88
M.S. Clark et al.
populations of the three-spined stickleback (Gasterosteus aculeatus) (cf. Cresko
et al. 2004, Colosimo et al. 2005). Allelic variants at this locus have led to the
reduction of pelvic plates in the freshwater ecotype of this species, a process that
has been associated with changes in predation risk.
For QTL mapping to become a commonplace methodology for studies of outbred
natural populations would require sampling of either large pedigrees, or extensive
series of sibling-pairs and the components of fitness measured in these individuals
(e.g. mammals: Beraldi et al. 2006). This is generally not possible without a massive
input of resources and a huge targeted breeding programme and hence is not really
an option, particularly if no commercial advantage is gained. The nearest example
related to this issue was a pilot study in the European sea bass. This reported crosses
among individuals with a poorly known pedigree and allowed the characterisation
of QTLs for body shape (Chatziplis et al. 2007), a trait of potential benefit to both
the aquaculture industry and par hasard the study of wild populations.
An alternative method to QTL mapping is association or linkage disequilibrium
mapping. This relies on the analysis of linkage between markers and trait loci that
are in linkage disequilibrium by genome scans of population samples, rather than
by pedigree analysis using QTLs. This approach has typically a much higher resolution than conventional pedigree analysis, but the efficiency of association mapping
depends on the number and distribution of markers used to scan the genome, and the
extent of linkage disequilibrium. This is a parameter itself that varies (Jorde 2000)
and is strongly reliant on population/species history (e.g. Backström et al. 2006) and
model of population structure (Yu et al. 2006). We are not aware of marine species
where such a method could be used in a near future to identify causative sequence
variants, as long as the number of markers in genome scans is low.
The use of genome scans using any of the markers cited above is important in
confirming that QTLs identified in contemporary populations have played a part in
adaptive phenotypic differentiation, driven by directional selection. By definition,
QTLs may be used to infer the genetic basis of adaptive traits underlying species
or population differences, but they do not rely per se on the effects selection may
have on corresponding adaptive traits (Hoekstra and Nachman 2003, Rogers and
Bernatchez 2005). Whilst genome scans rely on detecting potentially selected markers, the function and role of these loci on the construction of a given phenotype
needs to be ascertained. Nevertheless, if signs of selection as revealed by scans for
reduced within-population variability or increased between-population divergence
coincides with the chromosomal location of QTLs, this highlights the significance
of genes within these regions in adaptive evolution (Ellegren and Sheldon 2008).
Such a result has been recently presented by Rogers and Bernatchez (2005). They
integrated QTL mapping and genome scanning methods to analyse diverging sympatric pairs of the lake whitefish (Coregonus clupeaformis) species complex. This
was to test the hypothesis that differentiation between dwarf and normal ecotypes
at a growth associated QTL was maintained by selection. Indeed, their objective
consisted of evaluating growth as a phenotype–environment association, determining its genetic basis with QTL mapping, screening natural populations for outlier
levels of differentiation, and finally assessing observed patterns of divergence for
M.S. Clark et al.
populations of the three-spined stickleback (Gasterosteus aculeatus) (cf. Cresko
et al. 2004, Colosimo et al. 2005). Allelic variants at this locus have led to the
reduction of pelvic plates in the freshwater ecotype of this species, a process that
has been associated with changes in predation risk.
For QTL mapping to become a commonplace methodology for studies of outbred
natural populations would require sampling of either large pedigrees, or extensive
series of sibling-pairs and the components of fitness measured in these individuals
(e.g. mammals: Beraldi et al. 2006). This is generally not possible without a massive
input of resources and a huge targeted breeding programme and hence is not really
an option, particularly if no commercial advantage is gained. The nearest example
related to this issue was a pilot study in the European sea bass. This reported crosses
among individuals with a poorly known pedigree and allowed the characterisation
of QTLs for body shape (Chatziplis et al. 2007), a trait of potential benefit to both
the aquaculture industry and par hasard the study of wild populations.
An alternative method to QTL mapping is association or linkage disequilibrium
mapping. This relies on the analysis of linkage between markers and trait loci that
are in linkage disequilibrium by genome scans of population samples, rather than
by pedigree analysis using QTLs. This approach has typically a much higher resolution than conventional pedigree analysis, but the efficiency of association mapping
depends on the number and distribution of markers used to scan the genome, and the
extent of linkage disequilibrium. This is a parameter itself that varies (Jorde 2000)
and is strongly reliant on population/species history (e.g. Backström et al. 2006) and
model of population structure (Yu et al. 2006). We are not aware of marine species
where such a method could be used in a near future to identify causative sequence
variants, as long as the number of markers in genome scans is low.
The use of genome scans using any of the markers cited above is important in
confirming that QTLs identified in contemporary populations have played a part in
adaptive phenotypic differentiation, driven by directional selection. By definition,
QTLs may be used to infer the genetic basis of adaptive traits underlying species
or population differences, but they do not rely per se on the effects selection may
have on corresponding adaptive traits (Hoekstra and Nachman 2003, Rogers and
Bernatchez 2005). Whilst genome scans rely on detecting potentially selected markers, the function and role of these loci on the construction of a given phenotype
needs to be ascertained. Nevertheless, if signs of selection as revealed by scans for
reduced within-population variability or increased between-population divergence
coincides with the chromosomal location of QTLs, this highlights the significance
of genes within these regions in adaptive evolution (Ellegren and Sheldon 2008).
Such a result has been recently presented by Rogers and Bernatchez (2005). They
integrated QTL mapping and genome scanning methods to analyse diverging sympatric pairs of the lake whitefish (Coregonus clupeaformis) species complex. This
was to test the hypothesis that differentiation between dwarf and normal ecotypes
at a growth associated QTL was maintained by selection. Indeed, their objective
consisted of evaluating growth as a phenotype–environment association, determining its genetic basis with QTL mapping, screening natural populations for outlier
levels of differentiation, and finally assessing observed patterns of divergence for