Peer review of: Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex (2019)



Reviewers' Comments: 
 
Reviewer #1: 
Remarks to the Author: 
Overall the authors were very responsive to my comments on the previous version of the manuscript. 
I think the new manuscript is considerably stronger and more convincing than the first version. 
 
I have a number of remaining comments to improve the paper: 
 
1) Lines 121-125: I applaud the authors for doing the SFS analyses on similar sample sizes across 
populations. However, I think the results in Figure 2 are hard to directly interpret. It appears that the 
high effect mutations in the Alpine Ibex are skewed toward lower frequency, conditional on 
segregating. This itself is an interesting result, but I don’t think it by itself shows that “purifying 
selection acting more efficiently against highly deleterious mutations in Alpine ibex compared to 
Iberian ibex”. For example, there could just be fewer high impact mutations in the Iberian Ibex 
overall. I think the Rxy analysis (Figure 2E) better makes the point the authors are trying to make 
about strongly deleterious mutations being more effectively selected out in Alpine Ibex. 
 
2) Figure 2B: Indicate what the different colors mean. 
 
3) Line 183: It would be good to discuss Figure 3E (the Rxy analysis) here before talking about Figure 
4. 
 
4) Lines 210-211: Interestingly, it seems that GERP may do well with distinguishing neutral from 
selected mutations. However, GERP (and other conservation-based metrics) probably won’t do as well 
at distinguishing weakly deleterious from strongly deleterious mutations because both will not 
accumulate as fixed differences between species. This may be why explicitly considering mutations to 
premature stop codons shows evidence of purging (ie they are enriched for strongly deleterious 
mutations) while GERP does not. 
 
5) I still find Figure 5 to be a bit misleading. In the plot with the frequencies on the right, it seems like 
most of these mutations are absent from the Iberian Ibex. One may naively think that this implies 
more deleterious mutations in Alpine Ibex. However, these mutations in Figure 5 were ascertained as 
being found in Alpine Ibex. As such, it’s not surprising that they are at higher frequency in Alpine Ibex 
compared to Iberian. One solution could be to directly state this in the legend of Figure 5 to avoid the 
readers making improper comparisons. 
 
6) Lines 300-301: I think the authors do a good job at contrasting the results between weakly 
deleterious and strongly deleterious mutations. They correctly point out that the weakly deleterious 
can accumulate. However, I think the importance of weakly deleterious vs. strongly deleterious 
mutations for short-term extinction risk is a bit unclear. In other words, while the more weakly 
deleterious mutations are accumulating, they may not quickly lead to extinction. The Isle Royale wolf 
example demonstrate this contrast nicely. So, I would recommend that the authors discuss this 
subtlety a bit more at the end of the paper. 
 
7) Line 63: Close the “)”. 
 
8) Line 473: Please indicate that this gamma distribution on s only assumes deleterious mutations. 
 
9) Figure S14: What do the numbers at the top represent? “1” “1-2”, etc? 
 

10) Line 481: I’m not sure a burn in of 3000 generations is long enough to reach mutation-drift-
selection equilibrium for a population of size 1000. It would be good to run the burn in longer and 
show whether summary statistics of diversity look like those in the 3000 burn-in simulations. 
 
 
 
Reviewer #2: 
Remarks to the Author: 
The authors have addressed all my comments. 
 
 
 
Reviewer #3: 
Remarks to the Author: 
Authors have been addressing all comments raised by reviewers carefully and I feel that the 
modifications/explanations now helped to create a more concise version of the manuscript. 
I only have a few minor points: 
line 74/75: in the abstract you always refer to bottlenecks (plural) and in this paragraph you also 
indicate the one strong bottleneck in the 19th century (line 72) and then adding the following 
sentence “most extant populations….” While anyone familiar with the study system know that each 
mountain ridge or valley might have experienced additional bottlenecks the history is not clear to 
everyone. I would add another half sentence here explaining that there have been many local colonies 
established – mixing the whole Alpine ibex population with local colonies and their demography needs 
to be somehow explained – I do think this does not need comprehensive but could be done with a half 
additional sentence and rephrasing – especially as you bring some information in lines 164 onwards 
line 94 is redundant to line 70