization as nitrite transporter of several nitM proteins from different picocyanobacteria, showing also fruitful comparisons of their sequences that lead to characterize the c-terminal region of a-cyanobacterial NitM proteins as an inhibitory domain of nitrite transport.
| null | null |
R3 Other changes (1) p. 1 line 26, “α-cyanobacteira” has been changed to “α-cyanobacteria”.
| null | null |
life5010432_makarova
| 0 |
entitled “Functional Characterization of the FNT Family Nitrite Transporter of Marine Picocyanobacteria” is a very interesting piece of work since it shows the functional characterization as nitrite transporter of several nitM proteins from different picocyanobacteria, showing also fruitful comparisons of their sequences that lead to characterize the c-terminal region of a-cyanobacterial NitM proteins as an inhibitory domain of nitrite transport.
| null | null |
Functional annotation of genes through protein expression is highly needed in our time of exponentially growing sequence data.
| null | null |
life5010432_makarova
| 0 |
Round 1: and Author Response I found this research interesting, relevant and novel.
| null | null |
CC9605 is an open ocean strain and does not encounter high nitrite concentrations, while CC9311 is a coastal strain that deals with a range of nitrate/nitrite availability.
| null | null |
life5010432_makarova
| 0 |
(3) p. 5 line 5, “abbreviation” has been changed to “abbreviations”.
| null | null |
R2 This article will be of interest to general microbiologists, specialists in cyanobacteria, and especially researchers that conduct environmental research and also genome annotations.
| null | null |
life5010432_makarova
| 0 |
Such differences can be explained by habitat adaption of each strain.
| null | null |
Such differences can be explained by habitat adaption of each strain.
| null | null |
life5010432_makarova
| 0 |
R2 This article will be of interest to general microbiologists, specialists in cyanobacteria, and especially researchers that conduct environmental research and also genome annotations.
| null | null |
The characterized here gene, nitM, can serve as a molecular marker in environmental studies.
| null | null |
life5010432_makarova
| 0 |
It was particularly interesting to see the differences in protein functionality among the strains of marine Synechococcus.
| null | null |
Such differences can be explained by habitat adaption of each strain.
| null | null |
life5010432_makarova
| 0 |
(2) p. 2 lines 2–3, “α-cyanobacteiral” has been changed to “α-cyanobacterial”.
| null | null |
R2 This article will be of interest to general microbiologists, specialists in cyanobacteria, and especially researchers that conduct environmental research and also genome annotations.
| null | null |
life5010432_perova
| 0 |
CC9605 is an open ocean strain and does not encounter high nitrite concentrations, while CC9311 is a coastal strain that deals with a range of nitrate/nitrite availability.
| null | null |
It was particularly interesting to see the differences in protein functionality among the strains of marine Synechococcus.
| null | null |
life5010432_perova
| 0 |
Such differences can be explained by habitat adaption of each strain.
| null | null |
(2) p. 2 lines 2–3, “α-cyanobacteiral” has been changed to “α-cyanobacterial”.
| null | null |
life5010432_perova
| 0 |
The characterized here gene, nitM, can serve as a molecular marker in environmental studies.
| null | null |
The characterized here gene, nitM, can serve as a molecular marker in environmental studies.
| null | null |
life5010432_perova
| 0 |
Functional annotation of genes through protein expression is highly needed in our time of exponentially growing sequence data.
| null | null |
Functional annotation of genes through protein expression is highly needed in our time of exponentially growing sequence data.
| null | null |
life5010432_perova
| 0 |
R2 This article will be of interest to general microbiologists, specialists in cyanobacteria, and especially researchers that conduct environmental research and also genome annotations.
| null | null |
R3 Other changes (1) p. 1 line 26, “α-cyanobacteira” has been changed to “α-cyanobacteria”.
| null | null |
life5010432_perova
| 0 |
(2) p. 2 lines 2–3, “α-cyanobacteiral” has been changed to “α-cyanobacterial”.
| null | null |
entitled “Functional Characterization of the FNT Family Nitrite Transporter of Marine Picocyanobacteria” is a very interesting piece of work since it shows the functional characterization as nitrite transporter of several nitM proteins from different picocyanobacteria, showing also fruitful comparisons of their sequences that lead to characterize the c-terminal region of a-cyanobacterial NitM proteins as an inhibitory domain of nitrite transport.
| null | null |
life5010432_perova
| 0 |
Results also provide additional support to recently proposed archaeal phyla and halobacterial orders.
| null | null |
If all genomes from a taxon appear exclusively in a tree branch, the branch is said to be monophyletic.”
| null | null |
life5010949_makarova
| 0 |
About 180 archaeal genomes were used to calculate a new tree topology using CVTree.
| null | null |
It is the only described representative of a newly proposed phylum Nanoarchaeota and it cuts into the otherwise monophyletic phylum Euryarchaeota.
| null | null |
life5010949_makarova
| 0 |
This kind of research should be encouraged further because old taxonomic paradigms must be systematically reviewed based on new genomic data.
| null | null |
Even if defined in the future, it must be lineage-dependent.
| null | null |
life5010949_makarova
| 0 |
Even if defined in the future, it must be lineage-dependent.
| null | null |
It is the only described representative of a newly proposed phylum Nanoarchaeota and it cuts into the otherwise monophyletic phylum Euryarchaeota.
| null | null |
life5010949_makarova
| 0 |
This kind of research should be encouraged further because old taxonomic paradigms must be systematically reviewed based on new genomic data.
| null | null |
Round 1: and Author Response Summary Zuo et al.
| null | null |
life5010949_makarova
| 0 |
For example, it cannot be expected that the same degree of dissimilarity may be used to delineate classes in all phyla.
| null | null |
About 180 archaeal genomes were used to calculate a new tree topology using CVTree.
| null | null |
life5010949_makarova
| 0 |
I recommend acceptance for publication in Life Sciences journal.
| null | null |
Though a dissimilarity measure figures in the CVTree algorithm, it is not realistic to delineate taxa by using this measure at least for the time being.
| null | null |
life5010949_makarova
| 0 |
Perhaps an additional discussion point would be the advantages of using CVtree approach with regular concatenated proteins.
| null | null |
If all genomes from a taxon appear exclusively in a tree branch, the branch is said to be monophyletic.”
| null | null |
life5010949_makarova
| 0 |
present a comparative analysis of the taxonomic classification of the Archaea domain.
| null | null |
The idea to use whole genome data for archaeal phylogenies is interesting, as the 16S rRNA phylogenies can be poor in resolving relationships among archaeal lineage due to GC content bias in hyperthermophilic Archaea.
| null | null |
life5010949_makarova
| 0 |
It is the only described representative of a newly proposed phylum Nanoarchaeota and it cuts into the otherwise monophyletic phylum Euryarchaeota.
| null | null |
present a comparative analysis of the taxonomic classification of the Archaea domain.
| null | null |
life5010949_makarova
| 0 |
Evaluation I found major concerns along this manuscript, and suggest a substantial revision.
| null | null |
It is the only described representative of a newly proposed phylum Nanoarchaeota and it cuts into the otherwise monophyletic phylum Euryarchaeota.
| null | null |
life5010949_makarova
| 0 |
About 180 archaeal genomes were used to calculate a new tree topology using CVTree.
| null | null |
Though a dissimilarity measure figures in the CVTree algorithm, it is not realistic to delineate taxa by using this measure at least for the time being.
| null | null |
life5010949_makarova
| 0 |
For example, it cannot be expected that the same degree of dissimilarity may be used to delineate classes in all phyla.
| null | null |
However, I am personally not convinced that whole genomes bring additional advantages, or if we are better off by just using a conserved set of proteins.
| null | null |
life5010949_makarova
| 0 |
R13 Round 2: and Author Response Authors have substantially improved the article, including language corrections, and have provided extensive clarifications to all initial criticisms.
| null | null |
are describing a comprehensive analysis of archaeal phylogeny with a genome-based alignment free method, and then comparing the findings to 16S rRNA based phylogenies.
| null | null |
life5010949_makarova
| 0 |
It is the only described representative of a newly proposed phylum Nanoarchaeota and it cuts into the otherwise monophyletic phylum Euryarchaeota.
| null | null |
Even if defined in the future, it must be lineage-dependent.
| null | null |
life5010949_makarova
| 0 |
For example, it cannot be expected that the same degree of dissimilarity may be used to delineate classes in all phyla.
| null | null |
Round 1: and Author Response Summary Zuo et al.
| null | null |
life5010949_makarova
| 0 |
present a comparative analysis of the taxonomic classification of the Archaea domain.
| null | null |
For example, it cannot be expected that the same degree of dissimilarity may be used to delineate classes in all phyla.
| null | null |
life5010949_makarova
| 0 |
Here monophyly must be understood in a pragmatic way restricted to the given set of input data and the reference taxonomy.
| null | null |
Evaluation I found major concerns along this manuscript, and suggest a substantial revision.
| null | null |
life5010949_makarova
| 0 |
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