Many protein structural domains correspond to distinct exons. Neighboring exons often similar, as a result of internal gene duplications.
If two copies of a gene (or domain) are in close proximity to each other on the genome, then the probability for additional duplication in the region is greatly enhanced.
Suppose we have genes A and B in two different species. If A and B are related to each other via speciation, then they are orthologous. If they are related by duplication then they are paralogous.
Introns early vs Introns late debate. Introns early theory argues that introns were present in ancient genes as linkers between functional protein modules that are the exons. They are lost in prokaryotes. Introns late theory says that introns were integrated into functional genes only after the emergence of endosymbiotic process and eukaryotic cells.