Journal of Molecular Evolution

, Volume 61, Issue 5, pp 627–635 | Cite as

Genomic Approaches Reveal Unexpected Genetic Divergence Within Ciona intestinalis

  • Miho M. Suzuki
  • Teruaki Nishikawa
  • Adrian Bird


The invertebrate chordate Ciona intestinalis is a widely used model organism in biological research. Individuals from waters ranging from arctic to temperate are morphologically almost indistinguishable. However, we found significant differences in whole genomic DNA sequence between northern European and Pacific C. intestinalis. Intronic and transposon sequences often appear unrelated between these geographic origins and amino acid substitutions in protein coding sequences indicate a divergence time in excess of 20 MYA. This finding suggests the existence of two cryptic species within the present C. intestinalis species. We found five marker loci which distinguish the two genetic forms by PCR. This analysis revealed that specimens from Naples, Italy, have the Pacific-type genome, perhaps due to human-mediated marine transport of species. Despite major genomic divergence, the two forms could be hybridized in the laboratory.


Cionaintestinalis Cryptic species North European specimens Pacific specimens Genetic diversity Genome evolution 



We thank Rosaria De Santis (Stazione Zoologica A. Dohrn, Italy), Michael Thorndyke (Kristineberg Marine Research Station, Sweden), Nori Satoh (Kyoto University, Japan), and members of Craobh Haven (Oban, Scotland) for kindly providing the animals. We are grateful to Aileen Greig for technical assistance. This work was supported by grants from the Japanese Society for the Promotion of Science to M.M.S. and by a Programme Grant from the Wellcome Trust to A.B.


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Copyright information

© Springer Science+Business Media, Inc. 2005

Authors and Affiliations

  • Miho M. Suzuki
    • 1
  • Teruaki Nishikawa
    • 2
  • Adrian Bird
    • 1
  1. 1.The Wellcome Trust Centre for Cell, Biology The University of EdinburghEdinburghUK
  2. 2.The Nagoya University MuseumChikusa-kuJapan

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