Final answer:
Exon shuffling is thought to occur through homologous recombination, which allows for unequal crossing over of short DNA sequences in introns.
Step-by-step explanation:
Exon shuffling is thought to occur through homologous recombination in which short DNA sequences in two different introns misalign during meiotic synapsis, allowing for unequal crossing over. This leads to the production of a gene with a 'new' exon, resulting in a protein with a new domain and activity.