This is a well-conceived study and has been conducted using appropriate methods. The conclusion is sufficiently supported by the data.

I query the use of diversity metrics since none of the hypotheses concern diversity per se, rather the extent of overlap in parasite species and resistance genotypes between hosts. But this is a minor point and could be addressed by including an a priori hypothesis on diversity (this could be two-tailed to avoid retro-fitting expectation to data).

The introduction is well-written and comprehensive; could perhaps be abbreviated a little (e.g. the section on BZ-resistance history and mechanisms is not too necessary here). Methods, results and discussion are clear.

With regards to the likely spill-over and maintenance of resistant worms in ibex, originating from sheep, could it not also be possible that anthelmintic residues in the environment might lead to exposure of ibex worms and selection in situ?

Overall the study fails to conclude on the extent to which these worm populations are shared between hosts and the role of ibex in maintaining them and influencing genetic composition. This is sensible and justified and the authors are right to be cautious. All the same they might suggest more concretely what further studies are needed to answer this question – especially what is possible regarding longitudinal and intervention studies.

The English is generally excellent but could be improved slightly in places, e.g. typos / spelling lines 44, 138, 146, 153, 163, (non-exhaustive list).

In my opinion, the work is original and the manuscript is well written. The authors question the interface between domestic and wild ungulates and its consequences in terms of parasite transmission in mountain ecosystems, with issues for both pastoral activities and wildlife conservation. Overall, the description of the methods and the results are clear, with sufficient details and useful illustrations; the discussion is interesting and the conclusions are adequately supported by the results. I have only minor comments and some suggestions mainly to enrich the discussion.

Line 57: the results show that Ibex populations harbor resistant strains before the arrival of the sheep, showing that these strains were maintained for a year. However, there is no demonstration that this maintenance can last more than a year in the absence of sheep. The possible contribution of other wild ungulates that potentially frequent the pastures (as chamois) to the maintenance of the resistant strains has not be studied in the present works. Also, and given that the term reservoir refers to a capacity to maintain a pathogen over the long term without external input, I suggest to be more careful in the use of terms. My suggestion would be to reformulate with “and then could act as refuge or even contribute to maintain resistant GIN”. This comment also lead me to a question: is there any data, even in livestock, on the maintenance of the resistant strains in absence of any selection pressure (i.e. absence of the use of anthelminthics)? In my point of view, it would be interesting to discuss this point.

Line 81: the authors introduce the fact that resistances to several families of anthelmintics have been observed but their works focus only on benzimidazole resistance. It would be interesting to explain, in the introduction or the discussion, whether similar studies but for other anthelmintics would be possible and if not to explain why.

Line 176: the acronym ASV is used here for the first time in the manuscript, please explain it. 

Line 194 and following: to better understand the extent of the interfaces which are studied and in what proportion these interfaces are explored in the works, it would be useful to provide elements on the extent area of the massifs and that of the sampling locations where feces were collected (if data available).

In this Material and method section, I suggest gathering all the descriptive data on study sites in a table to make their vizualisation easier and to quickly identify differences between sites.

Line 214: please specify whether the term “individuals” concerns all age groups or only adults.

Line 219 and 222: the authors mention the presence of a goats on some pastures, but there is no further mention of goats afterwards. Since Ibex is phylogenetically closer to goat than to sheep, and that the parasitism of goats can differ from that of sheep, qualitatively and quantitatively, I would have found interesting to also explore the parasitism of the latters. I imagine that this was not done for understandable practical reasons, but I suggest that the authors address this point in the discussion (possible impact of the presence of goats on the nemabiome of Ibex?) in a paragraph that I suggest to add to discuss the possible role of other species (see my last comment).

Line 234: the authors explain that, when possible, they collected Ibex feces just after their deposit and in certain cases also during capture. In one of the files provided in appendix (Sample_description_Sheep_ivbex_all.csv), we can see that the data on the sex was registered during capture. Would it be possible to test a possible influence of sex on the results? As the use of pastures by males and females is not similar in space and time for Ibex, one hypothesis could be that the nemabiome are different. In the same way, for feces collected shortly after their emission, would it have been possible to note whether these feces was emitted by groups of males or females to test whether it affects the diversity of gastrointestinal nematode and the anthelmintic resistance?

Line 246/ table1: it is surprising that, in Belledonne, Ibex samples from 2018 and 2019 have been grouped together, without details on the number collected per year, any demonstration that the nemabiome composition is similar from one year to the next, and specification whether the pastoral pressure was similar from one year to the next (same flock size and composition?). This choice to group samples is all the more surprising as some feces were collected in July (in 2018) when one of the objectives of the work was to study parasitic diversity and resistance to anthelmintics before the arrival of the sheep (unless Belledonne is an exception, sheep are usually present on pastures since June). Finally, I did not understand why in the spreadsheet in Appendix there are 93 Ibex while table 1 indicates 80 Ibex samples in Belldone. This may be a misreading on my part, but I haven't seen any explanation of this difference. I have not compared data in detail for all the sites but it would be good to check the concordance of the numbers between the table and spreadsheet, or to explain why the data differ. In the same way, for Cerces MO, unless I am mistaken, the spreadsheet in appendix mention ibex samples in May 2019 but not in 2018, contrary to table 1. 

Line 539: it would be useful if the authors clarified that Ibex populations use areas grazed by sheep but most on the time at different times (months of the year or times of the day).

Line 543: the circulation of a pathogen being a prerequisite for its maintenance, I suggest to reverse circulation and maintenance in the sentence.

Finally, I would have found useful to add a point of discussion on the interest of exploring more widely the hosts possibly involved in the transmission and maintenance of nematodes, such as goats (see above) but also of other wild ungulates. The chamois is mentioned in line 122 but not later, although its role could also be questioned (densities sometimes high, spatio-temporal use of pastures different from that of ibex populations and certainly variable between sites).