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The genomics of coloration provides insights into adaptive evolution

Nature Reviews Genetics volume 21, pages 461–475 (2020)Cite this article

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A Publisher Correction to this article was published on 18 May 2020

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Abstract

Coloration is an easily quantifiable visual trait that has proven to be a highly tractable system for genetic analysis and for studying adaptive evolution. The application of genomic approaches to evolutionary studies of coloration is providing new insight into the genetic architectures underlying colour traits, including the importance of large-effect mutations and supergenes, the role of development in shaping genetic variation and the origins of adaptive variation, which often involves adaptive introgression. Improved knowledge of the genetic basis of traits can facilitate field studies of natural selection and sexual selection, making it possible for strong selection and its influence on the genome to be demonstrated in wild populations.

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Fig. 1: Different ways of making colour.
Fig. 2: Signalling through colour.
Fig. 3: Genetic architecture of colour loci.
Fig. 4: Development can shape evolution.
Fig. 5: An introgressed allele is responsible for the loss of phenotypic plasticity in snowshoe hares.
Fig. 6: Estimating natural selection.

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Acknowledgements

The authors thank everyone at the Butterfly Genetics Group at the University of Cambridge for useful discussion and comments on the manuscript. A.O. was supported by a UK Natural Environment Research Council doctoral training partnership (grant NE/L002507/1) and C.D.J. was supported by a European Research Council (grant 339873 Speciation Genetics) and UK Biotechnology and Biological Sciences Research Council grant BB/R007500/1.

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    Anna Orteu & Chris D. Jiggins

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Glossary

Association studies

Studies that correlate phenotypic variation with genetic variation. The most common methods are genome-wide association studies and quantitative trait locus mapping studies.

Polymorphism

The occurrence of two or more distinct phenotypes or morphs of a species within a population.

Genetic architecture

The genetic basis underlying variation in a phenotypic trait. The main characteristics are the number of loci, their interactions and effect sizes, and their relative positions in the genome.

Quantitative trait loci

Genomic regions at which there is a correlation between genetic variation and phenotypic variation in a trait of interest among individuals from a laboratory-generated cross.

Heterozygote advantage

A scenario in which the heterozygous genotype is fitter than either homozygous genotype.

Transposable element

A genetic element that can move from one position in the genome to another.

cis-regulatory element

(CRE). A genetic region that regulates expression of a coding sequence on the same DNA strand.

Selection coefficient

A measure of the difference in fitness between two genotypes, which are a necessary condition for the action of natural selection.

Negative frequency-dependent selection

An evolutionary process in which the fitness of a genotype or phenotype depends on its frequency in the population relative to other genotypes or phenotypes such that its fitness decreases as its frequency increases.

Purifying selection

The selective removal of deleterious alleles from the population.

Effective population size

The number of individuals in an idealized population that would show the same degree of genetic drift as seen in the real population.

Polygenic inheritance

Also known as polygenicity. The genetic control of a phenotype by multiple genes of small effect.

Genome-wide association study

(GWAS). A study that correlates genetic variation between individuals across the genome with phenotypic variation among those same individuals, typically in a wild population. Associated regions are inferred to contain causal variants controlling phenotypic variation. More generally known as ‘association studies’.

Stabilizing selection

A selective force that maintains the population phenotypic mean and eliminates extreme values.

Convergence

The independent evolution of similar features in different lineages or species.

Pleiotropy

The effect of a single mutation on multiple aspects of the phenotype.

‘Input–output’ genes

Genes that integrate complex spatiotemporal information and trigger alternative developmental outputs.

Phenotypic plasticity

The ability of a single genotype to produce a range of phenotypes depending on the environmental conditions.

Polyphenism

A type of phenotypic plasticity in which a single genotype can produce two or more discrete alternative phenotypes depending on the environmental conditions.

Reaction norms

Patterns of phenotypic expression of a single genotype across differing environmental conditions.

Balancing selection

Selective processes that maintain multiple alleles in a population, such as negative frequency-dependent selection and heterozygote advantage.

Introgression

The transfer of genetic material from one species to another through hybridization.

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Orteu, A., Jiggins, C.D. The genomics of coloration provides insights into adaptive evolution. Nat Rev Genet 21, 461–475 (2020). https://doi.org/10.1038/s41576-020-0234-z

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