Mitogenome Diversity and Phylogeny of Felidae Species

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This is an interesting paper, covering matrilineal evolution of felids. 37 of formally described 41 species are included, hence the diversity of the family is almost entirely covered. The most valuable part of the paper is the comparative analysis of evolutionary signal and structural evolution in different parts of mitochondrial genome, and the evaluation of the selective pressure on the different parts of the mitogenome.

The paper, however, needs to address several important issues before being accepted for publication. First of all, the inferred phylogeny does not look very different from other phylogenies, such as published in Werdelin et al. (2010) [I recommend to discuss this paper, which is not included in the reference list]; however, there are some differences in the tip branch topology. These differences may be related to the analysis of different parts of the genome (nuclear DNA in Werdelin et al., vs. mitogenome in this paper) and may reflect incomplete lineage sorting (ILS) or introgression at early stages of speciation. I strongly recommend authors discussing these inconsistencies, and parts of the topology changed related to the previous studies. I also suggest speaking about matrilineal phylogeny rather than about phylogeny of species, which is not the same.

Potential ILS or introgression patterns suggest that some closely related species from the same geographic region, such as Prionailurus spp. or Leopardus spp. may not be matrilineally monophyletic. The authors, probably randomly, used a single mitogenome for each studied species in their analysis, whereas there are many more felid mitogenome sequences in NCBI. I would suggest to overtake potential problems in reconstructing phylogeny, related to the infraspecific variations, by one of the following ways: (1) construct consensus sequences for each of the studied species, based on all mitogenomes, stored in NCBI, and run phylogenetic analysis based on these consensus sequences; (2) select randomly at least few sequences of each species (if more than one is available), concentrated on the geographically distant populations (e.g. applicable to Panthera pardus, Lynx Lynx, Felis sylvestris); (3) repeat the analyses with at least two more datasets including different samples of the same species. This will strongly increase the robustness of the analyses.

The use of CR in the analysis is questionable. In many publications, this part of the mitogenome is excluded from the analysis, because it may shade the phylogenetic pattern. The authors mention this gene only once, but did not show it on the figures. This has to be somehow explained.

I think that the authors might include a broader discussion about matrilineal evolution of felids, including the analysis of divergence times for individual genes, potential impact of selective pressure on phylogenetic reconstruction, and reasons for nucleotide composition differences in different mitochondrial genes.

Finally, authors several times mention conservation strategies, although it remains unclear how their results contribute in these strategies. Better remove these mentions, or explain in detail.

 

L 92 Ka/Ks ratio (non-synonymous vs synonymous mutations) should be explained here.

L 95 “or developing conservation genetic strategies” – unclear how. Explain.

L 149 Including control region in the dataset might bias the inference as a result of a high saturation level. I would recommend to repeat the analysis with the dataset excluding CR

L 154-155 what determines different length of the genomes? CR? Or other parts?

Fig. S2 is very difficult to follow. Perhaps it makes sense to re-draw this figure by showing only inconsistent branches/nodes for each dataset.

There are some discrepancies between the ML and BI trees based on the same 13PCGs+2rRNAs dataset. Usually, BI tree is considered to be more reliable; I would suggest to present this tree in the main text, and move Fig. 4 into supplementary material.

Comments for author File: Comments.pdf

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

This is a useful manuscript that uses mitogenomes to look at molecular evolution and phylogeny of felids. I thought that this was a well written manuscript and that it was reasonably clear. 

I only have a few thoughts and they are mostly around giving more rationale for why this research was done and why it might be useful.

Line 49: "the evolutionary history and adaptive mechanisms of felids remain central research topics in evolutionary and conservation biology." While this may be correct it would be useful for the authors to say more specifically why it is useful in this case. What specific issues are the authors attempting to shed light on with this analysis?

Line 52: "This unique evolutionary pattern" - All patterns are unique! Say what is interesting about this pattern.

Line 94: "Our findings are expected to provide a theoretical foundation for developing conservation genetic strategies for felids ..." Given that this is the focus of the paper, it would be useful if you could be more specific about the types of strategies that your data may inform upon. This manuscript is good on detail but poor on why we really want to know these things. You don't want this to come across as a data mining exercise where you extract some information just because you can....

Line 281: This section basically says there is much agreement with previous phylogenetic studies. I think that this could be a slightly larger section that perhaps looks at these comparisons in a little more detail. Where are the differences with previous studies? What does this mean for felid phylogeny understanding (and felid evolution understanding)?

 

 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

In its present shape, the paper is appropriate for publishing in MDPI Diversity. The appropriate changes are integrated into the manuscript, and if not, satisfactory replies to the comments are provided.