7 Genomic Approaches in Aquaculture and Fisheries
261
stickleback (McKinnon and Rundle 2002). Stickleback populations have invaded
repeatedly freshwater habitats after the last ice age throughout the northern hemisphere causing rapid genetic divergence. This leads to systematic adaptations of
phenotypic traits. For example, the reduction in the pelvic spine (Shapiro et al. 2006)
and body armour (Peichel et al. 2001) has been attributed to the Ptx1 and Eda genes
respectively. Interestingly, the trait body armour has been lost in freshwater populations many times in parallel due to the sorting of a rare allele of the Eda gene
in ancestral marine populations (Raeymaekers et al. 2007). The gene seems to give
a growth advantage, but it remains unclear whether it affected additional traits or
whether linked loci play a role (Barrett et al. 2008). Also mate choice (Boughman
2001), feeding (Schluter 1995) and parasite resistance (Kalbe and Kurtz 2006) have
diverged rapidly and in parallel. Parasite resistance in stickleback has been attributed
to a trade-off between innate immunity (MHC class I and II) and acquired immunity (Wegner et al. 2007). Increasingly, the significance of the gene cluster MHC has
been acknowledged; MHC diversity has been linked to many fitness traits, including
mate choice (Milinski et al. 2005).
Further developments of genomics and better insights into the genetic architecture of model organisms have made studies of multi-locus and multi-trait
adaptations in non-model organisms feasible. The above mentioned studies by
Oleksiak et al. (2002) and Larsen et al. (2007) using natural and managed populations, respectively, represent the first cases in marine fish where transcription
profiling was used to discriminate among populations. There is also interest for evolutionary models of parallel adaptive differentiation in physiological and behavioral
functions between species and among ecotypes. The dwarf morphotype of the whitefish Coregonus clupeaformis and the cisco C. artedi locally occupy sympatrically
the same limnetic ecological niche in North American freshwater lakes. C. clupeaformis has apparent adaptations to the limnetic trophic niche channeled through
transcriptional changes in functional genes involved in muscle contraction and energetic metabolism relative to the sympatric normal ecotype (Trudel et al. 2001). As
evidenced by a transcriptome analysis of both species using a heterologous microarray, each had the same genes involved in muscle contraction and energy metabolism,
but regulation was different (Derome and Bernatchez 2006).
A more detailed analysis of the mechanisms driving adaptive radiation in the
dwarf limnetic and normal pelagic ecotype of the whitefish C. clupeaformis was
involved in the analysis of physiological and behavioural traits. First, a comparative linkage analysis of the dwarf and normal ecotype showed a different genetic
architecture between the two types. Rogers et al. (2007) concluded that allopatric
divergence during the Pleistocene glaciations caused divergence and that subsequent ecological speciation occurred sympatrically. In a next step a QTL analysis of
a F 1 backcross family combined with a genome scan of both natural ecotype pairs
showed distinct differences in adaptive divergence and the role of divergent natural selection of traits. Significant QTL were associated with swimming behaviour
(which is important for habitat selection and predator avoidance), growth rate,
morphology (number of gill rakers and condition) and life history (more specifically the onset of maturity and fecundity). The natural sympatric pairs revealed a
261
stickleback (McKinnon and Rundle 2002). Stickleback populations have invaded
repeatedly freshwater habitats after the last ice age throughout the northern hemisphere causing rapid genetic divergence. This leads to systematic adaptations of
phenotypic traits. For example, the reduction in the pelvic spine (Shapiro et al. 2006)
and body armour (Peichel et al. 2001) has been attributed to the Ptx1 and Eda genes
respectively. Interestingly, the trait body armour has been lost in freshwater populations many times in parallel due to the sorting of a rare allele of the Eda gene
in ancestral marine populations (Raeymaekers et al. 2007). The gene seems to give
a growth advantage, but it remains unclear whether it affected additional traits or
whether linked loci play a role (Barrett et al. 2008). Also mate choice (Boughman
2001), feeding (Schluter 1995) and parasite resistance (Kalbe and Kurtz 2006) have
diverged rapidly and in parallel. Parasite resistance in stickleback has been attributed
to a trade-off between innate immunity (MHC class I and II) and acquired immunity (Wegner et al. 2007). Increasingly, the significance of the gene cluster MHC has
been acknowledged; MHC diversity has been linked to many fitness traits, including
mate choice (Milinski et al. 2005).
Further developments of genomics and better insights into the genetic architecture of model organisms have made studies of multi-locus and multi-trait
adaptations in non-model organisms feasible. The above mentioned studies by
Oleksiak et al. (2002) and Larsen et al. (2007) using natural and managed populations, respectively, represent the first cases in marine fish where transcription
profiling was used to discriminate among populations. There is also interest for evolutionary models of parallel adaptive differentiation in physiological and behavioral
functions between species and among ecotypes. The dwarf morphotype of the whitefish Coregonus clupeaformis and the cisco C. artedi locally occupy sympatrically
the same limnetic ecological niche in North American freshwater lakes. C. clupeaformis has apparent adaptations to the limnetic trophic niche channeled through
transcriptional changes in functional genes involved in muscle contraction and energetic metabolism relative to the sympatric normal ecotype (Trudel et al. 2001). As
evidenced by a transcriptome analysis of both species using a heterologous microarray, each had the same genes involved in muscle contraction and energy metabolism,
but regulation was different (Derome and Bernatchez 2006).
A more detailed analysis of the mechanisms driving adaptive radiation in the
dwarf limnetic and normal pelagic ecotype of the whitefish C. clupeaformis was
involved in the analysis of physiological and behavioural traits. First, a comparative linkage analysis of the dwarf and normal ecotype showed a different genetic
architecture between the two types. Rogers et al. (2007) concluded that allopatric
divergence during the Pleistocene glaciations caused divergence and that subsequent ecological speciation occurred sympatrically. In a next step a QTL analysis of
a F 1 backcross family combined with a genome scan of both natural ecotype pairs
showed distinct differences in adaptive divergence and the role of divergent natural selection of traits. Significant QTL were associated with swimming behaviour
(which is important for habitat selection and predator avoidance), growth rate,
morphology (number of gill rakers and condition) and life history (more specifically the onset of maturity and fecundity). The natural sympatric pairs revealed a