Genetic Diversity and Population Structure of the Chinese Mitten Crab (Eriocheir sinensis) from Six Different Lakes Using Microsatellites

Round 1

Reviewer 1 Report

The information provided is not clear making it difficult for the reader to understand the reasoning behind the techniques used and the conclusions taken. Authors should better explain the questions to be answered by each of the techniques used, as well as the information they put in the tables. The tables do not have captions and present acronyms that are not identified. I would greatly recommend the authors to reorganize the tables in order to facilitate their reading. As previously mentioned, the authors present many methods, measures and  statistics, but then do not discuss the results. Tables 1 and 2 are too large and there is no separation between the different results.

There are values ​​in table 3 that suggest doubts. Why is it that in some values ​​of the test statistic inequality appears? This result always displays a value, never a range of values. I also have doubts about some of the values ​​of the degrees of freedom. Authors should clarify how they came to that value. 

In my opinion, the article needs revisions in the following sections: results, discussion and conclusion sections.

Author Response

I have made relevant modifications to all the questions you raised

Author Response File: Author Response.pdf

Reviewer 2 Report

Manuscript Review

Journal: MDPI Fishes

Title: Genetic Diversity and Population Structure of the Chinese Mitten Crab (Eriocheir sinensis) from Six Different Lakes Using Microsatellites.

Authors: S. Su, J.D. Nsekanabo, B.P. Munganga, X. He, J.L. Li, F. Yu, M. Wang, Y. Tang.

Synopsis: The mitten crab is a nutritionally and commercially important sources of protein in China. Genetic studies were performed more than ten years ago to aid in developing managed protective areas for the crabs. However, no recent genetic assessments have followed as the rate of habitat loss and contamination has increased.  For this current study of genetic diversity among mitten crab populations from six lakes along the Yangtse River, microsatellite loci analysis was used. Across the six populations, 13 microsatellite loci were studied in 180 individuals from each population. In total 87 alleles were identified with an average of 6.69 alleles/loci. Neither null nor unique loci were found. Rather, all 13 loci were found in every population but the number of alleles varied between sites. Consequently, the genetic structure among the populations is more or less uniform. The among population genetic variation is much less than within population variance. None of the populations are genetically distinct and most appear to be in Hardy-Weinberg equilibrium. Since the crabs are catadromous, little selection, drift or preferential migration appears among the six lake population. Yangtze River mitten crabs appear to be genetically panmictic. 

Recommendation:  The information in this paper is publishable. However, it needs careful clarification and re-organization, especially the tables.  The manuscript should be re-organized in presentation before being accepted for publication.

Minor suggestions:

Line 66-71. Please specific which paper deals with microsatellites and which deals with mitogenomic loci.
Line 76. Change to “that time up to the present….”

Figure 1. What is the scale in kilometers?  Please add scale. Please put some reference latitude and longitude degrees on map.

Line 117. Tab.S1 was not included with review materials.

Line 139-141. Re-write this sentence, its meaning in unclear.?? “the find. clusters…”?

Line 147-148. There were no unique or private loci or alleles in the six populations, correct?

Line 155. Change to “0.017 for crab2 to 0.919 for Esin42”.

Table 1. Indicate that the names for microsatellite loci. Why are the loci not listed in numerical order? The population name column should be separate from the line of names for the microsatellite loci.

Data for observed alleles, effective number, observed heterozygosity, expected heterozygosity, and ratio test should be distinctly separated in this table. The table is so cluttered in appearance that is essentially unreadable.  Each of these could be in a separate table.

Line 166-167. “87 alleles, 180 individuals, 6 populations” is redundant. Remove to streamline.

Line 170-171. What does” accessed and showed variability and likelihood among the populations from 6 lakes” mean?  Please re-write. 

Line 174-178.  Name specifically which loci pairs exhibit linkage disequilibrium (p<0.05).

Table 2. Is this long table necessary in the paper? Why not make it Tab.S2? 

Table 3. Reorganize Tab 3. Collect and display all data for each model (IAM, TPM and SMM) together. In its current form, the table is not easily read.

Line 190. Insert “(Table 4)” after Shannon index.

Line 193. Remove first “(Tab.4).

Lines 194-195. Describe how polymorphism “level 2” and “level 1” is defined.

Tab 4. Reorganize. List microsatellite loci in order above, separate Shannon’s index from PIC data.

Tab 5. Label which are microsatellite loci across table.

Line 208. Are you sure this is data in Table 4? Can see it.

Line 210-211. Rewrite “…between the six populations was very low.”

Line 217-218. Remove “the 180 Chinese mitten crabs originating from”. Add “populations” after “lake”.

Line 246. “Respectively” is not need here.

Line 247-248. Rewrite to read…” The populations from the 6 lakes in China were found to be highly differentiated genetically”.

Line 252. Delete “Chinese mitten crabs”. Add “s” to “population”.

Line 253. After “principle” remove “thus” and add “.”. Start next sentence with “Since…”

Line 255. Drop “also”.

Line 256. Drop “comparing”.

Line 260. Remove “This paper used”. Rewrite “Three evolutionary models were used for the analysis of…”

Line 266. Rewrite, “…the crabs in the six lakes are locate….”

Line 267. Rewrite “… wasn’t much distance between them (Fig.1).”

Line 268-269. Rewrite “Since temperature differences are not large, there is little difference in the size of adult crabs.”

Line 270. Delete “in this article”.   Also change “crabs has” to “crabs have”.

Line 275. Delete comma after (2016).

Line 287-288. Delete “in Chinese mitten crabs”.

Author Response

I have made relevant modifications to all the questions you raised

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

In my opinion the manuscript needs to be improved. Few comments to the authors were showed as follows:

Table 1 is to big  so it can´t be read.

Line: 157 until 161: The author´s said:

“ The observed heterozygosity and expected  heterozygosity were not significantly (p<0.05) different among the six crab populations. Although not significant crabs from CD have the highest observed heterozygosity (0.595)  while those from GC have the lowest (0.531). The expected heterozygosity was highest (0.646) in crabs from GC while those from CD had the lowest (0.613). “

- what do you do?what was the test used? Where are these results?  We only have information about the “Effective number of alleles ” and the “Observed heterozygosity

”

In these paragraph the authors refer a table 4. But these table doesn´t belong to these section. Thus, it should not be referred to here.

Regarding to the paragraph:

“Analysis of genetic …variations can be observed in populations in six lakes”

In my opinion these information should be at the beginning of the section 3.1 second paragraph  should be at the beginning of the section 3.1.

Line 169: The section 3.2 must be separate from the text.

Line 175 until 177- the font is not the same

Table S2- whem we have a p- value close to zero it should be marked as follows “p<0.001” not <0.00000. Please modified that.

Table3. Decrease the number of decimal places so that the values ​​are all on the same line. I my opinion  they should consider only 3 decimal places in all tables   .

Line 210: “The pairwise Fst values across all six populations are given in Table 4.” Is the number of the table correct?

Line 212 until 215: “  The pairwise……. genetic differentiation between GC vs TH (0.0098) was the highest and the lowest was between CD vs TH (-0.0018).

Where is this information?

Suggestion: Changr the numbering in tables 7 and 8. The first to be referred to is 8 so it should be presented in 1st place and numbered as 7 and the AMOVA table should be the 8.

Line232: The table header is out of place.

Line 249: remove the sign “ and the dot before Fst.

Line 253: remove “<0.05”, it makes no sense to introduce the value in the discussion.

Line267: remove the dot.

Lines 279 and 280: In my opinion it makes no sense to introduce the  values in the discussion.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 3

Reviewer 1 Report

The authors  provided a revised version  of the manuscript  entitled “Genetic Diversity and Population Structure of the Chinese Mitten Crab (Eriocheir sinensis) from Six Different Lakes Using Microsatellites”.  In my opinion the current version has been  improved and  I recommend that the manuscript be accepted after the comments below are addressed.

Table 1: I would greatly recommend the authors to reorganize the table in order to facilitate their reading. The way the table is presented is not suitable for publication. Columns three through thirteen don´t have  the same width, the number of decimal places varies from zero to four.  It becomes difficult for the reader to identify the results presented in the different columns, since there is no separation between  the different results.

Suggestion:

- Table headers must be in bold;

-decrease the width of the first column, “Obs. nº of alleles”  or instead of having two columns they can reduce to one. The information that is in the 2nd column can be placed in the 1st. This reduction allows the other columns to be further separated.

- the other columns must all have the same width and the space between columns 7 “crab 8” and 8 “crab 11”;

- decrease the number of decimal places to two.

These changes can be made without distorting the information, and will improve the presentation of the table.

Line 169: add a space before and after the section 3.3

Line 194: add parentheses at the end of tab.4.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf