The Role of the Environment in Shaping the Genomic Variation in an Insular Wild Boar Population

Round 1

Reviewer 1 Report

The article by Fabbri and co-authors address another aspect of genetic variability of the well-studied population of wild boar on the island of Sardinia. The authors used SNP markers to confirm diversification of east-Sardinian wild boars from the population in the western part of the island, but also they demostrated that there is a deeper diversification within both western and eastern sub-populations. Moreover, they showed that this genetic variation is correlated to some environmental factors and hypothesized about genes that could be involved in the population diversification.
The article is well prepared from the points of view of methods and presentation. I have just a few minor comments:
Line 111: please explain the abbrevation MAF here when you use it for the first time
Line119 and further in the text: please use italics for the names of R packages and functions. Some readers could be not experts in R packages that you have used

Line 166: I think you better use "diversity" than "variability" when speaking of Shannon's index

Line 189: please use "LEA package"

Line 197: delete repeating citation

Lines 269-270: I'm not sure that "influence" is a correct term here. I think that here you deal with two correlated parameters, not with dependent variable which is unfluences by the independent one

Lines 280-282: same as for lines 269-270. You certainly cannot speak about the influence, because below you write that "the environmental contribution to the variation in the data was minor"

Line 297: It is 78% of the outliers detected by two methods, not the total outliers (n=1,536 line 294)

Line 298: what is "almost all"? 48 of 49 or less?

Line 335: GO terms - please explain

Line 399: "programs" is confusing, I think better use "methods", or "computer programs"

Line 405: I'm not sure I understand what do you mean. "Weak signals" is too general, please clarify what exactly did you expect.

Line 428: "ungulates" instead of "ungulate"

 

 

 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

In this manuscript titled “The Role of the Environment in Shaping the Genomic Variation in an Insular Wild Boar Population” the authors characterized the population structure in the Sardinian wild boar and sign of selection, testing the hypothesis that the environment has affected the detected genetic differentiation, starting from dataset of their previously study.

The manuscript deals with an interesting topic, with an adequate and well-developed approach both in the presentation of the results and in the statistics. Unfortunately it lacks some basic information and an adequate literature to support the claims. These shortcomings are very serious, because I think it is necessary to provide to the reader a complete picture of the state of the art, in particular for those works that have been developed on the same topic, in the same area and in some cases with the same methodologies. A critical issue also exists in the description of the experimental design and the study area.

 

In particular, below are the specific comments:

 

Line 33. It would be more correct to write “…similarly they can create a pattern of differentiation” rather than "similar pattern" 

 

Line 43. The sentence "another popular marker in population genetics studies" is superfluous. It could also be removed.

 

Line 46.  This statement should be supported by references.

 

Line 53. A recent study dealt with this topic considering Sardinian specimens was published on PNAS by Frantz et al 2019 (doi: 10.1073/pnas.1901169116). Maybe the authors missed it.

 

Line 56. A previous study analysing the genetic makeup of central-eastern Sardinian WB population with “a thousands of SNPs distributed across the genome” was published on Molecular Ecology by Petrelli et al 2021 (doi: 10.1111/mec.16238).  Maybe the authors missed it.

 

Line 59. Here the authors should better introduce the reader to the new concept that is about to be deal. The two periods seem to lack connection.

 

Line 66. There are more recent and comprensive contributions dealing with the plasticity of the wild boar. For example, see doi.org/10.3390/ land11060887.  Maybe the authors missed it too.

 

Lines 72 - 79. In lines 67-70, the authors emphasized the importance of demography and reproduction, in relation to this type of study, but do not bother to make an assessment of the population density (spatial variation) on the island or of any different reproductive capacities.

 

Line 82. No information is provided on the critical aspect of the study: the environmental variation found on the island. Only the altitudinal variation, however without any quantitative information is provided in Fig 1. All the notes on the environmental characteristics refer to the whole island (it does not useful for the  goal) or have no reference considering the figure 1. 

More, the names of massifs, lakes or other localities were not reported in map (although they were named in the text) and were difficult to localise unless referring to an Atlas. Also, it would be better to indicate that the study area is located in Italy, for readers who are not familiar with this geographic area. 

The authors should elaborate a more detailed map, reported  names, references to the environmental characteristics of the studied areas and their variation recorded within the island, to better interpret the arrangement of the samples. 

I suppose that the samples are collected according of environmental variables and not randomly.

 

Line 98. The samples used in this study are derived from previously published work. It would be more appropriate to write something like "Dataset selection and Quality Control” rather than “…Collection…”

 

Line 124. How can the reader localise “Nurra region” on the map provided by the authors in Fig.1?

 

Line 145 onwards. Was all the spatial information, sometimes even with an accuracy of 10 km, or using 1: 25000 maps, then simplified to NE, NO, CE etc…?

Furthermore, why is there no reference of these acronyms (NE, NO, EC, etc.) on the map of Fig.1? How does the reader understand which samples were classified as NE, NO etc, looking at the map in figure 1?

 

Lines 147-148. How did the authors determine that these climatic variables are significant for wild boar biology?

 

Line 235. This observation, and others on the structure of populations, suggest an effect of the gene flow, a factor that should be better exploited in the manuscript, both in the introduction and in the analysis of the results.

 

Lines 336 - 338. In Human, BBX plays an important role during the odontoblast differentiation of human DPSCs/progenitors….Extending this concept to bone development in wild boars is very hardly.

 

Line 361. The land use has changed significantly over time. The one detected today is profoundly different from that of a few millennia ago. The authors should take into account this.

 

Lines 368 - 371. This hyperbole is very difficult and to report similarities with domestication process in cows in this circumstance does not seem absolutely profitable, in my opinion. The time in which the mutations under selection traits on phenotypes appeared, cannot be deduced from these data.

 

Lines 371 - 373. What do the authors mean by this sentence? Please, clarify it

 

Line 422. Only il 3% of the genetic variation?

 

Lines 427 -428, quotes 80, 81 and 82 are absolutely inappropriate.

 

Line 436. This hypothesis has been already introduced previously in other published works, can the authors insert an appropriate literature?

 

 

Line 438. Interpretations on the results regarding BBx are scattered between results and discussion. The authors should revise a more homogeneous discourse on this issue.

 

 

Lines 460 - 471. It seems that the authors have neglected the consultation of an important slice of literature on these issues e.g.:

https://doi.org/10.1111/j.1365-2907.2010.00182.x  and doi:10.4404/hystrix-27.2-11489 - about “remarkably genomic diversity”;

doi:10.1111/eva.12383 - about “introgressive ibridization”

 

Ai et al. demonstrated a genetic adaptations to cold climate in pig populations from high-latitude Chinese regions, that might have been introgressed from an extinct Sus species, providing new insights into the role of introgression in adaptation among pigs species (https://doi.org/10.1038/ng.3199). The European pig was initially domesticated in the Near East and then subsequently introduced into Europe where they encountered free-living boar adapted to local conditions. The authors could consider also this possibility to explain the base of local adaptation of Sardinian wild boar to local conditions.

 

Thank you for the opportunity to review this manuscript

 

 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf