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• A high gene low that tended to homogenize the distribution of genotypic fre-
quencies in populations, thus masking potential local adaptation
• A lack of sensitivity to pollutants of the genetic markers used
The latter factor is particularly fundamental. Indeed, a selective pressure does not affect
the entire genome equally. The combination of different classes of molecular markers (neu-
tral markers vs. markers potentially under selection) is particularly interesting, and, as
described in Section 14.3, strong advances in genome typing has made this feasible for
many species at a large scale, called genome-wide sampling. Genome-wide sampling (mic-
rosatellites, AFLPs, nucleotide polymorphisms, etc.) is used to identify and separate locus-
specific effects (such as selection, mutation, assortive mating, and recombination) from
genome-wide effects (such as drift or bottlenecks, gene flow, and inbreeding). Genome-
wide effects inform us reliably about population demography and phylogenetic history,
whereas locus-specific effects help identify genes that are important for fitness and adap-
tation (Luikart et al. 2003). This approach, called “population genomics” (Black et al. 2001),
relies on the principle that neutral loci across the genome will be similarly affected by
demography and the evolutionary history of populations, and loci under selection will
often behave differently and therefore reveal “outlier” patterns of variation (Luikart et
al. 2003; Storz 2005). Population-genomics studies of adaptive molecular variation will
improve our understanding of the genetic mechanisms of speciation and will speed up
the discovery of genes that are important for health and human medicine (Black et al. 2001;
Jorde et al. 2001; Gibson and Mackay 2002) but also for biodiversity conservation (Luikart
et al. 2003). This approach has been applied to identify candidate loci responsible for local
adaptations among populations of the common frog
Rana temporaria
(Bonin et al. 2006) and
among populations of deer mice
Peromyscus maniculatus
distributed across altitudinal gra-
dients (Storz and Dubach 2004), and among ecotypes of lake whitefish
Coregonus clupeafor-
mis
(Campbell and Bernatchez 2004) and populations of intertidal snails (
Littorina saxatilis
)
(Wilding et al. 2001). The biggest hurdle encountered by this approach is the determination
of the relevance of specific polymorphisms to protein function. This field is called “func-
tional genomics” and requires (1) characterization of polymorphisms in both the cod-
ing and regulatory regions, (2) studies associating performances to protein variants, and
(3) studies combining genetic polymorphism and particular environments. For the
moment, this part is well documented for human diseases (cancer, Alzheimer, etc.), but
evidence remains scarce for aquatic organisms. The most significant example concerns
environmental adaptations in populations of the fish
F
.
heteroclitus
in the gene coding the
lactate dehydrogenase-B enzyme (LDH), a locus that has not, however, been discovered
by the genome typing approach. Both phenotypic (increased LDH activity) and genotypic
(changes in Ldh-B regulatory sequences) differences between populations distributed
along a steep thermal gradient have been found to be affected by natural selection, rather
than genetic drift (see the synthesis of Schulte 2001).
14.4.2 Transmission of Resistance to Contaminants
Resistance (or tolerance) to contaminants has been identified in many taxa, from micro-
organisms to vertebrates or plants (Amiard-Triquet 2011), considering (1) a physiologi-
cal acclimation of individuals or (2) heritable adaptive responses in a population where
contaminants can be considered selective factors. However, demonstrations of the resis-
tance (adaptive responses) of particular populations exposed to complex mixtures of
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