What affects power to estimate speciation rate shifts?

The
development of methods to estimate rates of speciation and extinction
from time-calibrated phylogenies has revolutionized evolutionary
biology by allowing researchers to correlate diversification rate
shifts with causal factors. A growing number of researchers are
interested in testing whether the evolution of a trait or a trait
variant has influenced speciation rates, and three modelling methods
– BiSSE, MEDUSA
and BAMM
– have been widely used in such studies. We simulated phylogenies
with a single speciation rate shift each, and evaluated the power of
the three methods to detect these shifts. We varied the degree of
increase in speciation rate (rate asymmetry), the number of tips, the
tip-ratio bias (ratio of number
of tips
with
each
character state) and the relative age in relation to overall tree age
when the rate shift occurred. All methods had good power to detect
rate shifts when the rate asymmetry was strong and the sizes
of the two lineages with the distinct speciation rates were
large. Even when lineage size was small, power was good
when
rate
asymmetry was
high.
In our simulated scenarios, small lineage sizes appear to affect BAMM
most strongly. Tip-ratio bias
influenced
the accuracy of speciation rate estimation but did not have a strong
effect on power to detect rate shifts. Based on our results, we
provide some suggestions to users of these methods.