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Using genomics to characterize evolutionary potential for conservation of wild populations.

Harrisson KA, Pavlova A, Telonis-Scott M, Sunnucks P - Evol Appl (2014)

Bottom Line: Genomics promises exciting advances towards the important conservation goal of maximizing evolutionary potential, notwithstanding associated challenges.For more typical conservations scenarios, we argue that screening genome-wide variation should be a sensible approach that may provide a generalized measure of evolutionary potential that accounts for the contributions of small-effect loci and cryptic variation and is robust to uncertainty about future change and required adaptive response(s).The best conservation outcomes should be achieved when genomic estimates of evolutionary potential are used within an adaptive management framework.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, Monash University Melbourne, Vic., Australia.

ABSTRACT
Genomics promises exciting advances towards the important conservation goal of maximizing evolutionary potential, notwithstanding associated challenges. Here, we explore some of the complexity of adaptation genetics and discuss the strengths and limitations of genomics as a tool for characterizing evolutionary potential in the context of conservation management. Many traits are polygenic and can be strongly influenced by minor differences in regulatory networks and by epigenetic variation not visible in DNA sequence. Much of this critical complexity is difficult to detect using methods commonly used to identify adaptive variation, and this needs appropriate consideration when planning genomic screens, and when basing management decisions on genomic data. When the genomic basis of adaptation and future threats are well understood, it may be appropriate to focus management on particular adaptive traits. For more typical conservations scenarios, we argue that screening genome-wide variation should be a sensible approach that may provide a generalized measure of evolutionary potential that accounts for the contributions of small-effect loci and cryptic variation and is robust to uncertainty about future change and required adaptive response(s). The best conservation outcomes should be achieved when genomic estimates of evolutionary potential are used within an adaptive management framework.

No MeSH data available.


Related in: MedlinePlus

Schematic of the molecular basis of evolutionary potential. (A) The components of evolutionary potential are divided into its epigenetic (i.e. nongenetic inheritance not attributable to DNA sequence) and genetic (i.e. sequence-based) components. (B) Evolutionary potential is further divided into different types of underlying variation based on function. (C) Examples of the different types of variation are listed. (D) Different types of variation differ in their typical individual effect size on phenotype. (E) The typical ability to detect signals of selection differs between methods, as indicated by the shaded bars. Additional information about the methods in (E) can be found in Table1. Signatures of selection on epigenetic variants that are in linkage disequilibrium with sequence-based variations can be indirectly captured by all of these methods.
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fig01: Schematic of the molecular basis of evolutionary potential. (A) The components of evolutionary potential are divided into its epigenetic (i.e. nongenetic inheritance not attributable to DNA sequence) and genetic (i.e. sequence-based) components. (B) Evolutionary potential is further divided into different types of underlying variation based on function. (C) Examples of the different types of variation are listed. (D) Different types of variation differ in their typical individual effect size on phenotype. (E) The typical ability to detect signals of selection differs between methods, as indicated by the shaded bars. Additional information about the methods in (E) can be found in Table1. Signatures of selection on epigenetic variants that are in linkage disequilibrium with sequence-based variations can be indirectly captured by all of these methods.

Mentions: In addition to supplementing the application of traditional quantitative genetic approaches in some conservation scenarios (see Using genomic advances to supplement application of traditional quantitative genetics approaches to conservation below) (Hill 2012), genomics, in as much as it can link genetic variation to adaptively important trait variation, also provides scope for alternative measures of evolutionary potential to be developed. A robust genomic estimator of evolutionary potential would comprise weighted estimates of all adaptive or potentially adaptive genetic (including coding, regulatory and cryptic, see below), and epigenetic, variation. However, determining the genetic changes and epigenetic mechanisms underlying evolution of novel phenotypes and developmental pathways is by far the biggest challenge facing evolutionary biologists (Mackay et al. 2009; Radwan and Babik 2012). There are two major components of evolutionary potential: genetic (DNA-sequence-based) and epigenetic (non-DNA-sequenced-based; Fig.1).


Using genomics to characterize evolutionary potential for conservation of wild populations.

Harrisson KA, Pavlova A, Telonis-Scott M, Sunnucks P - Evol Appl (2014)

Schematic of the molecular basis of evolutionary potential. (A) The components of evolutionary potential are divided into its epigenetic (i.e. nongenetic inheritance not attributable to DNA sequence) and genetic (i.e. sequence-based) components. (B) Evolutionary potential is further divided into different types of underlying variation based on function. (C) Examples of the different types of variation are listed. (D) Different types of variation differ in their typical individual effect size on phenotype. (E) The typical ability to detect signals of selection differs between methods, as indicated by the shaded bars. Additional information about the methods in (E) can be found in Table1. Signatures of selection on epigenetic variants that are in linkage disequilibrium with sequence-based variations can be indirectly captured by all of these methods.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231592&req=5

fig01: Schematic of the molecular basis of evolutionary potential. (A) The components of evolutionary potential are divided into its epigenetic (i.e. nongenetic inheritance not attributable to DNA sequence) and genetic (i.e. sequence-based) components. (B) Evolutionary potential is further divided into different types of underlying variation based on function. (C) Examples of the different types of variation are listed. (D) Different types of variation differ in their typical individual effect size on phenotype. (E) The typical ability to detect signals of selection differs between methods, as indicated by the shaded bars. Additional information about the methods in (E) can be found in Table1. Signatures of selection on epigenetic variants that are in linkage disequilibrium with sequence-based variations can be indirectly captured by all of these methods.
Mentions: In addition to supplementing the application of traditional quantitative genetic approaches in some conservation scenarios (see Using genomic advances to supplement application of traditional quantitative genetics approaches to conservation below) (Hill 2012), genomics, in as much as it can link genetic variation to adaptively important trait variation, also provides scope for alternative measures of evolutionary potential to be developed. A robust genomic estimator of evolutionary potential would comprise weighted estimates of all adaptive or potentially adaptive genetic (including coding, regulatory and cryptic, see below), and epigenetic, variation. However, determining the genetic changes and epigenetic mechanisms underlying evolution of novel phenotypes and developmental pathways is by far the biggest challenge facing evolutionary biologists (Mackay et al. 2009; Radwan and Babik 2012). There are two major components of evolutionary potential: genetic (DNA-sequence-based) and epigenetic (non-DNA-sequenced-based; Fig.1).

Bottom Line: Genomics promises exciting advances towards the important conservation goal of maximizing evolutionary potential, notwithstanding associated challenges.For more typical conservations scenarios, we argue that screening genome-wide variation should be a sensible approach that may provide a generalized measure of evolutionary potential that accounts for the contributions of small-effect loci and cryptic variation and is robust to uncertainty about future change and required adaptive response(s).The best conservation outcomes should be achieved when genomic estimates of evolutionary potential are used within an adaptive management framework.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, Monash University Melbourne, Vic., Australia.

ABSTRACT
Genomics promises exciting advances towards the important conservation goal of maximizing evolutionary potential, notwithstanding associated challenges. Here, we explore some of the complexity of adaptation genetics and discuss the strengths and limitations of genomics as a tool for characterizing evolutionary potential in the context of conservation management. Many traits are polygenic and can be strongly influenced by minor differences in regulatory networks and by epigenetic variation not visible in DNA sequence. Much of this critical complexity is difficult to detect using methods commonly used to identify adaptive variation, and this needs appropriate consideration when planning genomic screens, and when basing management decisions on genomic data. When the genomic basis of adaptation and future threats are well understood, it may be appropriate to focus management on particular adaptive traits. For more typical conservations scenarios, we argue that screening genome-wide variation should be a sensible approach that may provide a generalized measure of evolutionary potential that accounts for the contributions of small-effect loci and cryptic variation and is robust to uncertainty about future change and required adaptive response(s). The best conservation outcomes should be achieved when genomic estimates of evolutionary potential are used within an adaptive management framework.

No MeSH data available.


Related in: MedlinePlus