3) It might also be interesting to run an example of
a “non-standard” tree prior which we think might be empirically
relevant (e.g. diversity dependence). The authors mention this but I felt
that using a tree prior (which by the way does resemble diversity
dependence - or at least a decrease in speciation- given that most splits
are concentrated in the base of the tree) that is unknown might not be the
best narrative choice. As mentioned by the authors in the
introduction “Only new diversification models that result in a large
discrepancy between inferred and simulated phylogenies will be worth the
effort and computational burden to implement a species tree prior for in a
Bayesian framework.” In real life the utility of pirouete will be
associated with the “non-standard” tree priors from which we suspect (and
hence know them) might affect our inferences. Hence illustrating its
utility with an already “known” “non-standard” tree prior might be more
effective.
We agree. We rewrote the initial non-standard tree to resemble a
diversity-dependent tree, with a strong decrease in speciation rates.
[...]
[ ] Describe DD in text, with reference to Etienne and Haegeman, 2012
We agree. We rewrote the initial non-standard tree to resemble a diversity-dependent tree, with a strong decrease in speciation rates.