3 Populations and Pathways
105
age, sex, and genetic polymorphisms in natural populations. Several specific aspects
could be then considered with more attention:
• Identification of conserved genes that are up-regulated in response to toxicant
exposure (according to exposure time and toxicant concentration).
• Determination of how these gene expression profiles can be used to diagnose
stressors.
• Identification of genes that are most informative to incorporate into more specific
stress gene arrays for monitoring purposes.
In marine species, a particular effort has been focused on fishes (Sheader et al.
2006) and is underway in marine mollusc species. The toxicogenomic approach
will certainly present new opportunities to improve understanding of the molecular
mechanisms underlying toxic responses to environmental contaminants (Bradley
and Theodorakis 2002, Moore 2001).
3.5 Summary and Future Issues
This chapter summarises the current molecular tools available to the marine biologist for studying ecological questions. What is clear is that whilst new techniques are
continually being brought in (e.g. MPSS and 454 sequencing), their utility is reliant
upon a robust understanding of the underlying ecology and physiology of the species
under study. This often means identifying populations of the same species with
clear phenotypic contrasts, such that the contrast between phenotype and genotype
reveals a set of candidate genes for the further functional and genetic analyses of
a biological process. Equally adopting a rigorous experimental design using known
physiological knowledge will obviate many data interpretation problems. Hence a
holistic overview of ecological adaptation can only be obtained by a combination of
approaches. These are not restricted to genomics and must incorporate ecology and
physiology; indeed these are the disciplines that dictate the questions, populations
and experimental approaches used, with the molecular biology as an additional tool
in the armoury.
As regards future perspectives, undoubtedly the use of MPSS and 454 will
increase, as these techniques rapidly generate large amounts of genome data on
non-model species. Thus the traditional view of a non-model species, as a gene-poor
resource will change dramatically over the next few years. Each community should
concentrate on generating a number of “new model species” that are particularly
useful for answering ecological questions in their specific domain, be it aquaculture, hydrothermal vents or climate change and polar species. These species should
originate from a range of taxa across different feeding guilds, so that understanding
adaptation to a particular set of conditions is not limited to a single species. Indeed
this should ideally stretch from microbes through to higher predators, producing a
real gene to ecosystem understanding of our marine environment.
105
age, sex, and genetic polymorphisms in natural populations. Several specific aspects
could be then considered with more attention:
• Identification of conserved genes that are up-regulated in response to toxicant
exposure (according to exposure time and toxicant concentration).
• Determination of how these gene expression profiles can be used to diagnose
stressors.
• Identification of genes that are most informative to incorporate into more specific
stress gene arrays for monitoring purposes.
In marine species, a particular effort has been focused on fishes (Sheader et al.
2006) and is underway in marine mollusc species. The toxicogenomic approach
will certainly present new opportunities to improve understanding of the molecular
mechanisms underlying toxic responses to environmental contaminants (Bradley
and Theodorakis 2002, Moore 2001).
3.5 Summary and Future Issues
This chapter summarises the current molecular tools available to the marine biologist for studying ecological questions. What is clear is that whilst new techniques are
continually being brought in (e.g. MPSS and 454 sequencing), their utility is reliant
upon a robust understanding of the underlying ecology and physiology of the species
under study. This often means identifying populations of the same species with
clear phenotypic contrasts, such that the contrast between phenotype and genotype
reveals a set of candidate genes for the further functional and genetic analyses of
a biological process. Equally adopting a rigorous experimental design using known
physiological knowledge will obviate many data interpretation problems. Hence a
holistic overview of ecological adaptation can only be obtained by a combination of
approaches. These are not restricted to genomics and must incorporate ecology and
physiology; indeed these are the disciplines that dictate the questions, populations
and experimental approaches used, with the molecular biology as an additional tool
in the armoury.
As regards future perspectives, undoubtedly the use of MPSS and 454 will
increase, as these techniques rapidly generate large amounts of genome data on
non-model species. Thus the traditional view of a non-model species, as a gene-poor
resource will change dramatically over the next few years. Each community should
concentrate on generating a number of “new model species” that are particularly
useful for answering ecological questions in their specific domain, be it aquaculture, hydrothermal vents or climate change and polar species. These species should
originate from a range of taxa across different feeding guilds, so that understanding
adaptation to a particular set of conditions is not limited to a single species. Indeed
this should ideally stretch from microbes through to higher predators, producing a
real gene to ecosystem understanding of our marine environment.