84
M.S. Clark et al.
in a network involved in the physiological regulation of genes that led to the
expression of this phenotype at the individual or population levels (Feder 2007,
see also Crawford and Oleksiak 2007, Marden 2008). Some authors bring together
population and functional genomics to define environmental/ecological genomics
(e.g. Ungerer et al. 2008), whereas others define ecological genomics as a distinct
field (e.g. Wilson et al. 2005). We do not disagree with these different approaches
and it is clear that genomics sensu lato profoundly influences current biology. Here
we describe the use of the conceptual frameworks of population and/or quantitative genetics that have the potential for identifying and studying the genetic basis
of those traits affecting fitness that are key to natural selection (e.g. Ellegren and
Sheldon 2008). Such research is now commonplace in model species, and is increasingly used to study fundamental questions in ecology, phenotypic plasticity and
gene-environment interactions (reviewed in, e.g., Morin et al. 2004, Nielsen 2005).
Among the promising fields derived from population genomics is the understanding of complex evolutionary processes like patterns and rates of adaptation.
By examining large portions of the genome, population genomics can theoretically
disentangle locus specific-effects such as recombination, selection, epistatic interactions etc. that affect one or a few loci, from genome-wide effects affecting the
whole genome (bottlenecks, founder events, inbreeding). (e.g. Mitchell-Olds et al.
2007, Stinchcombe and Hoekstra 2008, Ellegren and Sheldon 2008). Some selective
processes may also act on the whole genome as a result of the long-term adaptation
of organisms over the course of evolution (i.e. thermal or pressure effects on protein
stability). Population genomics can be used to address ecological and environmental
issues such as biodiversity studies and marine ecosystems surveys with applications
to fisheries, monitoring of invasive species or design of Marine Protected Areas
(MPAs). They also offer great promise to address the phenomenon of trade-offs
that are expressed at the phenotypic level and dependent on the modulation of gene
expression and molecular processes (Roff 2007).
3.2.1 Analysis: Choices, Limitations and Considerations
3.2.1.1 Marker Type
The use of several genetic marker types including SNPs on the analysis of genetic
data and estimation of population parameters has been reviewed by Vasemägi and
Primmer (2005) and Ryynanen et al. (2007). The study of Vasemägi et al. (2005)
on Atlantic salmon can be used to illustrate issues about changes in heterozygosity, allele diversity, levels of population differentiation across sets of genetic
markers, and number of loci potentially under selection. They identified genetic signatures of divergent selection by screening 95 genomic and 78 EST derived miniand microsatellites for populations inhabiting contrasting natural environments
(salt, brackish, and freshwater habitats). They detected no significant variations in
heterozygosity, allele diversity or levels of population differentiation across anonymous or EST-SSRs loci when looking at all the populations surveyed as a whole.
M.S. Clark et al.
in a network involved in the physiological regulation of genes that led to the
expression of this phenotype at the individual or population levels (Feder 2007,
see also Crawford and Oleksiak 2007, Marden 2008). Some authors bring together
population and functional genomics to define environmental/ecological genomics
(e.g. Ungerer et al. 2008), whereas others define ecological genomics as a distinct
field (e.g. Wilson et al. 2005). We do not disagree with these different approaches
and it is clear that genomics sensu lato profoundly influences current biology. Here
we describe the use of the conceptual frameworks of population and/or quantitative genetics that have the potential for identifying and studying the genetic basis
of those traits affecting fitness that are key to natural selection (e.g. Ellegren and
Sheldon 2008). Such research is now commonplace in model species, and is increasingly used to study fundamental questions in ecology, phenotypic plasticity and
gene-environment interactions (reviewed in, e.g., Morin et al. 2004, Nielsen 2005).
Among the promising fields derived from population genomics is the understanding of complex evolutionary processes like patterns and rates of adaptation.
By examining large portions of the genome, population genomics can theoretically
disentangle locus specific-effects such as recombination, selection, epistatic interactions etc. that affect one or a few loci, from genome-wide effects affecting the
whole genome (bottlenecks, founder events, inbreeding). (e.g. Mitchell-Olds et al.
2007, Stinchcombe and Hoekstra 2008, Ellegren and Sheldon 2008). Some selective
processes may also act on the whole genome as a result of the long-term adaptation
of organisms over the course of evolution (i.e. thermal or pressure effects on protein
stability). Population genomics can be used to address ecological and environmental
issues such as biodiversity studies and marine ecosystems surveys with applications
to fisheries, monitoring of invasive species or design of Marine Protected Areas
(MPAs). They also offer great promise to address the phenomenon of trade-offs
that are expressed at the phenotypic level and dependent on the modulation of gene
expression and molecular processes (Roff 2007).
3.2.1 Analysis: Choices, Limitations and Considerations
3.2.1.1 Marker Type
The use of several genetic marker types including SNPs on the analysis of genetic
data and estimation of population parameters has been reviewed by Vasemägi and
Primmer (2005) and Ryynanen et al. (2007). The study of Vasemägi et al. (2005)
on Atlantic salmon can be used to illustrate issues about changes in heterozygosity, allele diversity, levels of population differentiation across sets of genetic
markers, and number of loci potentially under selection. They identified genetic signatures of divergent selection by screening 95 genomic and 78 EST derived miniand microsatellites for populations inhabiting contrasting natural environments
(salt, brackish, and freshwater habitats). They detected no significant variations in
heterozygosity, allele diversity or levels of population differentiation across anonymous or EST-SSRs loci when looking at all the populations surveyed as a whole.