90
M.S. Clark et al.
• Why so much effort (e.g. development of numerous markers, pedigrees, linkage map) for only one gene? Is this useful? Why not a candidate gene approach
that deals with a few well-known genes that would come from the available biochemical and physiological literature or other techniques such as microarrays
(see below, and, e.g., Ellegren and Sheldon 2008)?
Hence, although combining genome scan and QTL approaches can be useful in
identifying genomic regions of interest, the relevance of individual genes and their
surrounding cis- and trans-regulatory regions do necessitate extensive sequencing
of resources (e.g. BACs), and comparative genomics to identify genes of interest in
marine organisms.
3.3 Practical Application of Population Genomics in the Marine
Environment
There are a number of applications for the tools described above and population
genomics approaches, which inter-link with ecological issues:
3.3.1 Dispersal in the Sea: From Larval Development to Local
Adaptation and Speciation Processes
Understanding the extent of connectivity between marine populations is crucial, not
only for conservation purposes but also for fisheries management, as well as being a
means to increase our understanding of the functioning and evolution of populations
in the marine system. Comprehensive methodologies exist which means this issue
can be addressed from larval tracking through to gene analyses. Chapter 1 can be
consulted for more information on the specific area of larval identification, whilst
here three more general examples are provided of genome-based approaches that
fuel the debate about the patterns and extent of dispersal in the sea:
3.3.1.1 Pelagic Larval Studies
In species with a bentho-pelagic life cycle (the most frequent cycle in marine invertebrates) and in which adults are non-mobile, larvae are the major dispersal vector.
Larvae which are able to metamorphose (i.e. competent larvae) can delay their metamorphosis in response to biotic and abiotic factors (Hadfield 1998, Hadfield et al.
2001). This delayed metamorphosis may enhance the dispersal potential and the
connectivity between populations with implications on local adaptation, maintenance of species cohesiveness and population dynamics. Numerous studies have
nevertheless shown that evolutionary trade-offs exist between characteristics linked
to the dispersal abilities of the species and its cost, e.g. between the avoidance of
M.S. Clark et al.
• Why so much effort (e.g. development of numerous markers, pedigrees, linkage map) for only one gene? Is this useful? Why not a candidate gene approach
that deals with a few well-known genes that would come from the available biochemical and physiological literature or other techniques such as microarrays
(see below, and, e.g., Ellegren and Sheldon 2008)?
Hence, although combining genome scan and QTL approaches can be useful in
identifying genomic regions of interest, the relevance of individual genes and their
surrounding cis- and trans-regulatory regions do necessitate extensive sequencing
of resources (e.g. BACs), and comparative genomics to identify genes of interest in
marine organisms.
3.3 Practical Application of Population Genomics in the Marine
Environment
There are a number of applications for the tools described above and population
genomics approaches, which inter-link with ecological issues:
3.3.1 Dispersal in the Sea: From Larval Development to Local
Adaptation and Speciation Processes
Understanding the extent of connectivity between marine populations is crucial, not
only for conservation purposes but also for fisheries management, as well as being a
means to increase our understanding of the functioning and evolution of populations
in the marine system. Comprehensive methodologies exist which means this issue
can be addressed from larval tracking through to gene analyses. Chapter 1 can be
consulted for more information on the specific area of larval identification, whilst
here three more general examples are provided of genome-based approaches that
fuel the debate about the patterns and extent of dispersal in the sea:
3.3.1.1 Pelagic Larval Studies
In species with a bentho-pelagic life cycle (the most frequent cycle in marine invertebrates) and in which adults are non-mobile, larvae are the major dispersal vector.
Larvae which are able to metamorphose (i.e. competent larvae) can delay their metamorphosis in response to biotic and abiotic factors (Hadfield 1998, Hadfield et al.
2001). This delayed metamorphosis may enhance the dispersal potential and the
connectivity between populations with implications on local adaptation, maintenance of species cohesiveness and population dynamics. Numerous studies have
nevertheless shown that evolutionary trade-offs exist between characteristics linked
to the dispersal abilities of the species and its cost, e.g. between the avoidance of