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Thanks a lot for your final revision. I look forward to seeing the printed version of your paper!
# PeerJ Staff Note - this decision was reviewed and approved by David Roberts, a PeerJ Section Editor covering this Section #
Thanks a lot for your careful revision. The manuscript has improved a lot again and I look forward to seeing it published. However, I have a few minor details which I would like to ask you to address before I can finally accept the paper:
Results section and Table 1: please double-check the use of "phylogenetic relatedness" and "phylogenetic signal" so that the text matches the table and vice versa
line 247: replace "distributional" by "distribution"
line 325: replace "reatedness" by "relatedness"
line 684: replace "Doktor der Naturwissenschaften" by "Dissertation zur Erlangung des Grades
Doktor der Naturwissenschaften"
The current version has improved a lot, but another round of text polishing is still required. In the annotated file, I have made a number of suggestions which could improve the manuscript. I'd like to ask you to pay particular attention to a more precise wording and a more consistent terminology.
Figure 2: In the figure title and caption, it's ok to use the term "phylogeteic structure". But in the color scale legend, please replace it, e.g. by "phylogenetic signal" (see also my comments in the text).
Figure 3-5: In the caption, please use a consistent term for the temperature variable (instead of using range, range index and seasonality). Also, please add a note "See text for further details" or something similar to the captions, as it will be much easier to understand the figures when reading the results section.
(Right now, the annotated file is a pdf version. I will ask the editorial office to forward the word file to you, which should make it easier to edit the manuscript.)
I think that the presentation of this paper is now much improved. The analyses are clear and well-presented, and the arguments are effective.
See my concern about monophyly below.
I think that the paper now makes a clearer and more effective argument toward the points that it attempts to make. See my concern about monophyly below.
OK, so I raised this point in my first review... the group that is being analyzed is not monophyletic, and I do not like that. The authors responded that they are interested in the phylogenetic structure of the assemblage, and that their insights do not depend on monophyly. I think that an argument might be erected to the contrary, but let's accept the authors' proposition... in that case, then, why not expand the assemblage to include the entire set of species that seek arthropod food items while airborne ... some wood warblers, Tityra, and several other taxa should probably be included. Or maybe the entire field of phylogenetic structure of communities is OK with non-monophyly, and this concern should be ignored?
There is a misspelling in one of the in-text citations: (Wainwrigth & Reilly, 1994).
I am satisfied with the authors' responses to my comments and changes made to the manuscript and am happy for it to be published as is.
This paper is a valuable contribution to the literature investigating morphological variation across space and in relation to environmental factors as well as phylogenetic structure.
However, as pointed out by the reviewers and in my own comments (see annotated pdf), there are several issues related to the data, analyses and writing which need to be very carefully addressed before I can reconsider it for publication. It is very likely that it will be sent out for review again (to the same or maybe even new reviewers), so I ask you to really make an effort in revising the paper.
Apart from the detailed points raised by the reviewers which all need to be very carefully addressed, the manuscript needs a very thorough language revision with regard to spelling, grammar, and style. Without such a revision, ideally by a native speaker or a professional editing service, I will not be able to consider the revision. This includes a careful streamlining of the text - try to avoid redundancies, long sentences and complicated phrasing.
In my pdf annotations, I have also pointed out several issues regarding the analyses and data - partly repeating points raised by the reviewers as well - which should be addressed in your point-by-point reply, too.
That said, I found the paper very interesting in general and would like to stress that with a careful revision, it may definitely become publishable in PeerJ.
I look forward to receiving your revised manuscript!
As reviewer 2 (Anna Phillips) forgot to include a list of the references she mentioned in her review, she sent it to me and include the list here:
Papers mentioned in this review:
Calmaestra, R.G., and Moreno E. 2000. Ecomorphological patterns related to migration: a comparative osteological study with passerines. Journal of Zoology 252:495-501.
Campbell-Tennant, D.J.E., Gardner, J.L., Kearney, M.R., and Symonds, M.R.E. 2015. Climate-related spatial and temporal variation in bill morphology over the past century in Australian parrots. Journal of Biogeography 42:1163-1175.
Dawideit, B.A., Phillimore, A.B., Laube, I., Leisler, B., and Böhning-Gaese, K. 2009. Ecomorphological predictors of natal dispersal distances in birds. Journal of Animal Ecology 78:388-395.
Dehling, D.M., Fritz, S.A., Töpfer, T., Päckert, M., Estler, P., Böhning-Gaese, K., and Schleuning, M. 2014. Functional and phylogenetic diversity and assemblage structure of frugivorous birds along an elevational gradient in the tropical Andes. Ecography 37:1047-1055.
Fitzpatrick, J.W. 1985. Form, foraging behaviour, and adaptive radiation in the Tyrannidae. Ornithological Monographs 36:447-470.
Förschler, M.I., and Barlein, F. 2011. Morphological shifts of the external flight apparatus across the range of a passerine (Northern Wheatear) with diverging migratory behaviour. PLoS ONE 6:e18732.
Grant, P., and Grant, B.R. 2006. Evolution of character displacement in Darwin’s finches. Science 313:224-226.
Jønsson, K.A., Fabre, P.H., Fritz, S.A., Etienne, R.S., Ricklefs, R.E., Jørgensen, T.B., Fjeldså, J., Rahbek, C., Ericson, P.G.P., Woog, F., Pasquet, E., and Irestedt, M. 2012. Ecological and evolutionary determinants for the adaptive radiation of the Madagascan vangas. PNAS 109:6620-6625.
Miller, E.T., Zanne, A.E., and Ricklefs, R.E. 2013. Niche conservatism constrains Australian honeyeater assemblages in stressful environments. Ecology Letters 16:1186-1194.
Phillips, A.G., Töpfer, T., Rahbek, C., Böhning-Gaese, K., and Fritz, S.A. 2018. Effects of phylogeny and geography on ecomorphological traits in passerine bird clades. Journal of Biogeography 00:1-11. https://doi.org/10.1111/jbi.13383
Raposo do Amaral, F., Sheldon, F.H., Gamauf, A., Haring, E., Riesing, M., Silveira, L.F., and Wajntal, A. 2009. Patterns and processes of diversification in a widespread and ecologically diverse avian group, the buteonine hawks (Aves, Accipitridae). Molecular Phylogenetics and Evolution 53: 703-715.
Seeholzer, G., Claramunt, S., and Brumfield, R. 2017. Niche evolution and diversification in a Neotropical radiation of birds (Aves: Furnariidae). Evolution 71:702-715.
Sibly, R.M., Witt, C.C., Wright, N.A., Venditti, C., Jetz, W., and Brown, J.H. 2012 Energetics, lifestyle, and reproduction in birds. PNAS 109:10937-10941.
Winkler, H., and Leisler, B. 1992. On the ecomorphology of migrants. Ibis 134 suppl. 1: 21-28.
The manuscript is mostly clear in its presentation. Which is to say, the literature and background and figures and tables and such are all sufficient and acceptable. The English is pretty rough, though, and has quite a number of problems of subject-verb agreement and other grammatical problems. Which is to say, this manuscript needs a good, thorough editing pass by a native English speaker ... but this should not affect its consideration as a publishable contribution.
I have some major concerns about the design of the analysis... The major concern is the focus on the tyrannids OF MEXICO. That is, this is therefore explicitly a polyphyletic group. It is odd to develop such an analysis of a non-natural group, and there will be many biases and odd effects that will enter, because some of the lineages in the analysis will be lineages that are all included in the Mexican avifauna (e.g., Xenotriccus), and others for which one species has made it to Mexico, but 20 more have not (e.g., Platyrinchus or Zimmerius). I think that this design problem genuinely cripples the analysis, which is otherwise interesting and well executed.
How to fix this? The paper would benefit massively from either doing the hard work of expanding the dataset to a monophyletic group ... e.g., all of the tyrannids, or some major subclade ... which would therefore cross much of the Americas. OR one could pick a subclade that is endemic to some smaller area of analysis. This would reduce the number of species, but one would be analyzing a natural group.
See point 2 above...
The extent of the Los Tuxtlas highland area in Figure 1 is odd ... too extensive, and clearly including much lowland forest.
In Figure 3A, there are several places where a bright yellow dot is on top of a deep purple dot. This spatial coincidence of high and low phylostructure in the same place makes no sense at all.
Line 27-28: The abstract needs to be clear an precise since this is what influences the reader’s decision of whether to read the full article or not. To me the first sentence is not clear enough. The structure suggests that the authors imply that evolutionary history of taxa varies across geography, though based on the remainder of the article they clearly mean morphological variation across geographical space. Since the second sentence also refers to geographic variation of morphology, I would suggest leaving out the second half of the first sentence (“, which in turn also vary in geography”) which will avoid confusion in the readers and generally reduce repetition.
Line 33: to make the point very clear I suggest changing this to “phylogenetic structure of flycatcher assemblages of each locality”
Line 35: This should be “Linear mixed-effects models”
Line 44: traits themselves (bill, wing etc) do not increase. This should be changed to “morphological trait values increased”
Line 59: It would be beneficial to include some more recent work as well to complement Losos & Miles (1994), since these studies are still relevant and more recent work also exists. Furthermore it shows good knowledge of the literature on the side of the authors. E.g. Seeholzer et al. 2017; Phillips et al. 2018; Dehling et al. 2014; Raposo do Amaral et al. 2009
Line 59: “the accumulation of morphological diversity”?
Line 61-63: Suggest rephrasing. Speculation is not needed here: morphological variation is known to reflect species’ responses to biotic and abiotic factors, as traits are closely related to specific ecological niche dimensions such as diet and foraging behaviour (Grant & Grant 2006; Jonsson et al 2012), aerial movement and dispersal distance (Calmaestra & Moreno 2000; Dawideit et al 2009) and bipedal locomotion (Fitzpatrick 1985).
Line 66-68: I would have liked more detail here. How has evolutionary history been shown to influence geographic gradients? How do morphological traits vary with climate? i.e. bill shape and size for temperature regulation (see Campbell-Tennant et al. 2015)
Line 80: I find “morphological traits related to ecology” to be a more accurate description. Lifestyle traits are often more broadly defined and often connected to breeding (e.g. Sibly et al. 2012), whereas in this area of research, wing and bill sizes are often referred to as ecomorphological traits due to their close association with the species’ ecological niche (foraging, aerial movement etc). Perhaps the authors should consider using the term “ecomorphology” here and in other parts of their manuscript.
Line 219: “Brownian evolution” While Brownian motion can be used as a model of trait evolution, there is no such thing as “Brownian evolution”. The authors should keep it precise by writing “evolution following a Brownian motion model” (or similar) and should check the remainder of the manuscript for similar discrepancies (e.g. line 402).
Lines 238-263: In my opinion hypotheses and assumptions generally fit contextually better in the introduction, where an overall hypothesis was originally stated. The methods are in themselves already very long, so the manuscript would benefit from this section being moved to the introduction.
Line 294: “Table S3” does not seem to be the right table (this provides the PC1 factor loadings) I believe this should be Table S4.
Line 379-380: It would be helpful to the reader (this reader) if the text also clarified from which analyses these results are, especially because the explanation of patterns in morphological variation here could be from either the mixed effects models or calculations of phylogenetic signal. I presume, because of the mention of Table 3, that these are results for the mixed-effects models, but it would be good to clarify this in the sentence.
Line 429-445: In my opinion this paragraph is not suited to the discussion. Rather it serves as a justification for why the study is of interest. It would be better placed in the introduction.
Table 2: Important references have been overlooked for wing length: e.g. for locomotion – wing length and shape are very important factors in migration, and many members of the Tyrannidae clade are migratory species. This should not escape mention in this table, as wing shape also directly influences dispersal ability and evasive movements against predators. E.g. Winkler & Leisler 1992, Dawideit et al 2009; Förschler and Barlein 2011. Also, there is a stray bracket in the references for bill variation in this table. I suggest the authors proof read for similar editing errors.
Line 120-121: “Despite the obvious expectation…” I urge the authors to be careful about statements such as this. The statement of an “obvious expectation” will leave readers wondering why the authors would then expect something different. Since this is what the paper is investigating, I suggest the authors rephrase their statement to intrigue the readers as to why this relationship may behave differently than expected.
Line 137-139: A reference to the measuring method used is missing here. Did the authors follow the established techniques described in Eck et al. 2011, or another source? To allow reproducibility of each measurement on the specimens listed such a reference should be included.
Line 155: It is not clear to me why the authors seek to avoid morphological variations associated with sexual dimorphism, especially if as stated, variation between the sexes is lower than variation expected between species (Claramunt 2010). It is common practice to sample both male and females when analysing morphological differences between species, and in my opinion, the dataset would be more robust if these were included in the study. Furthermore, I am also missing details of how many specimens were measured per species. What was the distribution and the average number of specimens measured per species? At the moment these details are only available if they are pried painstakingly from the raw data, whereas they should be mentioned in the methods within the manuscript.
Line 162-164: I am concerned that through the transformation of bill values through a PCA they are no longer comparable with the wing length values which were not transformed with a PCA. My reasoning behind this is because I would assume that these values are no longer within the same scale. I would suggest instead creating a bill index as a single measure of bill shape; e.g. dividing bill height by bill length as a representation of diet and foraging behaviour (where bill height is considered to be one of the most informative variables e.g. Willson 1972; Grant & Grant 2006; Lederer 1975; Jonsson et al. 2012).
Line 176-179: I am not an expert in using climatic data. Do these methods provide enough detail to reproduce this aspect of the study?
Line 186: How were topographic variables related to morphological measurements? In linear regression models? More detail should be provided here…
Lines 232-234: Is there not sufficient occurrence data available for these species on public databases or in published research (e.g. GBIF data or range maps from the literature)? Why did the authors choose to use distributional hypotheses over actual observational data?
Line 277-298: This paragraph contains repetitions which could be removed. Since mixed-effects models are quite complex, the description should be crisp and clear. Shortening the paragraph and keeping statements precise and streamlined should help with this.
Line 453: I am surprised that the study conducted by Miller et al. (2013) is not mentioned here, or in the manuscript in general. It would be an interesting point of discussion considering the authors’ finding that climatic gradients explain variation in morphology, and finding a positive influence of phylogenetic membership in most communities, but with low phylogenetic signal. These results could suggest that these factors may also interact to influence morphological variation in assemblages. i.e. are morphological of more clustered assemblages more restricted in their climatic ranges? Miller et al. find that niche conservatism constrains honeyeater assemblages in arid regions.
Line 523-524: This to me suggests an interaction between temperature seasonality and phylogenetic structure on their influence on morphological variation, where phylogenetic structure modifies the effect of temperature seasonality on the morphological variation within assemblages. Did the authors test for such an interaction? If not, I would suggest that such a test should be done.
The article presents a well thought-out study with established and supported hypotheses and interesting, relevant objectives. In general I see this a publishable study relevant to the aims and scope of the journal. While the methods are presented with a good structure and with a lot of detail, I do have some concerns with some aspects methodology which I have outlined in the experimental design section.
The results have been described in detail and the authors paid attention to aiding the reader with their interpretation.
There were several places in the manuscript where grammar and syntax were incorrect (e.g. lines 76, 103-104, 317, and 384-385). In other areas of the manuscript, the sentences were very long and unnecessarily complicated (e.g. lines 48-51), or repeated aspects mentioned in previous sections (e.g. 302-305, which is described again in the methods of the actual experimental setup, and 277-298). Often these sentences could have been split in two and described a little simpler without a loss of detail. As a result I had trouble following many sentences. I think thorough copyediting and general proofreading is necessary throughout the article to correct grammar and reduce repetitions before resubmission.
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