The evolutionary landscape of alternative splicing in vertebrate species

Science. 2012 Dec 21;338(6114):1587-93. doi: 10.1126/science.1230612.


How species with similar repertoires of protein-coding genes differ so markedly at the phenotypic level is poorly understood. By comparing organ transcriptomes from vertebrate species spanning ~350 million years of evolution, we observed significant differences in alternative splicing complexity between vertebrate lineages, with the highest complexity in primates. Within 6 million years, the splicing profiles of physiologically equivalent organs diverged such that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are cis-directed. However, a subset of pronounced splicing changes are predicted to remodel protein interactions involving trans-acting regulators. These events likely further contributed to the diversification of splicing and other transcriptomic changes that underlie phenotypic differences among vertebrate species.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing*
  • Animals
  • Biological Evolution
  • Chickens / genetics
  • Evolution, Molecular*
  • Exons
  • Introns
  • Lizards / genetics
  • Mice / genetics
  • Mice, Inbred C57BL / genetics
  • Opossums / genetics
  • Phenotype
  • Platypus / genetics
  • Primates / genetics
  • RNA Splice Sites
  • Regulatory Sequences, Ribonucleic Acid
  • Species Specificity
  • Transcriptome*
  • Vertebrates / genetics*
  • Xenopus / genetics


  • RNA Splice Sites
  • Regulatory Sequences, Ribonucleic Acid

Associated data

  • GEO/GSE30352
  • GEO/GSE41338