title: Phase distribution of spliceosomal introns: implications for intron origin.
abstract: BACKGROUND
  The origin of spliceosomal introns is the central subject of the introns-early versus introns-late debate. The distribution of intron phases is non-uniform, with an excess of phase-0 introns. Introns-early explains this by speculating that a fraction of present-day introns were present between minigenes in the progenote and therefore must lie in phase-0. In contrast, introns-late predicts that the nonuniformity of intron phase distribution reflects the nonrandomness of intron insertions.
  
  
  RESULTS
  In this paper, we tested the two theories using analyses of intron phase distribution. We inferred the evolution of intron phase distribution from a dataset of 684 gene orthologs from seven eukaryotes using a maximum likelihood method. We also tested whether the observed intron phase distributions from 10 eukaryotes can be explained by intron insertions on a genome-wide scale. In contrast to the prediction of introns-early, the inferred evolution of intron phase distribution showed that the proportion of phase-0 introns increased over evolution. Consistent with introns-late, the observed intron phase distributions matched those predicted by an intron insertion model quite well.
  
  
  CONCLUSIONS
  Our results strongly support the introns-late hypothesis of the origin of spliceosomal introns.
authors.affiliation: Frontier Science Research Center, University of Miyazaki 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan. ndhung@med.miyazaki-u.ac.jp
authors.forename: Hung D
authors.initials: HD
authors.lastname: Nguyen
authors.forename: Maki
authors.initials: M
authors.lastname: Yoshihama
authors.forename: Naoya
authors.initials: N
authors.lastname: Kenmochi
mesh_terms: D000818:Animals; D003062:Codon / Q000235:genetics*; D005057:Eukaryotic Cells; D019143:Evolution, Molecular; D005658:Fungi / Q000235:genetics; D016678:Genome; D006801:Humans; D007438:Introns / Q000235:genetics*; D007448:Invertebrates / Q000235:genetics; D016013:Likelihood Functions; D008957:Models, Genetic; D016254:Mutagenesis, Insertional; D009154:Mutation; D010944:Plants / Q000235:genetics; D017381:Spliceosomes / Q000235:genetics*; D014714:Vertebrates / Q000235:genetics
chemical_list: D003062:Codon