7 Genomic Approaches in Aquaculture and Fisheries
255
But cases have been reported where eight microsatellites have the same information content as 18 SNPs (Artamonova 2007). This can, however, be compensated
for by the high and widespread genomic abundance facilitating huge numbers of
markers with good genomic coverage to be developed. Slightly more problematic
is the “ascertainment bias” (see Clark et al. 2005 and references therein), which is
the selection of loci from an unrepresentative sample of individuals or the use of a
method which provides a biased sample of loci. Ascertainment bias may not represent a major obstacle for SNP application in marine fish, as it is generally expected
to be particularly serious for highly structured species (see Chapter 3).
The development of new and more numerous genetic markers is not the only way
that the genomic revolution can contribute to our understanding of population structure in marine fish. Other methods such as the analysis of population differences in
gene expression can provide important pieces to the puzzle (Cossins and Crawford
2005). Microarrays for transcriptional analysis are an example. They have been
developed for a number of marine fish, primarily for model or aquaculture species
(see Wenne et al. 2007 and references therein) and have also been used to investigate gene expression in natural populations (e.g. killifish, Oleksiak et al. 2002).
This approach may provide new insights into the population structure of managed
species. Larsen et al. (2007) used a microarray to investigate potential differences
in gene expression between individuals from the North Sea and the Baltic Sea, two
different physical and biological environments, however with low levels of genetic
differentiation. A high number of genes were differentially expressed between fish
from the two populations experiencing similar conditions, thus strongly suggesting
population subdivision despite low levels of neutral genetic divergence. The results
suggest that population based management of marine fish should be enforced even
when migration rates appear to be relatively high.
7.7.2.2 Selection and Adaptation in Natural and Exploited Populations
The description of the demography of wild populations has been the primary
focus of population and conservation genetics for the last few decades (Beaumont
2005). Although the first genetic studies of marine fish were using markers such as
haemoglobin (Sick 1965) shown to be under selection, the quest for demographic
information to feed into the current management system of fisheries resources (see
section above), has also meant that (presumed) neutral markers are the choice
for marine fish species. However, the focus of the whole scientific field is shifting from studying neutral genetic variation alone to include inferences from gene
loci known – or suspected – to be under selection. The reasons for this change are
many. Generally, it can be said that adaptive variation represents the other side of
the evolutionary coin. That is, in order to understand the evolution of a species
it is crucial to know both how the genetic diversity is affected by demographic
processes (migration and genetic drift), and how traits and the underlying genes
are subject to selection, in turn improving the individual s chances of survival and
reproduction. Much has been learned from directly studying trait variation in natural
populations in the wild or under controlled conditions. However, many such studies
255
But cases have been reported where eight microsatellites have the same information content as 18 SNPs (Artamonova 2007). This can, however, be compensated
for by the high and widespread genomic abundance facilitating huge numbers of
markers with good genomic coverage to be developed. Slightly more problematic
is the “ascertainment bias” (see Clark et al. 2005 and references therein), which is
the selection of loci from an unrepresentative sample of individuals or the use of a
method which provides a biased sample of loci. Ascertainment bias may not represent a major obstacle for SNP application in marine fish, as it is generally expected
to be particularly serious for highly structured species (see Chapter 3).
The development of new and more numerous genetic markers is not the only way
that the genomic revolution can contribute to our understanding of population structure in marine fish. Other methods such as the analysis of population differences in
gene expression can provide important pieces to the puzzle (Cossins and Crawford
2005). Microarrays for transcriptional analysis are an example. They have been
developed for a number of marine fish, primarily for model or aquaculture species
(see Wenne et al. 2007 and references therein) and have also been used to investigate gene expression in natural populations (e.g. killifish, Oleksiak et al. 2002).
This approach may provide new insights into the population structure of managed
species. Larsen et al. (2007) used a microarray to investigate potential differences
in gene expression between individuals from the North Sea and the Baltic Sea, two
different physical and biological environments, however with low levels of genetic
differentiation. A high number of genes were differentially expressed between fish
from the two populations experiencing similar conditions, thus strongly suggesting
population subdivision despite low levels of neutral genetic divergence. The results
suggest that population based management of marine fish should be enforced even
when migration rates appear to be relatively high.
7.7.2.2 Selection and Adaptation in Natural and Exploited Populations
The description of the demography of wild populations has been the primary
focus of population and conservation genetics for the last few decades (Beaumont
2005). Although the first genetic studies of marine fish were using markers such as
haemoglobin (Sick 1965) shown to be under selection, the quest for demographic
information to feed into the current management system of fisheries resources (see
section above), has also meant that (presumed) neutral markers are the choice
for marine fish species. However, the focus of the whole scientific field is shifting from studying neutral genetic variation alone to include inferences from gene
loci known – or suspected – to be under selection. The reasons for this change are
many. Generally, it can be said that adaptive variation represents the other side of
the evolutionary coin. That is, in order to understand the evolution of a species
it is crucial to know both how the genetic diversity is affected by demographic
processes (migration and genetic drift), and how traits and the underlying genes
are subject to selection, in turn improving the individual s chances of survival and
reproduction. Much has been learned from directly studying trait variation in natural
populations in the wild or under controlled conditions. However, many such studies