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The authors examined in detail the genetic differentiation and population structure of two cownose ray Rhinoptera bonasus and R. brasiliensis in the Western Atlantic Ocean. The study reveals significant population genetic structure in both species, with distinct genetic clusters identified. Environmental variables, particularly benthic temperature and current velocity, were found to influence genetic diversity patterns. Migration patterns and genetic connectivity among populations were also explored, highlighting the role of environmental drivers in shaping genetic structure. The findings have important conservation implications and provide insights into the genetic variability of cownose rays in the region. The authors discuss their results with previous studies, address conservation relevance, and suggest future research directions.
The materials and methods section outlines the procedures and techniques employed to investigate the genetic variability and population structure of cownose rays in the Western Atlantic Ocean, providing a clear framework for the study's methodology. Analysis of sequences of COI and Cytb genes for both species to investigate genetic diversity, relationship with environmental variables, genetic structure, and demographic parameters. Environmental association analysis was performed to determine the correlation between oceanic landscape features and the genetic diversity of cownose rays, providing insights into how environmental variables may influence genetic patterns within and among populations. The population genetic structure of these species was assessed with Bayesian clusters in BAPS consistent with segregation patterns observed in haplotype networks based on COI and Cytb markers.
Results from the study provide valuable information about genetic diversity, population structure, and environmental factors affecting cattle-nosed rays in the Western Atlantic Ocean, contributing to the conservation and management of this species in the region. Significant population genetic structure was observed in both species, with distinct genetic clusters identified based on Bayesian analysis and haplotype networks. The study revealed varying patterns of genetic diversity within and among populations of cownose rays, indicating differences in gene flow and connectivity across the Western Atlantic Ocean. Benthic temperature and current velocity were identified as the most important environmental variables influencing genetic diversity in cownose rays, highlighting the role of environmental factors in shaping genetic patterns. The research expanded genetic data coverage along the distribution range of both species, providing a more comprehensive understanding of genetic variability from the eastern United States to Brazil, including the Gulf of Mexico. Evidence of migration patterns from northern localities, such as Chesapeake Bay, towards southern locations with higher temperatures, such as Cedar Key and Apalachicola Bay, was observed, indicating potential seasonal movements of cownose rays in response to temperature changes. Understanding the genetic variability and population structure of cownose rays is crucial for defining conservation units and implementing effective management strategies, especially in the context of climate change and habitat delimitation.
The article contributes to the growing body of knowledge on the genetics of marine species and, in my opinion, is suitable for publication because it highlights the importance of genetic studies in informing conservation efforts and sustainable management practices of cartilaginous fishes. Authors can check the minor corrections I have made in the text.
The paper on genetic variability and population structure of two cownose rays is well structured and the conclusions are substantiated by the results. Considering the level of the current knowledge related to these two species such papers are more than welcomed and after being revised according to the comments deserve publishing. The provided figures and tables are useful. The only comment is related to to checking the most recent literature which is not performed as it should be, thus the authors are advised to check the following reference and adjust their paper according to the recent results from studies:
Weber H. 2022. "Population Genetics Of Cownose Rays, Rhinoptera Spp. In The Western Atlantic"
Methods are described sufficiently and performed according to the current standards.
The only consideration is related to the procedure of obtaining tissue samples from specimens collected by fisheries at different localities: it would be good if the authors could provide the details of how (and by who) the field identification of the species was performed as it is a known fact that these species are sometimes confused with each other as the only external diagnostic characteristics to distinguish between both species are very limited.
The results are presented clearly and soundly. Conclusions are also well written and substantiated by the obtained results.
57-58 Although the distribution of these two species overlap in some areas they do not entirely occupy the same range, thus, divide the range distribution and describe it separately for both species.
107-109 please explain the process of the field identification of species
248-249 Could you give more explanation for „...although some individuals exhibited 100% similarity with individuals from the north...“
364: not true as it has been investigated, please see Weber H. 2022.
392-393: there are other data, please see Weber, 2022
References Weber et al., 2020 and Peterson et al., 2023 are mentioned in the main text but not listed in the References.
In References:
Correct order of Schwarz FJ references
The following references are listed but not cited in the main text:
Cockerham CC, Weir BS. 1993. Estimation of gene flow from F-statistics. Evolution 47:855–863
Peterson CT, Grubbs RD. 2023. Temporal community structure and seasonal climatic migration of coastal sharks and large teleost fishes in the northeast Gulf of Mexico. Canadian Journal of Fisheries and Aquatic Sciences.
Manuscript is clear, well written. Citations and structure fine, Results relevant to a group of rays that are poorly understood and reveal patterns worthy of publication for the science community to consider and study further.
Minor: Lines 191-195 need editing.
Line 503: correct "fo.und"
Table 3, should probably use Bonferroni test for each gene due to mulitiple tests on the same data set. This could make insignificant the p-values "Among Groups" for CO1 Scenario 2 and Cyt b Scenario 2. But overall findings stay the same.
A description of mtDNA as a haploid, maternally inherited molecule with all genes tightly linked together in contrast to nuclear genes is needed for readers who are not geneticists to put the results in context. This could be done in the Introduction and referred to again when results are being discussed to help explain why nuclear and mtDNA findings may have different explanations.
Table 3, should probably use Bonferroni test for each gene due to mulitiple tests on the same data set. This could make insignificant the p-values "Among Groups" for CO1 Scenario 2 and Cyt b Scenario 2. I expect overall findings will stay the same.
Findings are sound. Nothing to add.
Lines 191-195 need editing to fix incomplete sentence structure and make them more readable.
Line 503, "fo.und" needs to be corrected.
The following is something the authors might consider:
Paragraph (lines 503-514) discusses alternative explanations for patterns found in previously published nucllear genes compared to mtDNA in this study. One of the things that was most interesting to me was the use of BAPS (linked loci) to look at at population structure inferred from different genes on a tightly linked mtDNA genome not know to recombine. This is not how we used to do this years ago, but I like the approach. However, in using this approach, and when comparing to nuclear genes (which can recombine, even if linked), the author should, in my opinion, note for the non-geneticist reader that mtDNA (a haploid, maternally inherited genome) has an overall smaller effective population making it highly susceptible to bottlenecks or selective sweeps. Unfortunately, it's hard to which one without combining nuclear and mtDNA sequencing on the same samples. In other words, it's not at all unusual to note different patterns and surmise different pathways to explain them based on these different genomes. So in this paragraph, the explanation of "reproductive philopatry" can't really be rejected by biogeographic histories necessarily. This where we need more species showing this sort of pattern in the future in order to invoke concordance of pattern and support the historical biogeographic hypothesis.
In the next paragraph (lines 516-536) there is a discussion about benthic temperature and current velocity correlating to the mtDNA patterns. This suggests historical dispersal and selection influencing the results. These results too set the stage for further analysis, particularly with genomics to look for possible signals of selection attributed to warming temperatures since the last Ice Age that reshaped (expanded?) the distributions of these rays to their current patterns today. Then in the next paragraph, (Lines 538-546), a quick test of population expansions fails, yet the data signals in both species are present in other measures.
This is why reminding the reader that while mtDNA may not mutate as quickly as microsatellites, the molecule is highly sensitive to events or habitat shifts that influence population size either with bottlenecks or selective sweeps. In my experience, microsats don't always prove better than mtDNA. But those genes can give very different stories, which in combination, can be more interesting. Thus, a brief description of mtDNA as a haploid, maternally inherited molecule with all genes tightly linked together in contrast to nuclear genes is needed for readers who are not geneticists to put the results in context. This could be done in the Intro and reinforced when comparing mtDNA to previously published nuclear results.
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