We read this paper in my Eukaryotic Genomes class (more than 10 years ago…sigh). The paper suggests that you need to be proactive about getting rid of pseudogenes and transposable elements if you want to keep your genome small:
High intrinsic rate of DNA loss in Drosophila
DMITRI A. PETROV, ELENA R. LOZOVSKAYA & DANIEL L. HARTL
Nature 384, 346 – 349 (28 November 1996)
Differences in deletion rate may also contribute to the divergence in genome size among taxa, the so-called ‘C-value paradox’. Two reports find a positive correlation between genome size and intron size in a variety of taxa. In addition, the reduction in the intron size in birds, whose genome size is smaller than that of other tetrapods, has been inferred to be due to multiple separate deletions scattered along the introns. It is noteworthy that pseudogenes are much rarer in birds than in mammals. These results argue that differences in genome size among related organisms may be determined primarily by the variation in the genome-wide deletion rate, and not, for instance, by different rates of insertion of transposable elements.