Conservation Genetics of Clinch Dace Chrosomus sp. cf. saylori^†

Round 1

Reviewer 1 Report

The MS is well-written. The following observations need to be answered.

# What is the reason for heterogeneity in sample size in different creeks?

# Can the author use one terminology ( either creek or stream)?

# What might have prevented  Clinch Dace population# migration?

# How does the author relate genetic drift and inbreeding among the population as mentioned in Line 270?

# What is the effective population size of Clinch Dace in the respective creek and what about the sex ratio?

# What would be the impact of low heritability populations introductions to non-native streams?

Author Response

Please see the attachment 

Author Response File: Author Response.pdf

Reviewer 2 Report

Review of MS “Conservation Genetics of Clinch Dace Chrosomus sp. cf. saylori” submitted for publication to Fishes by Bourquin et al.

The authors collected Clinch Dace from seven streams and observed variation at nine selectively neutral microsatellite DNA loci to infer population genetic processes and identify units for conservation management. They conducted Bayesian cluster analysis，Estimated effective population sizes and m-ratios and calculated the FST values. The above results provide a reference for the conservation and management of this species.

I think this is a meaningful job, so I only have some suggestions for minor Revision.

1. I suggest merging Fig.S1 and Fig.1 as new Fig.1, so that readers can easily know what Clinch Dace looks like.

2. The text font format of the coordinate axis in Figure 2 needs to be adjusted

3. About the References, The connection between page numbers should be a “–”, not “-”.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 3 Report

Reviewer's report 

Date: 26 June, 2023 

Journal: Fishes

Manuscript ID: fishes-2482862

Type of manuscript: Article

Title: Conservation Genetics of Clinch Dace Chrosomus sp. cf. saylori

Authors: Rebecca Bourquin, Michael J Moore, Donald J Orth, Eric M Hallerman *

Using nine selectively neutral microsatellite loci, the authors have characterized within- and between-population genetic variability for the Clinch dace, a species of minnow (Chrosomus sp. cf. saylori). They found clear signals of inbreeding and other characteristics of small vulnerable populations.  The data are important and can be used for the future programs to restore the populations of this species. However, the manuscript contains multiple inaccuracies. At the present condition the manuscript is not appropriate for the journal Fishes.

Line 23: Change “…loss of alleles to recent genetic drift.” to  “…loss of alleles due to recent genetic drift.”

Line 54: Change: “… hence, it hence is vulnerable to local extirpation.” to “… it hence is vulnerable to local extirpation.”

Lines 79-81: The sample sizes vary enormously (from 3 up to 106). It can be problematic for many statistical tests. The authors need to make some comments how they overcome this obvious limitation. 

Line 106:  Change: “…amplificons” to “… amplicons…”

Line 122: Change: “…we the applied…” to “… we applied…”

Lines 163-165: Explain why you decided that the observed linkage disequilibrium was attributed to chance. 

Page 5, Table 2: This comment is not clear: “Bonferroni alpha = Bonferroni-corrected critical p-value.” Is Bonferroni correction for the H-W deviation? Please, explain. 

Lines 177-179: Consider English revision. 

Line 185: There is close correspondence between expected and observed heterozygosities (Table 2). How you explain in this case significant deviation from the H-W equilibrium? 

Lines 188-189: Consider English revision (“…three involving locus CypG30.”) 

Lines 206-208: The authors state that: “Greasy Creek, Hart Creek, and Middle Creek populations all had 206 mean FIS values that were significantly different from zero, suggesting inbreeding in those 207 populations (Table 4).” However, Table 4 shows just a single significant P-value (Hart Creek). Explain. 

Page 7, Figure 3: The designations are in very small font. Increase it to make possible to read. 

Lines 244-253: Consider English revision. 

Page 8, Table 6: Please, make the notes under the table connected with the table. 

Line 290: Change: “…management units…” to “…management units (MUs)…” and further use just abbreviation “MUs”. 

Reviewer's report 

Date: 26 June, 2023 

Journal: Fishes

Manuscript ID: fishes-2482862

Type of manuscript: Article

Title: Conservation Genetics of Clinch Dace Chrosomus sp. cf. saylori

Authors: Rebecca Bourquin, Michael J Moore, Donald J Orth, Eric M Hallerman *

Using nine selectively neutral microsatellite loci, the authors have characterized within- and between-population genetic variability for the Clinch dace, a species of minnow (Chrosomus sp. cf. saylori). They found clear signals of inbreeding and other characteristics of small vulnerable populations.  The data are important and can be used for the future programs to restore the populations of this species. However, the manuscript contains multiple inaccuracies. At the present condition the manuscript is not appropriate for the journal Fishes.

Line 23: Change “…loss of alleles to recent genetic drift.” to  “…loss of alleles due to recent genetic drift.”

Line 54: Change: “… hence, it hence is vulnerable to local extirpation.” to “… it hence is vulnerable to local extirpation.”

Lines 79-81: The sample sizes vary enormously (from 3 up to 106). It can be problematic for many statistical tests. The authors need to make some comments how they overcome this obvious limitation. 

Line 106:  Change: “…amplificons” to “… amplicons…”

Line 122: Change: “…we the applied…” to “… we applied…”

Lines 163-165: Explain why you decided that the observed linkage disequilibrium was attributed to chance. 

Page 5, Table 2: This comment is not clear: “Bonferroni alpha = Bonferroni-corrected critical p-value.” Is Bonferroni correction for the H-W deviation? Please, explain. 

Lines 177-179: Consider English revision. 

Line 185: There is close correspondence between expected and observed heterozygosities (Table 2). How you explain in this case significant deviation from the H-W equilibrium? 

Lines 188-189: Consider English revision (“…three involving locus CypG30.”) 

Lines 206-208: The authors state that: “Greasy Creek, Hart Creek, and Middle Creek populations all had 206 mean FIS values that were significantly different from zero, suggesting inbreeding in those 207 populations (Table 4).” However, Table 4 shows just a single significant P-value (Hart Creek). Explain. 

Page 7, Figure 3: The designations are in very small font. Increase it to make possible to read. 

Lines 244-253: Consider English revision. 

Page 8, Table 6: Please, make the notes under the table connected with the table. 

Line 290: Change: “…management units…” to “…management units (MUs)…” and further use just abbreviation “MUs”. 

Author Response

Please see the attached file.

Author Response File: Author Response.pdf

Round 2

Reviewer 3 Report

Reviewer's report 

Date: 07 July, 2023 

Journal: Fishes

Manuscript ID: fishes-2482862-peer-review-v2

Type of manuscript: Article

Title: Conservation Genetics of Clinch Dace Chrosomus sp. cf. saylori

Authors: Rebecca Bourquin, Michael J Moore, Donald J Orth, Eric M Hallerman *

The manuscript was significantly improved. It is appropriate now for the journal Fishes.