Comments to the Authors:
The manuscript “The antique genetic plight of the Mediterranean monk seal (Monachus monachus) by Salmona et al. investigates patterns of population structure and demography in the endangered Mediterranean monk seal. Using microsatellite data from contemporary and historical (i.e., from museum collections) monk seals collected throughout the species range, they observe patterns of population structure and isolation by distance, and find high levels of inbreeding in all populations. Using Approximate Bayesian Computation analyses, the authors find support for demographic models that include large declines in effective population size that likely occurred in antiquity.
I read the manuscript with great interest and I think that the findings have important implications for the conservation of monk seals. The data set is very valuable, as it includes comprehensive sampling from throughout species range and historical samples. Overall the quality of the work is very good and the results are clearly presented. I have some suggestions that may strengthen the paper even further.
Major comments:
Title: Use of the word antique here (and later in the manuscript) is non-standard for English. I would suggest revising the title to something like: The genetic plight of the Mediterranean monk seal (Monachus monachus) since antiquity.
Line 80: Figure 1: It would be easier to interpret the results if the color scheme in Figure 1C matched the color scheme in Figures 1A and 1 B. Also, the legend for W-Sahara in Figure 1C should be updated so it matches the plotted points.
Line 264: Where can the reader find specific details about models M180 and M181? Is that in Table S10? Also, should M180 and M181 be included in Figures S11, S12, or S13? I see that those figures contain schematic representations of the modeled demographic scenarios but it is not clear which schematics correspond to M180 and M181. Once you add that information to line 264, I think you can greatly simplify the information in Line 268 – maybe only refer to Figure 4 and Figures S30 and S31.
Figure 4: The nice results in Figure 4A are somewhat obscured by the current plot layout and I think that the figure can be edited slightly to improve legibility. I recommend the following adjustments: 1) Add population labels to the x-axis; 2) Do not use colors to represent geographic location – instead, use two colors (rather than point shape) to differentiate between the modern and historical samples; 3) Show either the 50% or 95% confidence intervals (not both); 4) Clarify what the labels “Other N1” and “other N2” represent. In Figure 4B, more readers might be familiar with the term “Anthropocene” than “Capitalocene”.
Line 376: I don’t quite see the Ne values you mention in the text in table S10. Please clarify what variable you are referring to here (is it N2?).
Minor comments:
Line 58: I would recommend that the sentence is rephrased so that it does not begin with “because”. Perhaps like this: Distinguishing between the respective impact of recent climate- and human-driven changes on the biosphere has proven challenging because Late Quaternary extinctions were caused by the superimposed effects of climate change and human activities from the Last Glacial Maximum (LGM) onwards.
Line 67: Non-standard use of the word posterior. I suggest replacing with “after”.
Lines 95– 96: It might be nice to provide time range estimates for the Bronze Age (~3,300 to 1,200 BCE). I also recommend writing centuries as Arabic numerals rather than Roman Numerals (i.e., 15th century vs. XVth century).
111: You write that habitat loss and overexploitation in the Mediterranean started as early as 10,000 years before present. It might be good to give an example of the archaeological evidence supporting this statement. Is it specific to seals or other marine taxa?
Lines 113 – 118: Please break up this sentence into 2-3 shorter sentences to improve readability.
Line 125: Non-standard use of the word confront. Consider replacing with “investigate”.
Line 134: Provide sample size information for recent samples (as you did with historical samples). Also, it would be nice to have a table somewhere (either in the main text or the electronic supplement) that summarizes the number of modern and historic samples analyzed for each geographic location.
Line 139: I suggest rewriting this sentence as: “…which suggested that after this period the species distribution fragmented into North Atlantic and eastern Mediterranean populations”.
Line 143: You don’t need to start a new paragraph here. Just proceed from the following one.
Line 144: Check phrasing of this sentence. Should “reconstructed” be a verb here?
Line 148: Clarify that the 25 historical samples were dated.
Line 150: Microsatellite should be singular here.
Line 163: Here and elsewhere: please substitute “nSSR” (or SSR) with “microsatellite” to have consistent use of terms throughout.
Line 165: This is a run-on sentence; perhaps a verb is missing?
Line 175: I don’t understand this sentence as it is currently written. Please clarify what distance metric you used and what is meant by the “spatial scale that maximizes the amount of variance explained”.
Line 196: It is a little confusing that you reference the model with K =2 clusters here, when you show the K=4 results in Figure 1. The K=4 model also supports the idea that there is differentiation between the Atlantic and Mediterranean samples, so I think you can reference it here instead.
Line 197: I recommend substituting the word “representing” for “mimicking”.
Line 200: Remove the word “representation”.
Line 201: Remove repetition of the word “clear”.
Line 203: In Figure 1, there is no Central-Eastern Mediterranean population. I think you meant to write Central Mediterranean population here?
Line 230: I think you should include a statement here (and perhaps in the methods as well) that allelic richness, observed heterozygosity, expected heterozygosity, etc., were estimated over all historical samples (rather than on a per-location basis) because the historical sample size was small. As written, the reader might misinterpret your statement to mean that you estimated all of these statistics for each geographic location using historical samples.
Line 238: It would be nice to include ~1 sentence of context about the Cabo Blanco mortality event – what caused it?
Line 298: I recommend replacing the word “upsurges” with “raises”.
Line 302: Sentence should be “…monitoring of potential breeding sites is systematized”.
Line 345: This is a very encouraging signal indeed!
Line 363: Please provide an approximate year range for Antiquity (that corresponds to the blue demarcation lines in Figure 4B).
Line 367: I would recommend incorporating a transition sentence as you move into discussing the Neolithic results. Perhaps you can refer to the estimated demographic event during the Neolithic in Figure 4b?
Line 383: Should be: Roman Empire’s
Line 388: Should be: Therefore (rather than wherefore). Also check the next couple of sentences for small typographic errors.
Line 399: A comma should come after e.g.
Figure 2E: Very cool results comparing inbreeding in modern and historical samples. Why do you think that inbreeding was higher in the historical Western Sahara samples? Might that result be due to small sample size? Or other factors?
Figure 3: You don’t need a period after km in the x-axis.