6
G.R. Carvalho et al.
and management (Pikitch et al. 2004), whereby the focus of effort has shifted from
individual components such as populations and species, to the interdependence of
communities and trophic levels. Initially, we will describe briefly the nature of
marine biodiversity, and then examine salient advances that have revolutionized our
ability to study its dynamics and distribution. The synthesis is not intended to be
comprehensive, but rather illustrates approaches and applications that are developed
further in accompanying chapters.
1.1.2 The Nature of Marine Biodiversity
Biodiversity is an all inclusive term to describe the variety of living organisms and
their environments, and it can be divided into four main components: (1) Genetic
diversity, that refers to the within-species genetic variation, a crucial determinant of
the ability of populations and species to withstand and recover from environmental
perturbations; (2) Species diversity, which describes the variety of species or other
taxonomic groups within an ecosystem, and represents the key identifiable units
that determine the complexity and resilience of habitats; (3) Ecosystem diversity,
that refers to the range of biological communities and the dynamics and nature of
their interdependence and interactions with the environment. Diversity at this level
is distinct from (1) and (2) in that it comprises both a living (biotic) and non-living
(abiotic) component; (4) Functional diversity, which includes the array of biological processes, functions or characteristics of a specific ecosystem. Some argue that
functional diversity may well be the most meaningful way of assessing biodiversity
because it does not necessitate the cataloguing of all species within an ecosystem,
and may thereby provide a tractable way for conserving marine natural systems.
Although such a view would be well supported by genomic approaches, its application is constrained by the usual need to relate diversity to function at different spatial
scales (Bulling et al. 2006, Naeem 2006), and the fact that many species and their
function are, as yet, undefined.
1.1.3 Empirical and Conceptual Advances
Genomics within the current context is a scientific discipline that studies the structure, function and diversity of genes and gene products in the genome of a species
with the aim of understanding the relationship between an organism and its biotic
and abiotic environment. Various advances at different biological levels have revolutionized our ability to analyze genome structure and function (Wilson et al.
2005): (1) At the level of DNA: including the development of high throughput DNA
sequencing, and recent enhancement using next generation sequencing technologies
(Rothberg and Leamon 2008); (2) At the level of gene expression (“transcriptomics”)
using microarray or digital gene expression technology; (3) At the level of protein products, with improved analysis of proteins (“proteomics”) using tandem
G.R. Carvalho et al.
and management (Pikitch et al. 2004), whereby the focus of effort has shifted from
individual components such as populations and species, to the interdependence of
communities and trophic levels. Initially, we will describe briefly the nature of
marine biodiversity, and then examine salient advances that have revolutionized our
ability to study its dynamics and distribution. The synthesis is not intended to be
comprehensive, but rather illustrates approaches and applications that are developed
further in accompanying chapters.
1.1.2 The Nature of Marine Biodiversity
Biodiversity is an all inclusive term to describe the variety of living organisms and
their environments, and it can be divided into four main components: (1) Genetic
diversity, that refers to the within-species genetic variation, a crucial determinant of
the ability of populations and species to withstand and recover from environmental
perturbations; (2) Species diversity, which describes the variety of species or other
taxonomic groups within an ecosystem, and represents the key identifiable units
that determine the complexity and resilience of habitats; (3) Ecosystem diversity,
that refers to the range of biological communities and the dynamics and nature of
their interdependence and interactions with the environment. Diversity at this level
is distinct from (1) and (2) in that it comprises both a living (biotic) and non-living
(abiotic) component; (4) Functional diversity, which includes the array of biological processes, functions or characteristics of a specific ecosystem. Some argue that
functional diversity may well be the most meaningful way of assessing biodiversity
because it does not necessitate the cataloguing of all species within an ecosystem,
and may thereby provide a tractable way for conserving marine natural systems.
Although such a view would be well supported by genomic approaches, its application is constrained by the usual need to relate diversity to function at different spatial
scales (Bulling et al. 2006, Naeem 2006), and the fact that many species and their
function are, as yet, undefined.
1.1.3 Empirical and Conceptual Advances
Genomics within the current context is a scientific discipline that studies the structure, function and diversity of genes and gene products in the genome of a species
with the aim of understanding the relationship between an organism and its biotic
and abiotic environment. Various advances at different biological levels have revolutionized our ability to analyze genome structure and function (Wilson et al.
2005): (1) At the level of DNA: including the development of high throughput DNA
sequencing, and recent enhancement using next generation sequencing technologies
(Rothberg and Leamon 2008); (2) At the level of gene expression (“transcriptomics”)
using microarray or digital gene expression technology; (3) At the level of protein products, with improved analysis of proteins (“proteomics”) using tandem