  An early burst of speciation followed by a subsequent slowdown in the rate of
diversification is commonly inferred from molecular phylogenies. This pattern
is consistent with some verbal theory of ecological opportunity and adaptive
radiations. One often-overlooked source of bias in these studies is that of
sampling at the level of whole clades, as researchers tend to choose large,
speciose clades to study. In this paper, we investigate the performance of
common methods across the distribution of clade sizes that can be generated by
a constant-rate birth-death process. Clades which are larger than expected for
a given constant-rate branching process tend to show a pattern of an early
burst even when both speciation and extinction rates are constant through time.
All methods evaluated were susceptible to detecting this false signature when
extinction was low. Under moderate extinction, both the gamma-statistic and
diversity-dependent models did not detect such a slowdown but only because the
signature of a slowdown was masked by subsequent extinction. Some models which
estimate time-varying speciation rates are able to detect early bursts under
higher extinction rates, but are extremely prone to sampling bias. We suggest
that examining clades in isolation may result in spurious inferences that rates
of diversification have changed through time.
