An Integrative Taxonomic Revision of the Freshwater Atyid Shrimps (Crustacea: Decapoda: Caridea) of Micronesia
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThis is a nice piece of work and a valuable contribution to carcinology. Therefore, this manus merits a significant revision to be really perfect. The major problem is that “An integrative taxonomic revision” and “morphological tree” are declared but not done/shown. I encourage authors to supplement the missing part of the integrative approach and enhance the discussion with a section devoted to phylogenetic relations and evolutionary trends within the group. Minor comments are below.
1. Introduction
Start with a paragraph introducing atyid shrimps
2. Materials and Methods
I am concerned by 'electrofishing' method, is that acceptable ethically?
Table 2. Sampling localities data. I think missing altitudes may be easily retrieved using precise coordinates and GIS software.
"The proportions of the various joints of the appendages" state which, present the table with measurements, and refer to this.
State which support values on the BI and ML trees you consider as statistically significant.
Provide morphological tree in addition to the molecular one.
3. Results.
"The phylogenetic tree obtained (Fig. 11)" You refer to Fig 11 before Fig 3. The tree merits being here; change figure numbers furthermore accordingly.
"The morphological study of the specimens confirmed the results of the molecular study in recognizing the 11 clades of the tree as separate species." the tree is not presented
Start with diagnoses of the genera (and probably family) before species, the reader needs understanding the generic morphology.
"Colour pattern Similar to Atyoida pilipes, variable, with dark spots and stripes all over the body". Just describe colour here, the reader is not obliged to imagine what Atyoida pilipes looks like, comparisons move to remarks.
"A. bisulcata. Randall" remove the dot
"Due to their high morphological variability, finding diagnostic characters to separate A. chacei sp. nov. from A. pilipes or A. tahitensis turned out to be a difficult task" use simplest statistical methods such as MDS or PCA to show they are different (example may be found, for example, in https://doi.org/10.1071/IS23034). MDS and PCA should work.
"This species prefers fresh and well-oxygenated waters" Oxygen measured (in this case give a value) or concentration just suggested (state the evidences: shallow, high speed stream?), same in Lines 446 and 549.
4. Discussion
How deep sea trenches may contribute in separation of fresh- and shalow-water shrimps? Geographic distance and currents - OK, but not the bottom morphology, remove.
Now discussion on phylogenetic relations.
Key for studied species
3.1 and 3.2 define in the key strongly reduced and well developed cornea (proportions to eyestalk?)
Author Response
- Introduction
Start with a paragraph introducing atyid shrimps
A: We added an introductory paragraph on atyids.
- Materials and Methods
I am concerned by 'electrofishing' method, is that acceptable ethically?
A: This is a standard method for sampling freshwater animals, we added a reference.
Table 2. Sampling localities data. I think missing altitudes may be easily retrieved using precise coordinates and GIS software.
A: We completed the missing altitudes.
"The proportions of the various joints of the appendages" state which, present the table with measurements, and refer to this.
A: We added a reference detailing our measurement method.
State which support values on the BI and ML trees you consider as statistically significant.
A: We specified the significant values.
Provide morphological tree in addition to the molecular one.
A: There must be a misunderstanding, we did not construct a morphological tree, we actually tried it in the past but without success due to the lack of discrete morphological characters in this group. The reviewer was probably misled by the terms “morphological analysis” which referred to the examination of the morphology to look for differences between molecular clades. We added a sentence to clarify.
- Results.
"The phylogenetic tree obtained (Fig. 11)" You refer to Fig 11 before Fig 3. The tree merits being here; change figure numbers furthermore accordingly.
A: The figure has been moved.
"The morphological study of the specimens confirmed the results of the molecular study in recognizing the 11 clades of the tree as separate species." the tree is not presented
A: See previously, the clades are from the molecular tree only.
Start with diagnoses of the genera (and probably family) before species, the reader needs understanding the generic morphology.
A: We added diagnoses for the family, genera and species complexes.
"Colour pattern Similar to Atyoida pilipes, variable, with dark spots and stripes all over the body". Just describe colour here, the reader is not obliged to imagine what Atyoida pilipes looks like, comparisons move to remarks.
A: We rephrased the sentence.
"A. bisulcata. Randall" remove the dot
A: Removed.
"Due to their high morphological variability, finding diagnostic characters to separate A. chacei sp. nov. from A. pilipes or A. tahitensis turned out to be a difficult task" use simplest statistical methods such as MDS or PCA to show they are different (example may be found, for example, in https://doi.org/10.1071/IS23034). MDS and PCA should work.
A: We have tried PCA but there is a lot of overlap because of the variability of the measured characters and the two groups are not well discriminated.
"This species prefers fresh and well-oxygenated waters" Oxygen measured (in this case give a value) or concentration just suggested (state the evidences: shallow, high speed stream?), same in Lines 446 and 549.
A: We do not have data on the oxygen concentration in the rivers, this sentence is based on observations of the water flow. We rephrased this to remove mentions of oxygen.
- Discussion
How deep sea trenches may contribute in separation of fresh- and shalow-water shrimps? Geographic distance and currents - OK, but not the bottom morphology, remove.
A: We are citing previous work that found a correlation between biogeographic breaks in amphidromous species and the presence of deep-sea trenches. This observation is confirmed by our results. The causality of this correlation is yet to be found, however.
Now discussion on phylogenetic relations.
A: This is not the purpose of the present study, a molecular analysis based on the 16S marker alone is not enough to discuss phylogenetic relationships (see the low support values for some of the deep nodes), it would require more markers from both nuclear and mitochondrial loci. The 16S tree is here to support our species hypotheses in recognizing them as separate clades and to support our identifications by providing sequences from outside the studied area.
Key for studied species
3.1 and 3.2 define in the key strongly reduced and well developed cornea (proportions to eyestalk?)
A: We clarified this
Reviewer 2 Report
Comments and Suggestions for AuthorsThe authors report and describe the shrimp biodiversity of Micronesia, a task of utmost importance given the current threats to biodiversity. Species are constantly under threat, and many disappear before even being described. The authors contribute to making species known, thereby facilitating measures for their protection and the preservation of their habitats in the future if needed.
The manuscript is well written, and the new species are well presented, while the authors have performed a significant amount of work from sampling to producing this MS. However, there are a number of small/medium issues that require the attention of the authors before the manuscript can be accepted for publication. Among the most significant are: 1) As the new species Atyoida chacei is more similar to A. pilipes and A. tahitensis please include also A. tahitensis in the phylogenetic tree and give the genetic distances between the three species. 2) While the paleogeographic aspect is intriguing, I believe it could be presented in a more concise manner. It currently feels somewhat repetitive and unnecessarily lengthy. 3) revise again some characters how they are described in relation to their figures given e.g. it is said in the txt that the telson of Caridina lobocensis doesnt have a median process while in the figure it is shown that it has. For the rest please refer to the attached PDF for specific corrections and suggestions.
Comments for author File: 
Comments.pdf
Author Response
1) As the new species Atyoida chacei is more similar to A. pilipes and A. tahitensis please include also A. tahitensis in the phylogenetic tree and give the genetic distances between the three species.
A: We added three sequences of A. tahitensis to the tree.
2) While the paleogeographic aspect is intriguing, I believe it could be presented in a more concise manner. It currently feels somewhat repetitive and unnecessarily lengthy.
A: We rephrased some parts to reduce redundancy.
3) revise again some characters how they are described in relation to their figures given e.g. it is said in the txt that the telson of Caridina lobocensis doesnt have a median process while in the figure it is shown that it has.
A: There were indeed errors in the descriptions, we corrected them.
For the rest please refer to the attached PDF for specific corrections and suggestions.
Figure 2: Improve analysis of figure so that letters can be seen clearly.
A: The resolution should be better in the final proofs and the figure will be clearer
Table 2: Coordinates of Babeldaob are eroneously written. Please correct as in Pohnpei and Guam
A: The coordinates formats have been homogenized
The material from Smithsonian is not mentioned in the M&M. Please give a full account of which material was processed in the M&M icluding an explanation for the stations numbering (e.g. a relevant reference).
Material from Naturalis again not given in the M&M.
Another museum material was taken from and not mentioned in the M&M
A: We added mentions to these collections in the material and methods.
only in this species the intermediate setate are described as plumose and not in the following species. Is there a reason for this?
A: No, this is a mistake, we added “plumose setae” to the other species descriptions
It will have been usefull if the authors provide the genetic distances (e.g. p-distance) between the three species especially since they are not clear morphological differences. How distinct is it from the rest C. seratirostris? How much is the genetic distance? Numbers help showcasing the diference.
A: We have added the genetic p-distances for information
“Colour pattern Unknown” Why? It is not orange? A colour photo of the species is given in 8C!!
A: Unfortunately, this particular specimen had already spent a few hours in ethanol, hence the orange coloration. However the patterns are still visible, so we changed our sentence.
In-text edits were all accepted and included.
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsI apologize for the delay of my review - I was at field. The Ms was sufficiently improved and I recommend this for publication. I only regret that:
1. "There must be a misunderstanding, we did not construct a morphological tree, we actually tried it in the past but without success due to the lack of discrete morphological characters in this group. The reviewer was probably misled by the terms “morphological analysis” which referred to the examination of the morphology to look for differences between molecular clades. We added a sentence to clarify."
Try to do this in the future using qualitative characters - look, for example a paper which should appear in 1-2 months: 10.1093/zoolinnean/zlae031
and
2. "This is not the purpose of the present study, a molecular analysis based on the 16S marker alone is not enough to discuss phylogenetic relationships (see the low support values for some of the deep nodes), it would require more markers from both nuclear and mitochondrial loci. The 16S tree is here to support our species hypotheses in recognizing them as separate clades and to support our identifications by providing sequences from outside the studied area."
I encourage authors to make phylogenetic and phylogeographic revisions in the future - I envy their opportunities of getting a material of this sort.
