Here today, gone tomorrow: How humans lost their body hair uofuhealthcare elife
. Your article has been reviewed by 3 peer reviewers, and the evaluation has been overseen by a Reviewing Editor and Molly Przeworski as the Senior Editor. The following individual involved in the review of your submission has agreed to reveal their identity: Peter H Sudmant .
– It would seem that relaxed selection following hair reduction could eventually result in the total absence of a gene or CNE in the dataset. Can RERconverge handle gene or CNE deletions, and would these events be detected in the current approach? 3) It is not clear if/how branch lengths are taken into account. It seems that short branches would be noisier compared to long branches. Of course, this might be the opposite for a a rapidly evolving region, if long branches are more saturated with changes. Does branch length need to be taken into account? Or does it make a difference?
We have incorporated these analyses – please see the response to Reviewer #3’s point for details. See response to Reviewer #3’s point here: 2) The numerous points raised by all three reviewers about clarity in your presentation of methods and results of the manuscript. Considering CNE deletions would likely be a fruitful avenue to find gains and losses associated with hairlessness and other convergent phenotypes. However, this is challenging due to uncertainty about the source of missing sequence and lack of standard likelihood models for indels. We believe addressing these challenges is beyond the scope of this paper.
For noncoding regions, the dearth of data is even more notable. We would need to have tissue- and timepoint-specific regulatory activity across many hairy and hairless species to fully understand the regulatory machinery underlying the phenotype. “In fact, over half of our top genes from show evidence of pseudogenization, and therefore are defunctionalized, in one or more hairless species .”1) Is the word"permulation" necessary? The overall analysis is a permutation, as the goal is to permute the hairless phenotype across the species set. My understanding is that the Brownian simulation is only to account for phylogenetic relationships.
3) It is not clear if/how branch lengths are taken into account. It seems that short branches would be noisier compared to long branches. Of course, this might be the opposite for a a rapidly evolving region, if long branches are more saturated with changes. Does branch length need to be taken into account? Or does it make a difference?
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