Program of the 2004 East Coast Worm Meeting - Caenorhabditis ...

33. A New Phylogeny Reveals Frequent Loss of Introns During Nematode Evolution
Ronald E Ellis 1 , Soochin Cho 2
1Department of Molecular Biology, UMDNJ - SOM, Stratford, NJ 08084
2Department of EEB, University of Michigan, Ann Arbor, MI 48109
Since introns were discovered 26 years ago, people have wondered how changes in
intron/exon structure occur, and what role these changes play in evolution. To answer these
questions, we have begun studying gene structure in nematodes related to C. elegans. As a first
step, we cloned a set of five genes from six different Caenorhabditis species, and used their
amino acid sequences to construct a detailed phylogeny of the genus. Our results show that C.
briggsae and C. remanei are sister species, and imply that mating systems have changed
frequently during recent nematode evolution.
Using this phylogeny, and the species C. sp. PS1010 as an outgroup, we were able to
determine which changes in intron/exon structure were caused by the deletion of ancestral
introns, and which were caused by the insertion of new introns. Our results show that nematode
introns are lost at a very high rate during evolution, almost 400-fold higher than in mammals.
These losses do not occur randomly, but instead favor some introns and do not affect others. By
contrast, intron gains are far less common than losses in these genes.
For years, people have focused on recombination between a gene and a cDNA copy of its
transcript as the primary cause of intron loss. However, we found that adjacent introns were not
likely to be lost together, as one might expect from this model, which implies that other
mechanisms are also important. Based on sequence data, we suggest that both simple deletions
and mutations at splice donor sites might play a significant role in causing the loss of introns
during evolution. Furthermore, each of these species has small introns, much like those in C.
elegans. The small size of these introns should increase the rate at which each type of loss
occurs, and could account for the dramatic difference in loss rate between nematodes and
mammals.
Because of the wealth of genomic data that will be generated for these species, we should
soon be able to expand our studies and determine the relative importance of these mechanisms
during evolution.