We consider a Yule process until the total population reaches size $n\gg 1$, and assume that neutral mutations occur with high probability $1-p$ (in the sense that each child is a new mutant with probability $1-p$, independently of the other children), where $p=p_n\ll 1$. We establish a general strategy for obtaining Poisson limit laws for the number of subpopulations exceeding a given size and apply this to some mutation regimes of particular interest. Finally, we give an application to subcritical Bernoulli bond percolation on random recursive trees with percolation parameter $p_n$ tending to zero.