Fig. S4.

Some chromosome arrangements for a hypothetical diploid genotype with 2n = 12 where eight chromosomes descend from the resident species (blue) and four ($\ell =4$) from the alien species (red). All alien chromosomes may be located on a single strand (A) or occur on the two strands (B and C). The number of ways that alien chromosomes can be positioned within each strand is given by $\left(\begin{array}{c}n\\ \nu \end{array}\right)$ and $\left(\begin{array}{c}n\\ \ell -\nu \end{array}\right)$ for left and right strands, respectively (Eq. S12), and the total number of combinations is the product of these two values. For example, there are 15 different ways to position 4 alien chromosomes on the right strand while having no alien chromosome on the left strand. This arrangement will result in two gamete types (one with no alien chromosomes and one with four) with the equal probability of 0.0208. The inset table provides the probability values for each of the five gamete types (i.e., $\nu \in \left\{0,\dots ,4\right\}$) that can be produced by a diploid genotype with n = 6 and $\ell =4$.