for publication in Evolution. Following the detailed reviews and suggestions from the Associate Editor Following the detailed reviews and suggestions from the Associate Editor, on our original submission, we have implemented extensive changes and included several additional analyses. We hope that you will agree that this revised version provides a stronger and more robust argument linking h l l l d l d b l b d stochastic population‐level processes, as modeled by neutral biodiversity theory, to the shape of the tree‐of‐life. A detailed response to comments from all reviewers and the Associate p Editor are provided below. Y i l Yours sincerely,
and I think readers of the I found this to be an interesting paper, and I think readers of the journal will find this to be interesting, too. However, there are some analyses that I would like to see clarified and/or included in the manuscript (or in supplementary material).... p ( pp y )
reviewer pulling out the heavy weapons does not necessarily result in manuscript death (or guarantee acceptance). SAVED BY THE EDITOR guarantee acceptance). Dear Dr. Davies: My suggestion is that in revising your MS you focus your efforts primarily on the methodological issues, particularly as highlighted by referee 3.
is, of course, ALWAYS more than could be done, more experiments to be performed, additional variables to consider, and simulations to be run. Key responses include showing a willingness to meet the reviewer’s Key responses include showing a willingness to meet the reviewer’s requests, but do not be afraid to make clear what is unreasonable (or impossible).
i t i th AND t it t d f bli ti The goal is to improve the paper AND get it accepted for publication. If additional experiments are required, make sure they DIRECTLY address the reviewer’s specific criticism(s). For rebuttal arguments, use facts and literature citations to support For rebuttal arguments, use facts and literature citations to support your points, NOT emotion or umbrage. R b th t i d i t d t th Remember that your revised manuscript and your responses to the reviewers’ comments will most likely be sent back to one or more of the original reviewers.
convince the reviewers – not the editor (usually). 2. Repeat all comments in full from the reviewers and provide p p a specific answer to each. 3. Be polite but not sycophantically so. 4 If the reviewer missed something you think is obvious say: 4. If the reviewer missed something you think is obvious say: “I have now made this more clear in the MS.” 5. Make an actual change whenever possible. This gives you more free passes when you can’t make changes.
to explore the influence of tree size. I ask this partly for my own curiosity, but more importantly because of the 'solution' the authors present. If I understand the solution correctly it results in many smaller 'subtrees' being analyzed. If there is any bias due to tree size, the solution itself may be biased. Because we find that K for the thinned trees converges on K for the full tree, our results suggest K is unbiased by tree size. However, to explore this aspect further, we now include additional simulations, estimating K i i t ( t d b th i ) d l d on various size trees (as suggested by the reviewer) randomly pruned from a larger tree of size n = 1000. Supporting our earlier inferences, we find no systematic bias in K with tree size (figure S2).
is the effect of inaccurate or invented branch lengths, a common problem with the sort of analyses that use unresolved trees. We make explicit the scope of our analysis in the first couple of sentences of the Discussion. We did not investigate phylogenetic error in either topology of branch lengths. This is an important area for further research; h d h ll d d h l l however, we predict such error will tend to decrease phylogenetic signal, opposite to the particular bias we focus on here.