A paper published online in Molecular Biology and Evolution claims to have "rigorous proof that [junk DNA was] added to DNA 'late' in the evolution of life on earth--after the formation of modern-sized genes, which contain instructions for making proteins" according to a press release from the National Institute of Standards and Technology, whose Center for Advanced Research in Biotechnology (CARB) was involved with the research (link)
The press release states:
Research from the CARB group appears to resolve a debate over the "early versus late" timing of the appearance of introns. Since introns were discovered in 1978, scientists have debated whether genes were born split (the "introns-early" view), or whether they became split after eukaryotic cells (the ones that gave rise to animals and their relatives) diverged from bacteria roughly 2 billion years ago (the "introns-late" view). Bacterial genomes lack introns. Although the study did not attempt to propose a function for introns, or determine whether they are beneficial or harmful, the results appear to rule out the "introns-early" view.
The CARB analysis shows that the probability of a modern intron's presence in an ancestral gene common to the genes studied is roughly 1 percent, indicating that the vast majority of today's introns appeared subsequent to the origin of the genes. This conclusion is supported by the findings regarding placement patterns for introns within genes. It long has been observed that, in the sequences of nitrogen-containing compounds that make up our DNA genomes, introns prefer some sites more than others. The CARB study indicates that these preferences are side effects of late-stage intron gain, rather than side effects of intron-mediated gene formation.
Ref: Wei-Gang Qiu, Nick Schisler, and Arlin Stoltzfus, "The Evolutionary Gain of Spliceosomal Introns: Sequence and Phase Preferences" MBE Advance Access published March 10, 2004, 10.1093/molbev/msh120