Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Opinion
  • Published:

Fish as models for environmental genomics


Fish offer important advantages for defining the organism–environment interface and responses to natural or anthropogenic stressors. Genomic approaches using fish promise increased investigative power, and have already provided insights into the mechanisms that underlie short-term and long-term environmental adaptations. The range of fish species for which genomic resources are available is increasing, but will require significant further expansion for the optimal application of fish environmental genomics.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Variation in gene expression within and between closely related species.
Figure 2: Transcript profiling as a phenotyping tool.
Figure 3: Distribution of fish genomic resources.

Similar content being viewed by others


  1. Gracey, A. Y. & Cossins, A. R. Application of microarray technology in environmental and comparative physiology. Annu. Rev. Physiol. 65, 231–259 (2003).

    Article  CAS  PubMed  Google Scholar 

  2. Randall, D. J., Burggren, W. & French, K. Animal Physiology: Mechanisms and Adaptations (W. H. Freeman, New York, 2002).

    Google Scholar 

  3. Oleksiak, M. F., Kolell, K. J. & Crawford, D. L. The utility of natural populations for microarray analyses: isolation of genes necessary for functional genomic studies. Mar. Biotech. 3, S203–S211 (2001).

    Article  CAS  Google Scholar 

  4. Berenbrink, M., Koldkjaer, P., Kepp, O. & Cossins, A. R. Evolution of complex systems: oxygen secretion in fish. Science 18 March 2005 [epub ahead of print].

  5. Venkatash, B. Evolution and diversity of fish genomes. Curr. Opin. Genet. Dev. 13, 588–592 (2003).

    Article  Google Scholar 

  6. Robinson-Rechavi, M. et al. Euteleost fish genomes are characterised by expansion of gene families. Genome Res. 11, 781–788 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Powers, D. A. Fish as model systems. Science 246, 352–358 (1989).

    Article  CAS  PubMed  Google Scholar 

  8. Kocher, T. D. Adaptive evolution and explosive speciation: the cichlid fish model. Nature Rev. Genet. 5, 288–298 (2004).

    Article  CAS  PubMed  Google Scholar 

  9. Boffelli, D., Nobrega, M. A. & Rubin, E. M. Comparative genomics at the vertebrate extremes. Nature Rev. Genet. 5, 456–465 (2004).

    Article  CAS  PubMed  Google Scholar 

  10. Gracey, A. Y., Troll, J. V. & Somero, G. N. Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Proc. Natl Acad. Sci. USA 98, 1993–1998 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Ton, C., Stamatiou, D. & Liew, C. -C. Gene expression profile of zebrafish exposed to hypoxia during development. Physiol. Genomics 13, 97–106 (2003).

    Article  CAS  PubMed  Google Scholar 

  12. Gracey, A. Y. et al. Coping with cold: an integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc. Natl Acad. Sci. USA. 101, 16970–16975 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Ju, Z., Dunham, R. A. & Liu, Z. Differential gene expression in the brain of channel catfish (Ictalurus punctatus) in response to cold acclimation. Mol. Genet. Genomics 268, 87–95 (2002).

    Article  CAS  PubMed  Google Scholar 

  14. Podrabsky, J. E. & Somero, G. N. Changes in gene expression associated with acclimation to constant temperatures and fluctuating daily temperatures in an annual killifish Austrofundulus limnaeus. J. Exp. Biol. 207, 2237–2254 (2004).

    Article  CAS  PubMed  Google Scholar 

  15. Hochachka, P. W. & Somero, G. N. Biochemical Adaptation (Princeton Univ. Press, New Jersey, 1984).

    Book  Google Scholar 

  16. Somero, G. N. & Hand, S. C. Protein assembly and metabolic regulation: physiological and evolutionary perspectives. Physiol. Zool. 63, 443–471 (1990).

    Article  CAS  Google Scholar 

  17. Pierce, V. A. & Crawford, D. L. Phylogenetic analysis of glycolytic enzyme expression. Science 276, 256–259 (1997).

    Article  CAS  PubMed  Google Scholar 

  18. Oleksiak, M. F., Churchill, G. A. & Crawford, D. L. Variation in gene expression within and among natural populations. Nature Genet. 32, 261–266 (2002).

    Article  CAS  PubMed  Google Scholar 

  19. Schulte, P. M., Glemet, H. C., Fiebig, A. A. & Powers, D. A. Adaptive variation in lactate dehydrogenase-B gene expression: role of a stress-responsive regulatory element. Proc. Natl Acad. Sci. USA 97, 6597–6602 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Williams, T. D., Gensberg, K., Minchin, S. D. & Chipman, J. K. A DNA expression array to detect toxic stress response in European flounder (Platichthys flesus). Aquat. Toxicol. 65, 141–157 (2003).

    Article  CAS  PubMed  Google Scholar 

  21. Oleksiak, M. F., Roach, J. L. & Crawford, D. L. Natural variation in cardiac metabolism and gene expression in Fundulus heteroclitus. Nature Genet. 37, 67–72 (2005).

    Article  CAS  PubMed  Google Scholar 

  22. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y. & Hattori, M. The KEGG resource for deciphering the genome. Nucleic Acids Res. 32, D277–D280 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Shapiro, M. D. et al. Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature 428, 717–723 (2004).

    Article  CAS  PubMed  Google Scholar 

  24. Nacci, D. E., Champlin, D., Coiro, L., McKinney, R. & Jayaraman, S. Predicting the occurrence of genetic adaptation to dioxin-like compounds in populations of the estuarine fish Fundulus heteroclitus. Env. Toxicol. Chem. 21, 1525–1532 (2002).

    Article  CAS  Google Scholar 

  25. Amores, A. et al. Zebrafish hox clusters and vertebrate genome evolution. Science 282, 1711–1714 (1998).

    Article  CAS  PubMed  Google Scholar 

  26. Polley, S. D. et al. Differential expression of cold-specific and diet-specific genes encoding two isoforms of the δ9-acyl-CoA desaturase in carp liver. Am. J. Physiol. 284, R41–R50 (2002).

    Google Scholar 

  27. Force, A. et al. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151, 1531–1545 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Chiang, E. F. L. et al. Two Sox9 genes on duplicated zebrafish chromosomes: expression of similar transcription activators in distinct sites. Dev. Biol. 231, 149–163 (2001).

    Article  CAS  PubMed  Google Scholar 

  29. Zweiger, G. & Scott, R. From expressed sequence tags to 'epigenomics': an understanding of disease processes. Curr. Opin. Biotechnol. 8, 684–687 (1997).

    Article  CAS  PubMed  Google Scholar 

  30. Renn, S. C. P., Aubin-Horth, N. & Hofmann, H. A. Biologically meaningful expression profiling across species using heterologous hybridization to a cDNA microarray. BMC Genomics 5, 42 (2004).

    Article  PubMed  PubMed Central  Google Scholar 

  31. Baum, M. et al. Validation of a novel, fully integrated and flexible microarray benchtop facility for gene expression profiling. Nucleic Acids Res. 31, e151 (2003).

    Article  PubMed  PubMed Central  Google Scholar 

  32. Moore, G., Devos, K. M., Wang, Z. & Gale, M. D. Cereal genome evolution- grasses, line up and form a circle. Curr. Biol. 5, 737–739 (1995).

    Article  CAS  PubMed  Google Scholar 

  33. Gale, M. D. & Devos, K. M. Plant comparative genetics after 10 years. Science 282, 656–659 (1998).

    Article  CAS  PubMed  Google Scholar 

  34. Jaillon, O. et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431, 946–957 (2004).

    Article  PubMed  Google Scholar 

  35. Woolfe, A. et al. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3, e7 (2005).

    Article  PubMed  Google Scholar 

  36. Meyers, B. C., Scalabrin, S. & Morgante, M. Mapping and sequencing complex genomes: let's get physical! Nature Rev. Genetics 5, 578–588 (2004).

    Article  CAS  Google Scholar 

  37. Schuler, G. et al. A gene map of the human genome. Science 274, 540–546 (1996).

    Article  CAS  PubMed  Google Scholar 

  38. Dear, P. H., Bankier, A. T. & Piper, M. B. A high-resolution metric HAPPY map of human chromosome 14. Genomics 48, 232–241 (1998).

    Article  CAS  PubMed  Google Scholar 

  39. Meyer, A. & Schartle, M. Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolutuion of novel gene functions. Curr. Opin. Cell Biol. 11, 699–704 (1999).

    Article  CAS  PubMed  Google Scholar 

  40. Epinat, J. C. et al. A novel engineered meganuclease induces homologous recombination in yeast and mammalian cells. Nucleic Acids Res. 31, 2952–2962 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Fan, L. C., Alestrom, A., Alestrom, P. & Collodi, P. Development of cell cultures with competency for contributing to the zebrafish germ line. Crit. Rev. Eukaryot. Gene Expr. 14, 43–51 (2004).

    Article  PubMed  Google Scholar 

  42. Nasevicius, A. & Ekker, S. C. Effective targeted gene 'knockdown' in zebrafish. Nature Genet. 26, 216–220 (2000).

    Article  CAS  PubMed  Google Scholar 

  43. Gasch, A. P. et al. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11, 4241–4257 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Whitehead, A. & Crawford, D. Variation in tissue-specific gene expression among natural populations. Genome Biology 6, R13 (2005).

    Article  PubMed  PubMed Central  Google Scholar 

  45. Rayl, A. How to create a successful fish tale? Scientist 15, 11–12 (2001).

    Google Scholar 

  46. Clark, M., Crawford, D. L. & Cossins, A. Worldwide genomic resources for non-model fish species. Comp. Func. Genomics 4, 502–508 (2003).

    Article  CAS  Google Scholar 

  47. Snape, J. R., Maund, S. J., Pickford, D. B. & Hutchinson, T. H. Ecotoxicogenomics: the challenge of integrating genomics into aquatic and terrestrial ecotoxicology. Aquat. Toxicol. 14, 143–154 (2004).

    Article  Google Scholar 

  48. Johnston, I. A., Vieira, V. L. A. & Temple, G. K. Functional consequences and population differences in the developmental plasticity of muscle to temperature in Atlantic herring Clupea harengus. Marine Ecol. Prog. Ser. 213, 285–300 (2005).

    Article  Google Scholar 

  49. Nilsson, G. E. & Lutz, P. L. Anoxia tolerant brains. J. Cereb. Blood Flow Metab. 24, 475–486 (2004).

    Article  PubMed  Google Scholar 

  50. Helfman, G., Collette, B. & Facey, B. The Diversity of Fishes (Blackwell Science, Malden, Massachusetts, 1997).

    Google Scholar 

  51. Aparicio, S. et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297, 1301–1310 (2002).

    Article  CAS  PubMed  Google Scholar 

  52. Katagiri, T. et al. Construction and characterization of BAC libraries for three fish species; rainbow trout, carp and tilapia. Anim. Genet. 32, 200–2004 (2001).

    Article  CAS  PubMed  Google Scholar 

  53. Nelson, J. S. Fishes of the world (John Wiley and Sons, New York, 1994).

    Google Scholar 

Download references


We thank M. Berenbrink for helpful discussions and comments and anonymous referees for comments. A.R.C. was supported by long-term funding from the UK Natural Environmental Research Council who also have supported the Liverpool Microarray Facility. D.L.C. was supported by grants from the US National Science Foundation Biocomplexity Programme and the US National Heart Lung and Blood Institute.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Andrew R. Cossins.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Related links

Related links


dbEST — Database of Expressed Sequence Tags


Gene Ontology

KEGG — Kyoto Encyclopedia of Genes and Genomes

Medaka Genome Project

Tetraodon Genome Browser

The Danio rerio Sequencing Project

The Fugu Genomics Project

Zebrafish Gene Collection



The increase in the frequency of a genetic variant in a population to 100%.


A low-copy vector for the construction of stable genomic libraries that uses the Escherichia coli F-factor origin for replication.


A hierarchical organization of concepts and nomenclature for molecular function, biological processes and cellular components. It constitutes a controlled vocabulary with orderly relationships between parent and daughter terms, onto which known genes are mapped, and provides a useful means of categorizing gene lists into functionally meaningful groupings.


(Also known as random drift.) A phenomenon whereby the frequency of a gene in a population changes over time because the number of offspring born to parents that carry the gene is subject to chance variation.


A simple method for ordering markers and determining the physical distances between them. It uses sub-haploid equivalents of randomly sheared DNA and requires the use of whole-genome amplification methods to carry out many PCR reactions.


An organization or 'clustering' of elements that best describes the relationships between them. A tree diagram or dendrogram is frequently used to represent the results of a cluster analysis, with cases of greatest similarity being adjacent to each other.


A family of genes involved in directing the morphological development of the body during early stages of life. In vertebrates they are clustered together on defined chromosomes and are widely believed to have originated by extensive duplication. The order of developmental expression over time is related to the position on the chromosome.


Cells or organisms that are derived from inbreeding or by genetic manipulation, and have identical or almost identical genomes.


A database comprising a collection of graphical pathway maps for metabolism, regulatory processes and other biological processes.


A non-degradable antisense oligonucleotide in which the sugar component is replaced by a morpholine ring structure. Morpholinos are currently used to block target-gene expression in zebrafish, Xenopus laevis and sea urchins. They bind stably to target mRNAs in order to block translation, and give more consistent phenotypes than traditional antisense oligonucleotides.


Variation in protein sequence that is not selectively important.


An evolutionary model that assumes that the selective advantage of the variation in a trait is insufficient to provide any fitness advantage. Changes in allele frequency are said to be the result of chance alone, or 'drift'.


Paralogous genes show homology because they originated as a result of duplication of a single ancestral gene.


(Quantitative trait loci). A genetic locus that is identified through the statistical analysis of quantitative traits (such as height in plants or body weight in animals). These traits are typically affected by more than one gene and also by the environment.


Cells produced by fusing irradiated donor cells that contain chromosomal fragments with recipient rodent cells to produce a panel of cell lines. Each of these cell lines contains fragments of donor chromosomes, which can be used to screen for physical linkage of genetic or physical markers. The resulting maps are indispensable tools for the positional cloning of candidate genes.


The genetic variation or heterozygosity that occurs between individuals in laboratory or natural populations.


Collinearity in the order of genes (or of other DNA sequences) in a chromosomal region of two species.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Cossins, A., Crawford, D. Fish as models for environmental genomics. Nat Rev Genet 6, 324–333 (2005).

Download citation

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing