Data from: Detecting evolutionarily significant units above the species level using the Generalized Mixed Yule Coalescent method

1. There is renewed interest in inferring evolutionary history by
modelling diversification rates using phylogenies. Understanding the
performance of the methods used under different scenarios is essential for
assessing empirical results. Recently we introduced a new approach for
analysing broadscale diversity patterns, using the Generalized Mixed Yule
Coalescent (GMYC) method to test for the existence of evolutionarily
significant units above the species (higher ESUs). This approach focuses
on identifying clades as well as estimating rates and we refer to it as
clade-dependent. However, the ability of the GMYC to detect the
phylogenetic signature of higher ESUs has not been fully explored, nor has
it been placed in the context of other, clade-independent approaches. 2.
We simulated >32,000 trees under two clade-independent models:
constant-rate birth-death (CRBD) and variable-rate birth-death (VRBD),
using parameter estimates from nine empirical trees and more general
parameter values. The simulated trees were used to evaluate scenarios
under which GMYC might incorrectly detect the presence of higher ESUs. 3.
The GMYC null model was rejected at a high rate on CRBD-simulated trees.
This would lead to spurious inference of higher ESUs. However, the support
for the GMYC model was significantly greater in most of the empirical
clades than expected under a CRBD process. Simulations with empirically
derived parameter values could therefore be used to exclude CRBD as an
explanation for diversification patterns. In contrast, a VRBD process
could not be ruled out as an alternative explanation for the apparent
signature of hESUs in the empirical clades, based on the GMYC method
alone. Other metrics of tree shape, however, differed notably between the
empirical and VRBD-simulated trees. These metrics could be used in future
to distinguish clade-dependent and clade-independent models. 4. In
conclusion, detection of higher ESUs using the GMYC is robust against some
clade-independent models, as long as simulations are used to evaluate
these alternatives, but not against others. The differences between
clade-dependent and clade-independent processes are biologically
interesting, but most current models focus on the latter. We advocate more
research into clade-dependent models for broad diversity patterns.