252
M.L. Cancela et al.
The field of marine population genetics has received a major impetus since the
end of the last millennium. Initially restricted to a small number of viruses, bacteria, model species and man, it is now being extended to an ever growing group
of taxa or even communities (metagenomics of microbial and picoplankton communities) (see Chapter 2 on Metagenomics). Fish genomics was initially limited
to the study of developmental biology and genetic architecture of model fish such
as Japanese pufferfish (Takifugu rubripes) and zebrafish (Danio rerio). Recently,
the number of fishes for which genome wide sequence information is available has
risen steadily (Cossins and Crawford 2005, Kocher and Kole 2008). Fish population genomics was applied first in the freshwater environment (e.g. Campbell and
Bernatchez 2004) and later on in the oceans (e.g. Larsen et al. 2007). However,
relatively few studies deal with marine population genomics, which is in line with
the poor overall focus on marine biodiversity (Hendriks and Duarte 2008). The following paragraphs therefore aim at integrating key studies in the field of population
genomics to gain an understanding of state-of-the-art and future direction of marine
fish population genomics.
7.7.2 State-of the Art in the Population Genomics of Fishes
7.7.2.1 Identifying Population Structure and Dynamics
In order to manage marine fisheries resources sustainably, one of the most pertinent questions to answer is how genetic and genomic variation in exploited fish is
distributed in time and space (Carvalho and Hauser 1998). By conducting genetic
analyses throughout the targeted species distribution, it is possible to determine
whether it consists of one large genetically homogenous unit where individuals are
mating randomly, or a smaller or larger number of semi-independent populations or
“stocks”, with various degrees of reproductive isolation, and their spatial dynamics (e.g. Sinclair 1988, Hanski and Gilpin 1997, Waples and Gaggiotti 2006). At the
same time analysis of historical tissue collections available in museums and fisheries
institutions all over the world (Nielsen and Hansen 2008) can provide inferences on
the temporal dynamics of the identified population structure and the demographic
trajectories of individual populations.
Failing to recognize the evolutionary relationships among spawning groups
within a species may have dire consequences for fisheries management. It may lead
to the over-exploitation of small, isolated, slow growing populations and ultimately
to their extirpation (Dulvy et al. 2003) and associated loss of intraspecific biodiversity. Accordingly, management and conservation of fisheries resources has to be
population based. Here genetics has traditionally been playing an essential role in
delineating population structure to assist fisheries managers.
Population genetic analyses of fish have been conducted for more than five
decades. In general the number of populations and levels of genetic differentiation among populations is low for marine compared to freshwater and anadromous
fish (Ward et al. 1994). This may be attributed to higher levels of migration and
M.L. Cancela et al.
The field of marine population genetics has received a major impetus since the
end of the last millennium. Initially restricted to a small number of viruses, bacteria, model species and man, it is now being extended to an ever growing group
of taxa or even communities (metagenomics of microbial and picoplankton communities) (see Chapter 2 on Metagenomics). Fish genomics was initially limited
to the study of developmental biology and genetic architecture of model fish such
as Japanese pufferfish (Takifugu rubripes) and zebrafish (Danio rerio). Recently,
the number of fishes for which genome wide sequence information is available has
risen steadily (Cossins and Crawford 2005, Kocher and Kole 2008). Fish population genomics was applied first in the freshwater environment (e.g. Campbell and
Bernatchez 2004) and later on in the oceans (e.g. Larsen et al. 2007). However,
relatively few studies deal with marine population genomics, which is in line with
the poor overall focus on marine biodiversity (Hendriks and Duarte 2008). The following paragraphs therefore aim at integrating key studies in the field of population
genomics to gain an understanding of state-of-the-art and future direction of marine
fish population genomics.
7.7.2 State-of the Art in the Population Genomics of Fishes
7.7.2.1 Identifying Population Structure and Dynamics
In order to manage marine fisheries resources sustainably, one of the most pertinent questions to answer is how genetic and genomic variation in exploited fish is
distributed in time and space (Carvalho and Hauser 1998). By conducting genetic
analyses throughout the targeted species distribution, it is possible to determine
whether it consists of one large genetically homogenous unit where individuals are
mating randomly, or a smaller or larger number of semi-independent populations or
“stocks”, with various degrees of reproductive isolation, and their spatial dynamics (e.g. Sinclair 1988, Hanski and Gilpin 1997, Waples and Gaggiotti 2006). At the
same time analysis of historical tissue collections available in museums and fisheries
institutions all over the world (Nielsen and Hansen 2008) can provide inferences on
the temporal dynamics of the identified population structure and the demographic
trajectories of individual populations.
Failing to recognize the evolutionary relationships among spawning groups
within a species may have dire consequences for fisheries management. It may lead
to the over-exploitation of small, isolated, slow growing populations and ultimately
to their extirpation (Dulvy et al. 2003) and associated loss of intraspecific biodiversity. Accordingly, management and conservation of fisheries resources has to be
population based. Here genetics has traditionally been playing an essential role in
delineating population structure to assist fisheries managers.
Population genetic analyses of fish have been conducted for more than five
decades. In general the number of populations and levels of genetic differentiation among populations is low for marine compared to freshwater and anadromous
fish (Ward et al. 1994). This may be attributed to higher levels of migration and