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M.L. Cancela et al.
the environmental variables. Hence the hydrodynamics of the habitat in which
marine organisms live shapes the ecosystem. But the environment in which marine
organisms live is also shaped by the ecosystem itself, which is defined by the community of organisms, their composition, interactions and dynamics (Scheffer et al.
2005). Predator-prey and socio-behavioural interactions, host-pathogen dynamics
and random forces influence the inhabiting species and populations and hence the
full ecosystem make-up. To some extent the influence is exerted through the phenotype of these organisms, where biological traits of importance are their life-history,
ecological niche and evolution.
Population genomics is the investigation of the genetic basis of adaptation and
speciation at the genome scale (Bonin 2008), or loosely defined it is simply population genetics on a large scale. Its foundation can be traced back to human genetics
by separating locus-specific effects from genome-wide effects. Since that time,
genomics has been shown to hold much promise for generating knowledge from the
poorly and difficult to study species of the open ocean (Derelle et al. 2006, Yooseph
et al. 2007).
We will start this section by taking a closer look at some of the key issues on
intraspecific evolution of fishes.
1. Since speciation is an ongoing and gradual process, the distinction between
species, subspecies and population is not always unambiguous. Hybridisation
between taxa is a common feature across the tree of life. This issue is further
complicated by the presence of numerous cryptic taxa across the tree of life,
including the fishes (Colborn et al. 2001; see Chapter 3 on Barcoding).
2. Fish are free-living organisms and have as a rule free-living larvae (and often
free-floating eggs). The small dimension of eggs and larvae makes that they are
associated with the plankton. Juveniles and adults in contrast, actively control
their movements. However, the behaviour of parents and larvae makes them
disperse less than expected, and show some level of retention (Jones et al.
2005). This encourages a pattern of genetic structuring, albeit subtle (see further). Frontal systems, large-scale eddies, depth, coastal topography and bottom
type shape these patterns.
3. Many oceanic fish taxa are characterised by huge census numbers (Palumbi
2004). However, recruitment is such that numbers may fluctuate between cohorts
(see further). If the breeding cycle is limited to just a few years, large differences in adult numbers may be observed. Variable recruitment results in an
effective population size that is several orders of magnitude smaller than the
census size (Hauser et al. 2002). It might make these populations less robust to
demographic changes than thought previously. “Sweepstake” survival of entire
family groups at the early stages of the life history leaves an imprint on the next
cohort (Hedgecock 1994). This fits with the classical “Match-Mismatch” hypothesis of Hjort (1914) (reformulated by Cushing 1969), which states that survival
of a cohort depends on the overlap between prey (the phyto- and zooplankton)
and predator (fish larva), or alternatively the fish larvae as prey for higher level
predators.
M.L. Cancela et al.
the environmental variables. Hence the hydrodynamics of the habitat in which
marine organisms live shapes the ecosystem. But the environment in which marine
organisms live is also shaped by the ecosystem itself, which is defined by the community of organisms, their composition, interactions and dynamics (Scheffer et al.
2005). Predator-prey and socio-behavioural interactions, host-pathogen dynamics
and random forces influence the inhabiting species and populations and hence the
full ecosystem make-up. To some extent the influence is exerted through the phenotype of these organisms, where biological traits of importance are their life-history,
ecological niche and evolution.
Population genomics is the investigation of the genetic basis of adaptation and
speciation at the genome scale (Bonin 2008), or loosely defined it is simply population genetics on a large scale. Its foundation can be traced back to human genetics
by separating locus-specific effects from genome-wide effects. Since that time,
genomics has been shown to hold much promise for generating knowledge from the
poorly and difficult to study species of the open ocean (Derelle et al. 2006, Yooseph
et al. 2007).
We will start this section by taking a closer look at some of the key issues on
intraspecific evolution of fishes.
1. Since speciation is an ongoing and gradual process, the distinction between
species, subspecies and population is not always unambiguous. Hybridisation
between taxa is a common feature across the tree of life. This issue is further
complicated by the presence of numerous cryptic taxa across the tree of life,
including the fishes (Colborn et al. 2001; see Chapter 3 on Barcoding).
2. Fish are free-living organisms and have as a rule free-living larvae (and often
free-floating eggs). The small dimension of eggs and larvae makes that they are
associated with the plankton. Juveniles and adults in contrast, actively control
their movements. However, the behaviour of parents and larvae makes them
disperse less than expected, and show some level of retention (Jones et al.
2005). This encourages a pattern of genetic structuring, albeit subtle (see further). Frontal systems, large-scale eddies, depth, coastal topography and bottom
type shape these patterns.
3. Many oceanic fish taxa are characterised by huge census numbers (Palumbi
2004). However, recruitment is such that numbers may fluctuate between cohorts
(see further). If the breeding cycle is limited to just a few years, large differences in adult numbers may be observed. Variable recruitment results in an
effective population size that is several orders of magnitude smaller than the
census size (Hauser et al. 2002). It might make these populations less robust to
demographic changes than thought previously. “Sweepstake” survival of entire
family groups at the early stages of the life history leaves an imprint on the next
cohort (Hedgecock 1994). This fits with the classical “Match-Mismatch” hypothesis of Hjort (1914) (reformulated by Cushing 1969), which states that survival
of a cohort depends on the overlap between prey (the phyto- and zooplankton)
and predator (fish larva), or alternatively the fish larvae as prey for higher level
predators.