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Detecting genetic responses to environmental change

Key Points

  • Neutral genetic markers can be used to monitor environmental change if populations undergo drastic reductions in size and interruptions in gene flow with other populations.

  • Several attempts to monitor pollution stress with neutral markers have failed, yet serial sampling and new methods of analysis are likely to increase the power of neutral markers to detect populations under stress.

  • Adaptive genetic markers can be identified with various techniques including microarrays, QTL mapping, biochemical studies leading to candidate genes, and genome scans. QTL approaches in particular are improving rapidly to provide faster ways of identifying candidate genes.

  • Microarray approaches can provide powerful ways of identifying candidate pathways and genes when combined with comparisons of naturally or artificially diverged populations.

  • Allelic changes in adaptive markers have been linked to a variety of environmental stresses, including climate change and chemical toxicants.

  • The types of genes and processes involved in adaptive responses overlap across species because of common mechanisms, restricted sets of genetic options for dealing with particular stresses and constraints on evolutionary pathways.

  • DNA decay in candidate genes could be used to rapidly assess the adaptive potential of species to particular types of stresses. Decay is likely to reflect species with little adaptive potential and indicate evolutionary constraints.

Abstract

Changes in environmental conditions can rapidly shift allele frequencies in populations of species with relatively short generation times. Frequency shifts might be detectable in neutral genetic markers when stressful conditions cause a population decline. However, frequency shifts that are diagnostic of specific conditions depend on isolating sets of genes that are involved in adaptive responses. Shifts at candidate loci underlying adaptive responses and DNA regions that control their expression have now been linked to evolutionary responses to pollution, global warming and other changes. Conversely, adaptive constraints, particularly in physiological traits, are recognized through DNA decay in candidate genes. These approaches help researchers and conservation managers understand the power and constraints of evolution.

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Figure 1: Relation between population size and genetic variation.
Figure 2: Evolution at a candidate locus depending on its effect and genetic background.

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Acknowledgements

We are grateful for discussions with M. Blows, G. Broggini, L. Harshman, V. Kellermann, C. Sgrò, J. Van Buskirk and B. van Heerwaarden during the preparation of this Review. We would also like to thank three anonymous reviewers for comments on the manuscript. This work was undertaken while A.A.H. held a Federation Fellowship from the Australian Research Council. The work was supported by the Swiss National Science Foundation (Grant 3100A0-116270 to Y.W.), and a Commonwealth Environment Research Facilities Significant Project Grant.

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Glossary

Plastic change

A change in phenotypic expression, but not in the genotype, because of environmental change.

Inbreeding depression

A decline in fitness owing to inbreeding that is caused by the expression of (deleterious) alleles in the homozygote state.

Neutral genetic marker

A sequence of DNA that is polymorphic within a population or a species and that is not under selection (for example, a microsatellite).

Gene flow

The exchange of genes between populations that is caused by the dispersal of propagules or individuals.

Clinal

Referring to a gradual change along a geographic axis in allele frequencies or phenotypes.

Effective population size

The size of the population that contributes to the next generation — it determines the importance of genetic drift and the amount of inbreeding.

Microsatellite marker

A non-coding section of DNA consisting of short repeats of 1–4 nucleotides.

Coalescent method

A method of reconstructing population history by simulating the genealogy of genes back to the most recent common ancestor of all alleles currently in the population.

Likelihood method

The estimation of an unknown parameter based on its likelihood of producing the observed data (for example, population size is estimated based on a change in heterozygosity).

Approximate Bayesian computation method

A method that compares summary statistics calculated from the data with those produced by a simulation model in which parameters are drawn at random.

Moment-based method

An approach in which the 'true' population parameters are equated to parameters obtained from observed samples (mean, variance and so on).

cDNA-amplified fragment length polymorphism (cDNA-AFLP) expression profiling

A fingerprinting method that allows the genome-wide analysis of expression in any species without the need for prior sequence information. The mRNA of an organism is reverse transcribed to cDNA, then cut and fused with small adaptor sequences. The amount of adaptor represents the expression levels of the gene attached to it.

Selective sweep

A reduction in genetic variation in DNA that surrounds a locus that is under strong directional selection.

Directional selection

Natural selection that favours phenotypes or genotypes on one side of a distribution.

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Hoffmann, A., Willi, Y. Detecting genetic responses to environmental change. Nat Rev Genet 9, 421–432 (2008). https://doi.org/10.1038/nrg2339

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