Anthropogenic activities have increased the rate of biological extinction many-fold. Recent empirical studies suggest that projected extinction may lead to extensive loss to the Tree of Life, much more than if extinction were random. One suggested cause is that extinction risk is heritable (phylogenetically patterned), such that entire higher groups will be lost. We show here with simulation that phylogenetically clustered extinction risks are necessary but not sufficient for the extensive loss of phylogenetic diversity (PD) compared to random extinction. We simulated Yule trees and evolved extinction risks at various levels of heritability (measured using Pagel's ). At most levels of heritability ( in range of 0 to 10), mean values of extinction risk (range 0.25 to 0.75), tree sizes (64 to 128 tips), tree balance and temporal heterogeneity of diversification rates (Yule and coalescent trees), extinction risks do not substantially increase the loss of PD in these trees when compared to random extinction. The maximum loss of PD (20% above random) was only associated with the combination of extremely excessive values of phylogenetic signal, high mean species' extinction probabilities, and extreme (coalescent) tree shapes. Interestingly, we also observed a decline in the rate of increase in the loss of PD at high phylogenetic clustering of extinction risks. Our results suggest that the interplay between various aspects of tree shape and a predisposition of higher extinction risks in species-poor clades is required to explain the substantial pruning of the Tree of Life.