Harnessing genomics for delineating conservation units

doi:10.1016/j.tree.2012.05.012

Trends in Ecology & Evolution

Volume 27, Issue 9, September 2012, Pages 489-496

https://doi.org/10.1016/j.tree.2012.05.012 Get rights and content

Genomic data have the potential to revolutionize the delineation of conservation units (CUs) by allowing the detection of adaptive genetic variation, which is otherwise difficult for rare, endangered species. In contrast to previous recommendations, we propose that the use of neutral versus adaptive markers should not be viewed as alternatives. Rather, neutral and adaptive markers provide different types of information that should be combined to make optimal management decisions. Genetic patterns at neutral markers reflect the interaction of gene flow and genetic drift that affects genome-wide variation within and among populations. This population genetic structure is what natural selection operates on to cause adaptive divergence. Here, we provide a new framework to integrate data on neutral and adaptive markers to protect biodiversity.

Section snippets

New tools for an old problem: delineating conservation units using genomic data

The rapid increase in the availability of genomic data (see Glossary) is quickly transforming how long-standing questions are addressed and answered in evolution 1, 2, 3, 4, ecology [5], and now conservation 6, 7, 8. Genomics has the potential to revolutionize understanding of adaptive differentiation and the delineation of CUs within species 7, 9. In particular, next-generation sequencing makes it easier to integrate information from neutral and adaptive loci to characterize CUs and adaptive

When should genomics be used to define CUs?

Before using genomic data to define CUs, the first consideration is whether a population genomic approach should be used as opposed to a more standard approach such as a population genetic analysis using microsatellite loci. We argue that genomic data will usually be better than microsatellite data for delineating CUs, as genomic data allow quantification of adaptive variation. Microsatellite data can be used to define ESUs and MUs, but are generally inadequate for characterizing adaptive

Premises of new genomic framework

Based on the above considerations, we developed a new framework for delineating CUs and quantifying adaptive differences among them (Box 3). Our framework is based on two premises. First, different classes of marker should be used for delineating ESUs versus MUs. Second, there may be important adaptive differences among ESUs and MUs that should be tested for and quantified using loci under divergent selection. Below, we describe each of these points in more detail.

The first premise of our new

Future directions

Many outstanding questions need to be answered to learn how best to take advantage of the power of genomic data to delineate CUs and characterize adaptive differentiation among them. Chief among these are: which analyses are most appropriate and effective for testing for adaptive differentiation using outlier loci? How many SNP loci are needed to delineate different CUs accurately and characterize spatial patterns of adaptation? When will incorporating genomic data change delineation of CUs or

Acknowledgments

We thank P. Craze, G. Luikart, J.M. Robertson, D.A. Tallmon, R.S. Waples and three anonymous reviewers for providing helpful suggestions that greatly improved this paper. This research was supported by NSF grants DEB 1046408 and DEB 1146489 to W.C.F., DEB 1022196 to J.K.M., and DEB 0742181 to F.W.A. P.A.H. received support from NIH/NCRR grant P20RR16448 to L. Forney.

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Trends in Ecology & Evolution

OpinionHarnessing genomics for delineating conservation units

Section snippets

New tools for an old problem: delineating conservation units using genomic data

When should genomics be used to define CUs?

Premises of new genomic framework

Future directions

Acknowledgments

Trends Ecol. Evol.

Trends Ecol. Evol.

Trends Ecol. Evol.

Trends Ecol. Evol.

Trends Ecol. Evol.

Biol. Conserv.

Trends Ecol. Evol.

Trends Ecol. Evol.

Trends Ecol. Evol.

Trends Ecol. Evol.

Trends Ecol. Evol.

Curr. Biol.

Trends Ecol. Evol.

A guide to the genomics of ecological speciation in natural animal populations

Ecol. Lett.

Genomics and the future of conservation genetics

Nat. Rev. Genet.

Genetics and the Conservation of Populations

Adaptive evolutionary conservation: towards a unified concept for defining conservation units

Mol. Ecol. 10

Pacific salmon, Oncorhynchus spp., and the definition of ‘species’ under the Endangered Species Act

Mar. Fish. Rev.

Metapopulation Biology: Ecology, Genetics, and Evolution

Adaptive vs. neutral genetic diversity: implications for landscape genetics

Landsc. Ecol.

The gap between the concept and definitions in the Evolutionarily Significant Unit: the need to integrate neutral genetic variation and adaptive variation

Ecol. Res.

Conservation units and translocations: strategies for conserving evolutionary processes

Hereditas

Predicting the probability of outbreeding depression

Conserv. Biol.

Field guide to next-generation DNA sequencers

Mol. Ecol. Resour.

Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout

Mol. Ecol. Resour.

RAD in the realm of next-generation sequencing technologies

Mol. Ecol.

The impact of predation on life-history evolution in Trinidadian guppies (Poecilia reticulata)

Evolution

Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags

PLoS Genet.

Maintenance of genetic variability under joint effect of mutation, selection and random drift

Genetics

A mathematical theory of natural and artificial selection. VI. Isolation

Proc. Camb. Philos. Soc.

Evolution in Mendelian populations

Genetics

Gene flow in natural populations

Annu. Rev. Ecol. Syst.

Variation in resistance and virulence in the interaction between Arabidopsis thaliana and a bacterial pathogen

Evolution

Local adaptation, patterns of selection, and gene flow in the Californian serpentine sunflower (Helianthus exilis)

Evolution

The power and promise of population genomics: from genotyping to genome typing

Nat. Rev. Genet.

Opinion
Harnessing genomics for delineating conservation units