Evidence for Genetic Hybridization between Released and Wild Game Birds: Phylogeography and Genetic Structure of Chukar Partridge, Alectoris chukar, in Turkey
Round 1
Reviewer 1 Report
Comments to Authors:
In their work, Albayrak et al. carry out a thorough genetic analyses of chukar partridges (Alectoris chukar) from Turkey in order to explore their genetic makeup and look for possible signatures of human-mediated introgressive hybridization, or better, intraspecific genetic admixture, indicative of gene flow between captive and wild populations. For this purpose, the Authors use two mitochondrial DNA and ten microsatellite loci. As such, the study is certainly not novel in the techniques used, but a similar study on this species from Turkey was still awaiting and it represents a valuable integration to the “saga” of Alectoris studies carried out mostly on other Mediterranean Alectoris and in the western Mediterranean. The methodological approach used by the Authors is correct, they performed several analysis, and the overall structure of the MS is good. Nevertheless, the MS suffer from lack of clarity in a number of passages, punctuation is not used consistently, repetitions and wordiness are a concern; some formal aspects (i.e. correct spelling of scientific names, consistency with the use of symbols and abbreviations) are disregarded. Grammar mistakes and awkward phrasing do occur. The best thing would be to make a native speaker go through the MS before it is newly submitted.
For reasons of practicality, I opted to provide my edits and comments in the pdf attached to this submission. I have tried to improve myself a number of passages, and I hope that the Authors will appreciate my efforts by accepting the changes proposed, otherwise they just risk delaying the acceptance of their MS.
Please, note that in the edited version of the MS both corrections and comments can be visualized by placing the cursor on the deleted or highlighted text. Some edits deal also with the tables.
There is ample room for improvements also concerning the figures, as duly indicated in the text. As far as the tree provided in the Supplementary Material, please note that the correct spelling is “Barbanera”, not “Barbaranea”. By the way, it is awkward to indicate “Barbanera” as opposed to “Turkish haplotype”: I suggest to rather indicate the country and or subspecies next to the square parentheses.
Even if probably not requested by the journal, I recommend the Authors to deposit their microsatellite genotypes in a public repository like Dryad in order for other researchers to use these data in their own research.
Comments for author File: 
Comments.pdf
Author Response
Comments to Authors:
In their work, Albayrak et al. carry out a thorough genetic analyses of chukar partridges (Alectoris chukar) from Turkey in order to explore their genetic makeup and look for possible signatures of human-mediated introgressive hybridization, or better, intraspecific genetic admixture, indicative of gene flow between captive and wild populations. For this purpose, the Authors use two mitochondrial DNA and ten microsatellite loci. As such, the study is certainly not novel in the techniques used, but a similar study on this species from Turkey was still awaiting and it represents a valuable integration to the “saga” of Alectoris studies carried out mostly on other Mediterranean Alectoris and in the western Mediterranean. The methodological approach used by the Authors is correct, they performed several analysis, and the overall structure of the MS is good. Nevertheless, the MS suffer from lack of clarity in a number of passages, punctuation is not used consistently, repetitions and wordiness are a concern; some formal aspects (i.e. correct spelling of scientific names, consistency with the use of symbols and abbreviations) are disregarded. Grammar mistakes and awkward phrasing do occur. The best thing would be to make a native speaker go through the MS before it is newly submitted.
Responce: Thank you very much for positive comment. The ms checked and improved with native speaker
For reasons of practicality, I opted to provide my edits and comments in the pdf attached to this submission. I have tried to improve myself a number of passages, and I hope that the Authors will appreciate my efforts by accepting the changes proposed, otherwise they just risk delaying the acceptance of their MS.
Responce: Thank you very much for valuable effort on the ms. The ms was improved with using all suggestion
Please, note that in the edited version of the MS both corrections and comments can be visualized by placing the cursor on the deleted or highlighted text. Some edits deal also with the tables.
Responce: They were done
There is ample room for improvements also concerning the figures, as duly indicated in the text. As far as the tree provided in the Supplementary Material, please note that the correct spelling is “Barbanera”, not “Barbaranea”. By the way, it is awkward to indicate “Barbanera” as opposed to “Turkish haplotype”: I suggest to rather indicate the country and or subspecies next to the square parentheses.
Responce: They were done.
Even if probably not requested by the journal, I recommend the Authors to deposit their microsatellite genotypes in a public repository like Dryad in order for other researchers to use these data in their own research.
Responce: They were done.
peer-review-20121662.v1.pdf
Responce: Thank you very much for your suggestion and correlations. The ms was improved using the edit
Author Response File: Author Response.pdf
Reviewer 2 Report
This manuscripts represents an in-depth but parochial report on the genetic structure of chukar partridges in Turkey. Overall, it is very well executed and written. The analyses appear to be appropriate and thorough.
The sole thing I would have preferred to see in the Introduction is a broader review, or at least citations of literature on the subject, of lessons learned from genetic admixture (both successes and failures) in non-game species resulting from reintroduction efforts, for example in falcons or parrots, or of game species on a more global scale. This could include a review of consequences, as well as changes in planning and protocols. The authors clearly intended to focus this study more narrowly, but I think it would be of relevance and interest to a broader audience if the manuscript was couched in a larger context that has received more attention.
I found the discussion somewhat disappointing in comparison to all preceding sections. The many analyses and results deserve justification and explanation in a manner that would make them more accessible to any but a select audience of population geneticists, including Turkish wildlife managers. The writing of the Discussion was less polished, to the extent that some sentences were unclear or that I had to read them repeatedly to decipher their intent. Examples follow.
311-313: I had to re-read this run-on sentence too many times to make sense of the last phrase regarding the CAN population.
315-318: “When only wild and only captive populations were evaluated themselves, it was found that the captive populations were more different from each other (FST = 0.24). This differentiation of captive populations may be due to the fact that bloodlines used by breeding stations are reinforced with Chukar Partridges from the wild.” The second sentence does not logically follow from the first. It needs explanation. If captive populations were more different from one another than wild populations were from one another, then how could reinforcement of captive bloodlines from wild ones result in greater differences among captive ones?
334-337: Reference to both mallard and partridge in this sentence is utterly confusing. Is this a word-processing error?
341-342: Taken literally, this statement seems to contradict the previous sentence. Admixture could “reduce genetic diversity” in a metapopulation, but not within populations.
Typos: 350 lineages is misspelled; 359 may is misspelled; chukar is capitalized or not inconsistently.
328-329: What is the explanation for this observation, be it a matter of record or speculative?
323-326: To the extent that it is already known that “bred and raised chukars or their hybrids from captivity are always risks for wild populations (322-323)”, it raises the question of what the present manuscript offers that is novel or enlightening. The manuscript would be much improved if this aspect could be better developed.
4.2-4.3 How do the authors reconcile remediation of the loss of heterozygosity on the one hand (4.2) and preservation of genetic structure (4.3) on the other?
4.3 In conclusion, more-specific recommendations about release policies (e.g., numbers, origin, transportation) would likely be helpful for wildlife managers or legislators. Again, the manuscript would be of broader interest if it included a statement framing the historical and existing genetic differentiation between populations. How significant was this differentiation relative to that in other species that have been recognized as deserving of conservation interventions?
Author Response
This manuscripts represents an in-depth but parochial report on the genetic structure of chukar partridges in Turkey. Overall, it is very well executed and written. The analyses appear to be appropriate and thorough.
Responce: Thank you very much for the positive comments. We did not give detail response in the below because we made major revisions with your suggestion and comments. You can find the changes in the changes file
The sole thing I would have preferred to see in the Introduction is a broader review, or at least citations of literature on the subject, of lessons learned from genetic admixture (both successes and failures) in non-game species resulting from reintroduction efforts, for example in falcons or parrots, or of game species on a more global scale. This could include a review of consequences, as well as changes in planning and protocols. The authors clearly intended to focus this study more narrowly, but I think it would be of relevance and interest to a broader audience if the manuscript was couched in a larger context that has received more attention.
Responce: We added two falcon and one parrot references
I found the discussion somewhat disappointing in comparison to all preceding sections. The many analyses and results deserve justification and explanation in a manner that would make them more accessible to any but a select audience of population geneticists, including Turkish wildlife managers. The writing of the Discussion was less polished, to the extent that some sentences were unclear or that I had to read them repeatedly to decipher their intent. Examples follow.
Responce: The ms were improved and rewritten some paragraphs
311-313: I had to re-read this run-on sentence too many times to make sense of the last phrase regarding the CAN population.
Responce: The paragraph was changed
315-318: “When only wild and only captive populations were evaluated themselves, it was found that the captive populations were more different from each other (FST = 0.24). This differentiation of captive populations may be due to the fact that bloodlines used by breeding stations are reinforced with Chukar Partridges from the wild.” The second sentence does not logically follow from the first. It needs explanation. If captive populations were more different from one another than wild populations were from one another, then how could reinforcement of captive bloodlines from wild ones result in greater differences among captive ones?
Responce: The paragraph was improved and rewritten
334-337: Reference to both mallard and partridge in this sentence is utterly confusing. Is this a word-processing error?
Responce: They are fixed
341-342: Taken literally, this statement seems to contradict the previous sentence. Admixture could “reduce genetic diversity” in a metapopulation, but not within populations.
Responce: Previous sentence was improved
Typos: 350 lineages is misspelled; 359 may is misspelled; chukar is capitalized or not inconsistently.
Responce: They seems to be correct. All species names are capitalized.
328-329: What is the explanation for this observation, be it a matter of record or speculative?
Responce: These are our results which is given in Table 6
323-326: To the extent that it is already known that “bred and raised chukars or their hybrids from captivity are always risks for wild populations (322-323)”, it raises the question of what the present manuscript offers that is novel or enlightening. The manuscript would be much improved if this aspect could be better developed.
Responce: The sentences were improuved
4.2-4.3 How do the authors reconcile remediation of the loss of heterozygosity on the one hand (4.2) and preservation of genetic structure (4.3) on the other?
Responce: Captive chukars have few haplotypes and released chukars should be reduce the heterozigoty due to continuously gene flow from breeding station to wild populations.
4.3 In conclusion, more-specific recommendations about release policies (e.g., numbers, origin, transportation) would likely be helpful for wildlife managers or legislators. Again, the manuscript would be of broader interest if it included a statement framing the historical and existing genetic differentiation between populations. How significant was this differentiation relative to that in other species that have been recognized as deserving of conservation interventions?
Responce: The paragraph was improved as clearly understood.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
The authors made a good job in accepting most of the changes proposed in the previous round. The quality of the MS improved conspicuously, but there are still a number of issues to address.
Importantly, when GenBank resources are used, the accession number should be given. The author must be able to know exactly which records have been used. Consequently, this info should be provided in Table 1 and in the tree of the supplementary figure.
In this respect - and I don’t want to repeat it again - the Authors are warmly welcomed to correct the “Barbaranea 2009” to “Barbanera 2009”. A misspelled surname is not matter for a philosophical debate: it should be just corrected.
Comments for author File: Comments.pdf
Author Response
Comments to Authors:
The authors made a good job in accepting most of the changes proposed in the previous round. The quality of the MS improved conspicuously, but there are still a number of issues to address.
Importantly, when GenBank resources are used, the accession number should be given. The author must be able to know exactly which records have been used. Consequently, this info should be provided in Table 1 and in the tree of the supplementary figure.
In this respect - and I don’t want to repeat it again - the Authors are warmly welcomed to correct the “Barbaranea 2009” to “Barbanera 2009”. A misspelled surname is not matter for a philosophical debate: it should be just corrected.
Response: Thank you very much for the positive comment. The GenBank accession numbers were given in the supplementary figure. The misspelled surname was corrected in the supplementary figure. We corrected the surname in the first revision but unfortunately, we forgot the upload it.
peer-review-20811672.v2.pdf
Response: Thank you very much for your valuable editing effort. We accept all your suggestion and improve them with your comment except for the title.
Author Response File: Author Response.pdf
