Diversity and skepticism are vital for comparative biology: a response to Donoghue and Edwards (2019)

Several objections raised by Donoghue and Edwards (2019) regarding a recent paper of ours (Beaulieu and O'Meara, 2018) provide a good opportunity to discuss the different uses of phylogenies to understand evolutionary history.Are small-scale studies more informative and prone to less error?Or, as we argue, do studies at different scales carry their own benefits and costs?Is ascertainment bias, a term we use to describe how individual clades chosen for study may represent a biased sample of life, a potentially critical problem for macroevolutionary studies?Donoghue and Edwards (2019) recently argued that the ascertainment bias we highlighted is not as problematic as we claimed.In fact, they pointed to our own simulations as evidence, which showed that despite the increased variance, analyses of many smaller, variable subclades produced, on average, reasonable estimated rates of the larger and more inclusive clade.We disagree with their interpretation and expand on the ways ascertainment bias may affect our conclusions about the mode and tempo of evolution, and we also highlight areas where more research is needed.Finally, there is a disagreement over whether it is more informative to understand parameters of a process (e.g., rate of trait evolution) or inferred details of a particular history (e.g., ancestral states).We address these issues in reverse order, as each builds toward the next. MODELS, UNITS, AND NATURAL HISTORYA key difference between Donoghue and Edwards (2019) and our view centers on the value of parameter estimation.For example,