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Thank you very much for resubmitting this very nice manuscript. I am very pleased to see this moving forward for publication. We appreciate that you have chosen PeerJ!
Dear authors, I appreciate your modifications of the manuscript, it reads like a great piece of work now.
Thank you very much for your interesting and timely manuscript. The reviewers suggest some streamlining and clarification of background material, along with suggestions to aid in clarifying the presentation. Primarily in the introduction careful editing by a native English speaker would help in terms of readability, but beyond this section the readability is very good. The figures are very clear, and it is entirely up to the authors, but one is tempted to suggest it is a shame that the gorgeous bird drawing in S1 is not in the main figure 1!
We suggest minor revisions because we believe that it will be straightforward for the authors to revise the manuscript draft to incorporate the overwhelming majority of the reviewers comments. I am confident that the resultant paper will be a clear, interesting and valuable contribution. I look forward to seeing this revised version!
Your manuscript "Historical and current introgression in a Mesoamerican hummingbird species complex" summarizes an interesting biogeographic study, which is of general interest, especially for researchers of biodiversity. I would like to see it published in PeerJ, but have some major concerns about data interpretation and partly data generation, which I summarized in more detail in the attached document. I'm also not satisfied with data presentation, which in my opinion often lacks a clear structure, contains numerous repetitions and partly too many details. Furthermore, I recommend to have the next manuscript version checked by a native speaker.
The research topic introgression is highly relevant and meaningful. I appreciate the sufficient sampling as well as the wealth of data generation and analyses, which follow a high but not particularly innovative technical standard. I have some concerns about the feasibility of the utilized methods to study "historical and current introgression", which I also summarized in more detail in the attached document.
see attached document
I suggest substantial rewriting of parts of the manuscript and an indication in the title that this study tackles introgression from a biogeographic perspective.
This manuscript describes the population histories of three Amazilia hummingbird species (A. beryllina, A. cyanura, and A. saucerottei) with parapatric distributions in Central America. The authors scored variation in mtDNA sequences (3 loci), microsatellite lengths (12 loci), and plumage coloration (10 characters), and also modeled distributions based on current locality records and current, last glacial maximum, and last interglacial environmental variables. The mtDNA analyses find a lack of species monophyly, recent divergence among species, and evidence of non-symmetrical isolation-with-migration. The microsatellite analyses find evidence for three genetic clusters with distributions consistent with known geographic barriers (Isthmus of Tehauntepec and Nicaraguan Depression), with some individuals showing signs of admixture. The plumage color analyses find that samples in the central portion of the range have phenotypes that are intermediate of those at the north/southern limits of the combined range. The distribution models give evidence of niche conservatism and potential range expansions and contractions that may have contributed to historical isolation and secondary contact.
The manuscript could be improved with a clearer presentation of background material, hypotheses, and potential outcomes in the introduction (the writing and grammar could be improved in the introduction and discussion sections). For example, the first paragraph attempts to provide background on the effects of introgression and climatic fluctuations on shaping evolution. The content here seems limited, particularly with respect to potential patterns of genetic structure. It is not clear to me why this paragraph is limited to mtDNA introgression/isolation. More details on the effects of isolation and gene flow on the (nuclear) genome would be useful to the reader. The authors could weave in their relevant information on climatic shifts and also introduce the importance of geographic barriers. Also, it seems important that the authors introduce the difficulty of differentiating incomplete lineage sorting and introgression.
I also found the four “divergence scenarios involving admixture” in the last paragraph of the introduction to be rather confusing. Number 3 is particularly confusing because it mentions “have not introgressed in the past” and “will show admixture only if gene flow has currently occurred,” which seems conflicting. I think some of the confusion stems from an implicit assumption that the mtDNA and microsatellites could provide conflicting signals, without giving the appropriate background information on this possibility. These possible scenarios should be more clear (simplified and reduced?). Also, I think that the discussion should re-visit the scenarios and explicitly state which one(s) is supported by the results.
The experimental design of the study was well conceived and executed. The study features impressive sampling, with data collected from ≥ 145 specimens for these analyses; outgroup sampling was also included when appropriate. The use and deposition of voucher specimens in the study is critical and should be applauded. The analyses conducted in each section of the methods appear relevant and complete, with consideration of program/analysis settings and parameters (although I do not have expertise in Maxent). The methods and results sections were generally well-written, and the figures and tables clearly illustrate key results.
The authors have deposited voucher specimens in natural history collections and also archived mtDNA sequences in GenBank (but not yet released). Is does not appear that microsatellite length polymorphism or plumage scoring results have been archived.
Figure 1D shows the STRUCTURE results based on msat data. These show three clusters that roughly correspond to north of the Isthmus of Tehauntepec, Nuclear Central America (between Isthmus of Tehauntepec and Nicaraguan Depression), and south of the Nicaraguan Depression. The black bars between clusters correspond to the Isthmus of Tehauntepec and Nicaraguan Depression, but this might not be immediately obvious. Perhaps small arrows from these titles to the bars might make it more explicit? The samples in this plot are ordered according to their geography (northwest to southeast). Individuals with evidence of genetic admixture appear scattered throughout the plot. That is, admixture does not appear more common near the isthmus and depression barriers. I found this pattern interesting and think that it deserves more attention in the discussion (e.g., what are some possible scenarios/mechanisms for this pattern?)
Overall, the complex has clinal variation in plumage colors, with evidence of genetic introgression/admixture among species. Given these recovered patterns in genetic and plumage variation, the authors might want to add their viewpoint on taxonomy of this species complex in the discussion.
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