| The intron-exon structure of eukaryotic genes has been intensely studied for three decades, yet fundamental questions remain: (1) when and how did introns first arise? (2) how are introns gained and lost? (3) what were the roles of selection, population size, and drift in establishing current gene structures. I compare intron-exon structures of eukaryotic orthologs and provide partial answers to these questions. I find that very old eukaryotic ancestors were intron-rich, and that most modern introns are very old, dating back hundreds of millions of years. More recent evolution has been characterized by general and often dramatic reduction in intron number. Rates of intron gain and loss, as well as the ratio of the two processes, vary considerably between lineages. These rates are insufficient to explain the large number of introns present in very deep eukarotic ancestors, suggesting that early eukaryotes experienced a massive intron invasion of a scale not since seen. Introns appear to be lost via gene conversion by reverse transcriptase products of spliced mRNA transcripts; the mechanism of intron gain is much less certain, with recently gained Drosophila and Caenorhabditis introns showing opposite signatures. Proposed models of intron invasion in response to recent decreases in population size are analyzed and found to be inadequate. In addition, I develop a phylogenetic method utilizing intron position conservation and find that intron conservation in metazoans and plants supports the ecdysozoa grouping. |
