Chapter 3
Populations and Pathways: Genomic
Approaches to Understanding Population
Structure and Environmental Adaptation
Melody S. Clark, Arnaud Tanguy, Didier Jollivet, François Bonhomme,
Bruno Guinand, and Frédérique Viard
Abstract The field of Genomics has essentially been fuelled by medical research
with developments in human gene therapy, such as the Human Genome Project.
This major international undertaking resulted in a significantly increased sequencing capacity, a dramatic decrease in the time and cost of sequencing and also the
computational effort required for the analysis. Marine biologists are taking advantage of this high throughput technology, hence, the tools are now available to answer
questions that would have not been possible even five years ago. Genomics, in terms
of studying DNA, can effectively define the genetic structure of populations and as
a consequence the mapping of species boundaries, approximate drift in populations
and accurately measure biodiversity. Studying transcribed sequences (RNA) enables
the identification of changes at the cellular level associated with the adaptation of
species to particular habitats and now, in our changing environment, predicts their
ability to survive perturbation.
The aim of this chapter is to familiarize the reader with the most commonly used
genomic techniques that are available for population and adaptation studies. These
encompass both DNA based methodologies for population studies and RNA based
techniques for expression studies. Which technique is used largely depends on the
species under study and the resources available. In environmental research it is
important to understand that “resources” does not just refer to money for sequencing
and library production, but also access to starting material and the ability to store
the material successfully, often under difficult conditions. For example, a cruise to
investigate a particular hydrothermal vent may only happen once in a researcher’s
lifetime and so material will be scarce, numbers will be limited and it may not be
possible to store the material at a low enough temperature to prevent RNA degradation (thereby excluding expression studies). Also species availability tends to be on
what is there at the time, rather than being able to perform a calculated choice for
which species is the best to study. In other studies such as aquaculture or invasive
M.S. Clark (B)
Ecosystems, British Antarctic Survey, Natural Environment Research Council, Cambridge CB3
0ET, UK
e-mail: mscl@bas.ac.uk
73
J.M. Cock et al. (eds.), Introduction to Marine Genomics,
Advances in Marine Genomics 1, DOI 10.1007/978-90-481-8639-6_3,
C
Springer Science+Business Media B.V. 2010
Populations and Pathways: Genomic
Approaches to Understanding Population
Structure and Environmental Adaptation
Melody S. Clark, Arnaud Tanguy, Didier Jollivet, François Bonhomme,
Bruno Guinand, and Frédérique Viard
Abstract The field of Genomics has essentially been fuelled by medical research
with developments in human gene therapy, such as the Human Genome Project.
This major international undertaking resulted in a significantly increased sequencing capacity, a dramatic decrease in the time and cost of sequencing and also the
computational effort required for the analysis. Marine biologists are taking advantage of this high throughput technology, hence, the tools are now available to answer
questions that would have not been possible even five years ago. Genomics, in terms
of studying DNA, can effectively define the genetic structure of populations and as
a consequence the mapping of species boundaries, approximate drift in populations
and accurately measure biodiversity. Studying transcribed sequences (RNA) enables
the identification of changes at the cellular level associated with the adaptation of
species to particular habitats and now, in our changing environment, predicts their
ability to survive perturbation.
The aim of this chapter is to familiarize the reader with the most commonly used
genomic techniques that are available for population and adaptation studies. These
encompass both DNA based methodologies for population studies and RNA based
techniques for expression studies. Which technique is used largely depends on the
species under study and the resources available. In environmental research it is
important to understand that “resources” does not just refer to money for sequencing
and library production, but also access to starting material and the ability to store
the material successfully, often under difficult conditions. For example, a cruise to
investigate a particular hydrothermal vent may only happen once in a researcher’s
lifetime and so material will be scarce, numbers will be limited and it may not be
possible to store the material at a low enough temperature to prevent RNA degradation (thereby excluding expression studies). Also species availability tends to be on
what is there at the time, rather than being able to perform a calculated choice for
which species is the best to study. In other studies such as aquaculture or invasive
M.S. Clark (B)
Ecosystems, British Antarctic Survey, Natural Environment Research Council, Cambridge CB3
0ET, UK
e-mail: mscl@bas.ac.uk
73
J.M. Cock et al. (eds.), Introduction to Marine Genomics,
Advances in Marine Genomics 1, DOI 10.1007/978-90-481-8639-6_3,
C
Springer Science+Business Media B.V. 2010