3 Populations and Pathways
97
given the success of the assay in the lab, the relative stress levels of environmentally sampled animals could then be examined. The reason being that if no HSP70
expression was detected in these animals, the logical conclusion would be that these
genes were inactive under that particular set of circumstances, given the fact that the
genes had been characterised and there was a working and accurate assay. In fact
this proved not to be the case and indicated that control of these genes was more
complex depending on whether the stress applied was short-term acute (experimental) or longer term chronic (environmental) (Clark et al. 2008d, Clark and Peck
2009).
Although this is a single gene example and would not be considered as
“genomics” per se, it does demonstrate the complexity of environmental genomics
and the requirement to integrate different disciplines: ecology, through physiology
to gene expression and genomics. It also serves to highlight, that to date, the majority of environmental stress monitoring in invertebrate species has used the HSP70
gene family (to great effect), with relatively few examples of a genomics approach.
Hence this following section will include some single gene examples, where they
serve to demonstrate molecular approaches to an environmental question, which can
then be expanded to a genomics approach.
3.4.1 Defining Habitat Limits: Biogeography
The question of “which animal inhabits which environment and why?” is fundamental to ecology. Population genetics is often seen as at least a partial answer to
this question as this discipline can document DNA differences between populations,
and say that population X is not the same as population Y even though they look
very similar. The markers used in this type of analysis are generally neutral markers (i.e. do not code for genes) and hence not under selection pressure. Identifying
differences in neutral DNA between populations does not answer the fundamental
question of why species “chose” to live where they do and what particular adaptations they need to survive in their chosen environment (also see Section 3.2.1.3).
In the past we have been able to document morphological, physiological and biochemical environmental adaptations, but with molecular biology, this can be taken
to the more detailed scale of the cellular level, the level at which all these phenotypic adaptations are controlled. It is now possible to investigate the transcriptional
and proteomic profiles of different populations living under different environmental
conditions and manipulate these to investigate the nature of the underlying cellular
changes. Such knowledge, apart from providing an answer to the question of habitat “choice”, will also enable us to predict how animals will adapt in the face of
perturbation, in particular climate change.
This type of work is of great relevant to ectotherms, of which those in the marine
environment are prime examples, where one might expect tight linkage between the
environmental temperature and species distribution patterns (Somero 2002). To a
large extent this field of research has concentrated on inter-tidal species, as these
97
given the success of the assay in the lab, the relative stress levels of environmentally sampled animals could then be examined. The reason being that if no HSP70
expression was detected in these animals, the logical conclusion would be that these
genes were inactive under that particular set of circumstances, given the fact that the
genes had been characterised and there was a working and accurate assay. In fact
this proved not to be the case and indicated that control of these genes was more
complex depending on whether the stress applied was short-term acute (experimental) or longer term chronic (environmental) (Clark et al. 2008d, Clark and Peck
2009).
Although this is a single gene example and would not be considered as
“genomics” per se, it does demonstrate the complexity of environmental genomics
and the requirement to integrate different disciplines: ecology, through physiology
to gene expression and genomics. It also serves to highlight, that to date, the majority of environmental stress monitoring in invertebrate species has used the HSP70
gene family (to great effect), with relatively few examples of a genomics approach.
Hence this following section will include some single gene examples, where they
serve to demonstrate molecular approaches to an environmental question, which can
then be expanded to a genomics approach.
3.4.1 Defining Habitat Limits: Biogeography
The question of “which animal inhabits which environment and why?” is fundamental to ecology. Population genetics is often seen as at least a partial answer to
this question as this discipline can document DNA differences between populations,
and say that population X is not the same as population Y even though they look
very similar. The markers used in this type of analysis are generally neutral markers (i.e. do not code for genes) and hence not under selection pressure. Identifying
differences in neutral DNA between populations does not answer the fundamental
question of why species “chose” to live where they do and what particular adaptations they need to survive in their chosen environment (also see Section 3.2.1.3).
In the past we have been able to document morphological, physiological and biochemical environmental adaptations, but with molecular biology, this can be taken
to the more detailed scale of the cellular level, the level at which all these phenotypic adaptations are controlled. It is now possible to investigate the transcriptional
and proteomic profiles of different populations living under different environmental
conditions and manipulate these to investigate the nature of the underlying cellular
changes. Such knowledge, apart from providing an answer to the question of habitat “choice”, will also enable us to predict how animals will adapt in the face of
perturbation, in particular climate change.
This type of work is of great relevant to ectotherms, of which those in the marine
environment are prime examples, where one might expect tight linkage between the
environmental temperature and species distribution patterns (Somero 2002). To a
large extent this field of research has concentrated on inter-tidal species, as these