Genetic Characterization of Endangered Indian Mithun (Bos frontalis), Indian Bison/Wild Gaur (Bos gaurus) and Tho-tho Cattle (Bos indicus) Populations Using SSR Markers Reveals Their Diversity and Unique Phylogenetic Status

Round 1

Reviewer 1 Report

The language needs some minor but significant improvements (some examples marked).

I would suggest to remove big part of the Results explanations, if possible, to Discussion section.  And vice versa, such details like microsatellite markers used or not and why, should be moved from Discussion to Material and Methods section.

There is no need to describe the same result several times. For instance, the Authors presented the same results of molecular variance analysis in the text, in the table and in the graph.

Please, consider using consistent names for subpopulations throughout the manuscript. In Fig.5 the subpopulations are named Pop1, Pop2 and Pop3, while in the text SP1, SP2 and SP3 or just by the breed name in graphs. It might be confusing.

I would be very careful with alternative usage of FIS and inbreeding. Microsatellite based FIS has not much in common with actual inbreeding. It just gives information if in the population, at certain studied moment, the animals mated more or less in relatedness. The source of reliable inbreeding is either pedigree analysis or genomic parameter Runs of Homozygosity. You definitely cannot state, based on FIS values, that the population is inbred or not and how much (lines 503 – 510).

Also, use consistent nomenclature as to the breed name: Mithun, Gaur or mithun, gaur, depends on the convention.

When explaining origin, relationships between breeds, their locations and probable migrations routes, a simplified map would be very useful. If the Authors would remove some other figures with doubled information, that would create space for few maps maybe?

I suggest to enrich Conclusions and implement some crucial informations drived from the project in this section. And What actualy is the 'unique phylogenetic status' of the described subpopulations, mentioned in the title? The text hardly refers to that.

The manuscript brings some new genetic data on the rare Asian bovines and has potential, but needs improvement.

Comments for author File: Comments.pdf

Author Response

Please see the attachment. Thank you.

Author Response File: Author Response.pdf

Reviewer 2 Report

The paper is an interesting examination of the relationships among guar, mithuns, and tho-tho.  The research described here can make important contributions to the conservation and management of these species.  However, before this can happen, there is some confusion in the interpretation of the results that will need to be corrected.  In the results and discussion sections, the authors state that Arunachal mithuns are distinct from Manipur, Mizoram, and Nagaland mithuns.  They also state that Mizoram mithuns are similar with Manipur, Nagaland, and Arunachal mithuns.  However, this isn't supported by the results described in the paper.  Structure, PCA, and neighbour-joining results show that Arunachal and Nagaland form one clade, while Manipur and Mizoram form another clade.  This disparity has a major impact on the conclusions of the paper, and needs to be corrected.  

Comments for author File: Comments.pdf

Author Response

Please see the attachment. 

Thank you.

Author Response File: Author Response.pdf

Reviewer 3 Report

Manuscript entitled “Genetic Characterization of endangered Indian Mithun (Bos frontalis), Indian Bison/ wild gaur (Bos gaurus) and Tho-Tho cattle (Bos indicus) populations using SSR markers reveals their diversity and unique phylogenetic status”.

In this paper, the authors investigate population structure and genetic diversity of rare Indian bovines, Mithun, Bison and Tho-Tho cattle. The topic is of interest for the field, it is very important to analyze endangered, rare, and at risk livestock populations, and it is important to collect information at a molecular level, but the main problem is microsatellites. Microsatellite markers are not used anymore for diversity studies in mammals. My advice is to delete or at least reduce all the parts relating to microsatellites and emphasize analysis of cytochrome b. 

The results section is described very well, the only flaw is that the authors added comments and considerations, which should be found in the discussion section.

The Discussion section is very difficult to read, numerical values are once again considered, as in the results section, and it becomes difficult (or impossible) to follow the flow of ideas.

Conclusions are not supported by results, at least not completely, the authors expressed some concepts that are beyond the scope of the research, please delete: “Marker trait association analysis using phenotypic and genotypic data will help in detection of useful markers linked with economically useful traits. In Mithun hybridization programme one parent should be taken from either Arunachal or Nagaland population and another parent from Manipur or Mizoram to get better segregate genotypes with higher growth and better economic traits.”.

Line 45-46: please explain, or add some reference.

Line 52: “On the other hand” please delete.

Line 67-68: those microsatellites were recommended long ago when they were thought to be informative. Unfortunately, the evidence has shown that they are not reliable. For this reason, they have been replaced by other types of markers, such as e.g. SNPs.

Line 70: The references numbers 17, 18, 19, 20, 21, 22, 23, 24, 25 refer to plant research. I think it is not appropriate to use such references, unless they are justified or discussed, which is not the case.

Line 83: “It was decided to test microsatellite markers that have been developed for cattle 83 [32]”, here you are citing a 1996 project. In 1996 it was correct to think that microsatellites provided valid and useful information, now it is no longer so.Line 109-112: “their native breeding tracts” please rephrase.

Table 1: Table1 might be provided as supplementary material.

Author Response

Please see the attachment.

Thank you. 

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

The paper is an interesting examination of the relationships among guar, mithuns, and tho-tho.  The research described here can make important contributions to the conservation and management of these species.  I am glad to see that the confusion surrounding the grouping of different mithun populations has been fixed, and the authors now discuss their results appropriately. 

Comments for author File: Comments.pdf

Author Response

Please see the attachment.

Best regards,

Sabyasachi Mukherjee

Corresponding Author

Author Response File: Author Response.docx

Reviewer 3 Report

The manuscript has been improved.

Author Response

Dear Sir/Ma’m,

Thank you so much for considering our manuscript “Genetic Characterization of endangered Indian Mithun (Bos frontalis), Indian Bison/ wild Gaur (Bos gaurus) and Tho-Tho cattle (Bos indicus) populations using SSR markers reveals their diversity and unique phylogenetic status”.

Thank you very much for your valuable suggestions for further improvement and kind consideration of our manuscript. We hope our revised manuscript has addressed all the issues satisfactorily and shall be considered for publication now.

With best regards,

Sabyasachi Mukherjee

Corresponding Author