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Adaptive evolution and explosive speciation: the cichlid fish model

Nature Reviews Genetics volume 5, pages 288298 (2004) | Download Citation



The cost of DNA sequencing continues to fall, which makes it feasible to develop genomic resources for new model species that are well suited for studying questions in evolutionary biology. The thousands of closely related cichlid fishes in the lakes of East Africa are an ideal model system for understanding the genetic basis of vertebrate speciation. Genomic techniques are helping to integrate empirical and theoretical studies by identifying the genes that underlie the phenotypic differences among species.

Key points

  • The spectacular radiation of 2,000 species of cichlid fishes in East Africa is an ideal model system and natural laboratory for studying evolutionary processes.

  • The explosive speciation of cichlids is probably due to a combination of forces, including natural selection on ecological traits, sexual selection on male colour patterns, and possibly genetic conflicts over the sex ratio.

  • Genomic approaches promise to unify theoretical and empirical studies by identifying the genes that are responsible for adaptive differences.

  • An array of genomic resources has been developed for cichlids, including genetic and physical maps, and microarrays of expressed sequences.

  • Quantitative trait mapping is identifying the genetic basis for differences in jaw and tooth shape among species.

  • Orange-blotch, a sex-linked intraspecific colour polymorphism that features in several models of speciation, is due to a single dominant gene in a Lake Malawi cichlid.

  • Marked variation in visual spectral sensitivity among species is due to differences in the expression of the opsin genes.

  • The development of new model systems for the study of evolution and speciation is now practical, and will provide another window on the function of vertebrate genes.

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I thank R.C. Albertson, K. Carleton, M. Kidd, O. Seehausen, J.T. Streelman and the anonymous reviewers for helpful discussions and comments. My work on cichlid fishes has been supported by the US National Science Foundation and the US Department of Agriculture.

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  1. Hubbard Center for Genome Studies, University of New Hampshire, Suite 400, Environmental Technology Building, 35 Colovos Road, Durham, New Hampshire 03824, USA.

    • Thomas D. Kocher


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The author declares no competing financial interests.



Where an allele is favoured in one sex and selected against in another.


Speciation that involves the differentiation of geographically separate populations.


Selection among individuals of one sex that is exerted through competition for mates, or the mating preferences of the opposite sex.


The evolutionary relationships of a group of organisms, which are often depicted as a tree diagram.


The morphological characteristics of an animal that relate to its intake of food.


(LD). A measure of genetic associations between alleles at different loci, which indicates whether certain allelic combinations are more common than expected.


A process of runaway evolution of male traits and female mating preferences under sexual selection, which Ronald A. Fisher is credited with recognizing.


The tendency for co-existing species to differ in their niche requirements.


An opening in the egg capsule through which spermatozoa enter.


The entry of several sperm into one egg.


Genes in host organelles such as mitochondria, or in intracellular parasites such as Wolbachia, that are typically passed from mother to offspring through the cytoplasm.


The preferential transmission of one gamete genotype over another genotype, in which the genotypes in question might derive from the same meiosis.


The persistent differential methylation of parental genes that results in the expression of the allele from only one parent in the offspring.


Conservation of the linkage relationship among genes between two species.


The analysis of single-nucleotide-polymorphism alleles in population-based studies to identify loci that are associated with a particular phenotype.


An approach to gene mapping that looks for associations between a particular phenotype and allelic variation.


The genealogical history of alleles within a population.

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