Does Functionality Condition the Population Structure and Genetic Diversity of Endangered Dog Breeds under Island Territorial Isolation?

Round 1

Reviewer 1 Report

The presented manuscript entitled “Does functionality condition the population structure

and genetic diversity of endangered dog breeds under island territorial isolation?” is a comprehensive and interesting study focused on the genetic diversity of two dog breeds. The presented study is well written and prepared based on a large number of animals. The methods are properly selected and designed. I recommend the presented manuscript to publication and suggest some corrections.

Minor comments:

I suggest uniforming the naming of Ca Rater breeds. In the main text and tables, you used ‘Ca Rater’ name while at the Figures (3, 4, 5), you used ‘Ca de Rater’ name. If it is necessary please explain, if not uniform.  

Lines 183 – 186 – it is not clear if the genetic data used in the present study was obtained within this study or you used data from the previous report. If the genetic analysis was a part of the present study you should show more details about biological material collected from dogs, Ethics Committee agreement as well as STR analysis details.

Author Response

Comments and Suggestions for Authors

The presented manuscript entitled “Does functionality condition the population structure

and genetic diversity of endangered dog breeds under island territorial isolation?” is a comprehensive and interesting study focused on the genetic diversity of two dog breeds. The presented study is well written and prepared based on a large number of animals. The methods are properly selected and designed. I recommend the presented manuscript to publication and suggest some corrections.

Response: We thank the reviewer for his/her comments.

Minor comments:

I suggest uniforming the naming of Ca Rater breeds. In the main text and tables, you used ‘Ca Rater’ name while at the Figures (3, 4, 5), you used ‘Ca de Rater’ name. If it is necessary please explain, if not uniform.  

Response: naming for Ca de Rater breed was unified.

Lines 183 – 186 – it is not clear if the genetic data used in the present study was obtained within this study or you used data from the previous report. If the genetic analysis was a part of the present study you should show more details about biological material collected from dogs, Ethics Committee agreement as well as STR analysis details.

Response: No biological samples were taken for this manuscript. The genetic analyses described here base on pedigree records as it has been performed in other dog breeds [1-3].

1. Jansson, M.; Laikre, L. Pedigree data indicate rapid inbreeding and loss of genetic diversity within populations of native, traditional dog breeds of conservation concern. PloS one 2018, 13, e0202849.
2. Leroy, G.; Mary-Huard, T.; Verrier, E.; Danvy, S.; Charvolin, E.; Danchin-Burge, C. Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse. Genetics Selection Evolution 2013, 45, 1.
3. Calboli, F.C.; Sampson, J.; Fretwell, N.; Balding, D.J. Population structure and inbreeding from pedigree analysis of purebred dogs. Genetics 2008, 179, 593-601.
4. appliedbiosystems. User Guide: Canine ISAG STR Parentage Kit (2014); Thermo Fisher Scientific: Waltham, Massachusetts, USA, 2017.

Ethics committee agreement was not needed. We clarified this in the section below.

Ca de Rater Mallorquí Club and Associació de Criadors i Propietaris del Ca Pastor Mallorqui - Club del Ca de Bestiar gave their informed consent for the use of pedigree data before the study was performed. As biological samples were not taken further permission request was not necessary. The study was conducted in accordance with the Declaration of Helsinki. The Spanish Ministry of Economy and Competitivity through the Royal Decree Law 53/2013 and its credited entity, the Ethics Committee of Animal Experimentation from the University of Córdoba, permitted the application of the protocols present in this study as cited in the 5^th section of its 2^nd article, as the animals assessed were used for credited zootechnical use. This national Decree follows the European Union Directive 2010/63/UE, from the 22nd of September of 2010.

Reviewer 2 Report

The manuscript entitled “Does functionality condition the population structure and genetic diversity of endangered dog breeds under island territorial isolation?” deepens the genealogical and evolutionary history of two endangered autochthonous dog breeds inhabiting the Island of Majorca. The study presents a valuable and complete overview on the genetic composition along the generations of dog breeds of commercial interest. However, I would try to make this work a little more of broad interest to readers from different areas. Certainly, I would shorten the length of the entire manuscript, to be more easily affordable. After having made some cuts and solved few minor issues, I consider this work suitable for publication on Animals.

These are my minor comments:

• The introduction is too long and not always contains only scientific informations. For example, the paragraph at lines 69-79 can be limited to just a couple of lines. The same is true for the following paragraphs.
• Are these two breeds found outside Spain?
• Line 186: please specify amplification and genotyping protocols/conditions for the use of the Dog core STR panel.
• To which period do all the “historical” values shown in the tables of this study refer?
• Given that in the analyses the “Ca Rater” sample is always bigger than the “Ca de Bestiar” sample, have you considered the effect of the different sample sizes on the results obtained?
• Figure 3: please insert the name of the Island in the caption of the figure.
• Table 5: the first column would be more readable if the parameter-rows related to the same value-row had a shorter line-spacing than the others.
• Some Spanish words are still present in the text (see line 487 and 494).
• The discussion can also be shortened quite a lot.
• Are all the references in Spanish and all those related to a conference proceeding downloadable on the web? Please check.

Author Response

Comments and Suggestions for Authors

The manuscript entitled “Does functionality condition the population structure and genetic diversity of endangered dog breeds under island territorial isolation?” deepens the genealogical and evolutionary history of two endangered autochthonous dog breeds inhabiting the Island of Majorca. The study presents a valuable and complete overview on the genetic composition along the generations of dog breeds of commercial interest. However, I would try to make this work a little more of broad interest to readers from different areas. Certainly, I would shorten the length of the entire manuscript, to be more easily affordable. After having made some cuts and solved few minor issues, I consider this work suitable for publication on Animals.

Response: We thank the reviewer for his/her kind comments

These are my minor comments:

• The introduction is too long and not always contains only scientific informations. For example, the paragraph at lines 69-79 can be limited to just a couple of lines. The same is true for the following paragraphs.

Response: We followed reviewer suggestion and reduced the introduction 368 words.

• Are these two breeds found outside Spain?

Response: Only in certain occasions, but are becoming popular among people from Germany which come to the Archipelago. Still any of those animals was considered in the pedigree data.

• Line 186: please specify amplification and genotyping protocols/conditions for the use of the Dog core STR panel.

Response: The Canine ISAG STR Parentage Kit (2014) is an optimized reagent kit for the analysis of the 22 short tandem repeat (STR) loci recommended by the International Society of Animal Genetics (ISAG) in 2014 for canine parentage determination, that is to check the validity of the pedigree file. Amplification and genotyping protocols can be consulted in appliedbiosystems [4].

• To which period do all the “historical” values shown in the tables of this study refer?

Response: As stated in lines 180 to 182 “between January 1987 and September 2017 for the historical population of CR. Contrastingly, for CB, historical pedigree file includes 385 animals (49.61% sires; 50.39% dams) born between June 1994 and April 2018.”

• Given that in the analyses the “Ca Rater” sample is always bigger than the “Ca de Bestiar” sample, have you considered the effect of the different sample sizes on the results obtained?

Response: According to Gibbons and Chakraborti [5], the estimated probability of a Type I error is controlled (in the sense of being reasonably close to the attainable level) by Mann-Whitney Test, Student’s t Test and independent Median t tests when the variances are equal, regardless of the sample sizes. However, it was controlled by the alternate t test (independent median t tests) for unequal variances with unequal sample sizes.

5. Gibbons, J.D.; Chakraborti, S. Comparisons of the Mann-Whitney, Student’s t, and Alternate t Tests for Means of Normal Distributions. The Journal of Experimental Education 1991, 59, 258-267, doi:10.1080/00220973.1991.10806565.

• Figure 3: please insert the name of the Island in the caption of the figure.

Response: Name of the island was added following the reviewer suggestion.

• Table 5: the first column would be more readable if the parameter-rows related to the same value-row had a shorter line-spacing than the others.

Response: We agree and followed reviewer suggestion.

• Some Spanish words are still present in the text (see line 487 and 494).

Response: Sorry. We corrected them.

• The discussion can also be shortened quite a lot.

Response: Reviewer suggestions were followed and discussion was reduced 300 words. Overal manuscript was reduced two pages.

• Are all the references in Spanish and all those related to a conference proceeding downloadable on the web? Please check.

Response: Yes, all the information that we used was extracted from documents that can be found in the web, sometimes in repositories or historical libraries with scanned documents, but some of them were found in specialized sites.