Preface
vii
of a species to adapt to perturbations of the environment are particularly important for predicting the effects of climate change or other anthropogenic factors. The
chapter begins with an overview of the methodologies available for analyses at both
the DNA and RNA level and then goes on to discuss the relative merits of the tools
available with respect to the type of question that is being addressed. Finally, the
chapter uses some examples to illustrate how genomic approaches have been and
are being used in different contexts to answer questions about the structure and
dynamics of populations and ecosystems in the marine environment.
The next two chapters concentrate on the impact of genomics on metazoan
research. Chapter 4 describes how genomic approaches have been used to improve
our understanding of the phylogeny of the metazoans. Early attempts to deduce
the evolutionary history of the metazoans, based solely on morphological and
developmental features, were susceptible to errors, due to factors such as morphological simplification of previously complex lineages and difficulties inherent in
scoring and evaluating this type of feature. The introduction of gene-based phylogenetic methods led to a revolution in this field, leading to what is known as the
“New View” of animal phylogeny, but certain relationships within the metazoans
remained unresolved or controversial. Phylogenomic approaches, employing much
more complete, “genome-scale” datasets, are now being employed to address these
questions. This chapter describes how genome information is being used in phylogenomic studies and provides some examples of important insights produced by
these approaches such as the recent re-evaluation of chordate relationships.
Chapter 5 looks specifically at the evolution of complexity in the animal lineage. Extension of work with model organisms to a much broader range of species,
including many marine animals, has provide a more complete view of the evolution
of complexity in the metazoans, particularly in terms of the underlying molecular
genetic processes. These studies challenge the assumption that descendants are necessarily more complex than their ancestors and show that simplification has occurred
in several lineages. By dissecting the molecular processes at work at different stages
of evolution, these studies have shed light on several major evolutionary transitions,
such as the transition to multicellularity or the origin of germ layers.
Chapter 6 focuses on the use of genomic methods to study marine algae. The
term “algae” assembles a very diverse collection of taxonomic groups that all
share one feature, the ability to carry out photosynthesis. These organisms play
an important role in the planet’s geochemical cycles and they are a rich source of
novel biomolecules and bioprocesses. The important contribution of both genome
sequencing and metagenomic analyses to the recent acceleration in our understanding of the biology of marine algae is discussed. The chapter also underlines the
importance of the recent development of model organisms for several major algal
groups.
Aquaculture is a rapidly expanding sector worldwide but the genomics resources
available in this area remain poorly exploited. Chapter 7 discusses the application of
genomic approaches to fish and shellfish and discusses how the data generated can
be exploited to address aspects such as reproduction, growth and nutrition, product
vii
of a species to adapt to perturbations of the environment are particularly important for predicting the effects of climate change or other anthropogenic factors. The
chapter begins with an overview of the methodologies available for analyses at both
the DNA and RNA level and then goes on to discuss the relative merits of the tools
available with respect to the type of question that is being addressed. Finally, the
chapter uses some examples to illustrate how genomic approaches have been and
are being used in different contexts to answer questions about the structure and
dynamics of populations and ecosystems in the marine environment.
The next two chapters concentrate on the impact of genomics on metazoan
research. Chapter 4 describes how genomic approaches have been used to improve
our understanding of the phylogeny of the metazoans. Early attempts to deduce
the evolutionary history of the metazoans, based solely on morphological and
developmental features, were susceptible to errors, due to factors such as morphological simplification of previously complex lineages and difficulties inherent in
scoring and evaluating this type of feature. The introduction of gene-based phylogenetic methods led to a revolution in this field, leading to what is known as the
“New View” of animal phylogeny, but certain relationships within the metazoans
remained unresolved or controversial. Phylogenomic approaches, employing much
more complete, “genome-scale” datasets, are now being employed to address these
questions. This chapter describes how genome information is being used in phylogenomic studies and provides some examples of important insights produced by
these approaches such as the recent re-evaluation of chordate relationships.
Chapter 5 looks specifically at the evolution of complexity in the animal lineage. Extension of work with model organisms to a much broader range of species,
including many marine animals, has provide a more complete view of the evolution
of complexity in the metazoans, particularly in terms of the underlying molecular
genetic processes. These studies challenge the assumption that descendants are necessarily more complex than their ancestors and show that simplification has occurred
in several lineages. By dissecting the molecular processes at work at different stages
of evolution, these studies have shed light on several major evolutionary transitions,
such as the transition to multicellularity or the origin of germ layers.
Chapter 6 focuses on the use of genomic methods to study marine algae. The
term “algae” assembles a very diverse collection of taxonomic groups that all
share one feature, the ability to carry out photosynthesis. These organisms play
an important role in the planet’s geochemical cycles and they are a rich source of
novel biomolecules and bioprocesses. The important contribution of both genome
sequencing and metagenomic analyses to the recent acceleration in our understanding of the biology of marine algae is discussed. The chapter also underlines the
importance of the recent development of model organisms for several major algal
groups.
Aquaculture is a rapidly expanding sector worldwide but the genomics resources
available in this area remain poorly exploited. Chapter 7 discusses the application of
genomic approaches to fish and shellfish and discusses how the data generated can
be exploited to address aspects such as reproduction, growth and nutrition, product