3 Populations and Pathways
99
3.4.2 Microarrays: Identification of Biochemical Pathways
Involved in Adaptation
This section is concerned with the identification of more complex pathways and
how these change in relation to perturbation or natural environmental cycling. This
specifically refers to gene chips. Work in the field is relatively limited so far, as
considerable specialised molecular input is required: library production, generation
of gene chips, hybridization of the chips and analysis. None of this is trivial and
requires specialist skills only available in relatively few laboratories. It is possible
to use gene chips produced for a model organism to ask questions in a non-model
species, cf. Hogstrand et al. (2002) examining the response to zinc exposure in
rainbow trout (Oncorhynchus mykiss) using high density spotted arrays from the
Japanese pufferfish (Takifugu rupripes). Whilst this technique has been proved to
work effectively (reviewed in Buckley 2007, Kassahn 2008), the detected magnitude of fold difference in gene expression decreases across phylogenetic distance
(Renn et al. 2004) and this has to be considered as part of the experimental design.
Also, another problem of working on non-model species, is a restricted ability to
identify genes (also see Section 3.2.1.1) and more importantly putatively assign
function, as this is all based on sequence similarity with database entries, most of
which are vertebrates, in particular, mammals. As a result, gene chip analyses in
non-model species has been dominated by fish species, in particular those involved
in aquaculture and ecotoxicology (Wenne et al. 2007, Daib et al. 2008).
However, examples of environmentally-biased gene chip experiments are beginning to appear. These include the heat stress response of the inter-tidal porcelain
crab (Petrolisthes cinctipes) (Teranishi and Stillman 2007), cold stress in the common carp (Cyprinus carpio L.) (Gracey et al. 2004), daily fluctuating temperatures
in the annual killifish (Austrofundulus limnaeus) (Podrabsky and Somero 2004)
and the purely environmental sampling example of M. califorianus detailed above
(Place et al. 2008). Whilst these experiments document gene changes associated
with changing conditions and can for example, highlight pathways most readily
affected cf. protein folding, protein degradation and protein synthesis with heat
stress (Teranishi and Stillman 2006), the gene lists are long. Detailed analysis of all
genes is simply not logistically possible and these experiments essentially provide
candidate genes for future studies, e.g. stearoyl-CoA desaturase in cold adaptation
of the carp (Gracey et al. 2004). However without the initial broad brush stroke
approach of screening thousands of genes in the first place, it would not have been
possible to identify such candidates, which ultimately may help us understand the
fundamental nature of environmental adaptation.
3.4.3 Genome Plasticity and Seasonal Variation
One point to remember is that expression of the genome is not static. Unless a longterm study is undertaken, with many different samplings of the population, then
99
3.4.2 Microarrays: Identification of Biochemical Pathways
Involved in Adaptation
This section is concerned with the identification of more complex pathways and
how these change in relation to perturbation or natural environmental cycling. This
specifically refers to gene chips. Work in the field is relatively limited so far, as
considerable specialised molecular input is required: library production, generation
of gene chips, hybridization of the chips and analysis. None of this is trivial and
requires specialist skills only available in relatively few laboratories. It is possible
to use gene chips produced for a model organism to ask questions in a non-model
species, cf. Hogstrand et al. (2002) examining the response to zinc exposure in
rainbow trout (Oncorhynchus mykiss) using high density spotted arrays from the
Japanese pufferfish (Takifugu rupripes). Whilst this technique has been proved to
work effectively (reviewed in Buckley 2007, Kassahn 2008), the detected magnitude of fold difference in gene expression decreases across phylogenetic distance
(Renn et al. 2004) and this has to be considered as part of the experimental design.
Also, another problem of working on non-model species, is a restricted ability to
identify genes (also see Section 3.2.1.1) and more importantly putatively assign
function, as this is all based on sequence similarity with database entries, most of
which are vertebrates, in particular, mammals. As a result, gene chip analyses in
non-model species has been dominated by fish species, in particular those involved
in aquaculture and ecotoxicology (Wenne et al. 2007, Daib et al. 2008).
However, examples of environmentally-biased gene chip experiments are beginning to appear. These include the heat stress response of the inter-tidal porcelain
crab (Petrolisthes cinctipes) (Teranishi and Stillman 2007), cold stress in the common carp (Cyprinus carpio L.) (Gracey et al. 2004), daily fluctuating temperatures
in the annual killifish (Austrofundulus limnaeus) (Podrabsky and Somero 2004)
and the purely environmental sampling example of M. califorianus detailed above
(Place et al. 2008). Whilst these experiments document gene changes associated
with changing conditions and can for example, highlight pathways most readily
affected cf. protein folding, protein degradation and protein synthesis with heat
stress (Teranishi and Stillman 2006), the gene lists are long. Detailed analysis of all
genes is simply not logistically possible and these experiments essentially provide
candidate genes for future studies, e.g. stearoyl-CoA desaturase in cold adaptation
of the carp (Gracey et al. 2004). However without the initial broad brush stroke
approach of screening thousands of genes in the first place, it would not have been
possible to identify such candidates, which ultimately may help us understand the
fundamental nature of environmental adaptation.
3.4.3 Genome Plasticity and Seasonal Variation
One point to remember is that expression of the genome is not static. Unless a longterm study is undertaken, with many different samplings of the population, then