Rates of intron loss and gain: implications for early eukaryotic evolution

Abstract

We study the intron-exon structures of 684 groups of orthologs from seven diverse eukaryotic genomes and provide maximum likelihood estimates for rates and numbers of intron losses and gains in these same genes for a variety of lineages. Rates of intron loss vary from approximately 2 x 10(-9) to 2 x 10(-10) per year. Rates of gain vary from 6 x 10(-13) to 4 x 10(-12) per possible intron insertion site per year. There is an inverse correspondence between rates of intron loss and gain, leading to a 20-fold variation among lineages in the ratio of the rates of the two processes. The observed rates of intron gain are insufficient to explain the large number of introns estimated to have been present in the plant-animal ancestor, suggesting that introns present in early eukaryotes may have been created by a fundamentally different process than more recently gained introns.

Fig. 1.

General phylogenies for demonstrating the method. (A) External branch. (B) Internal branch. Arrows indicate the branches analyzed.

Fig. 2.

A Dollo parsimony reconstruction of the data for comparison with our results.

Fig. 3.

MLE of the numbers of intron losses and gains for 684 groups of orthologs. Number of introns present in modern species or previously estimated present in ancestors (50) are given in black. MLE of the number of intron losses and gains along each branch are given in blue and red, respectively. Blue branches are inferred to have experienced >1.5 losses per gain; red branches >1.5 gains per loss. (A) Initial estimates, excluding introns that are gained and subsequently lost along the same branch. (B) Final results, correcting for introns that are gained and subsequently lost along the same branch. The estimate of the number of introns present in the studied regions in the Plasmodium crown ancestor is derived assuming that the deepest branches had an average rate of loss (see Discussion).