1 Genomics in the Discovery and Monitoring
9
marine species from on-going environmental change and habitat disturbance make
it increasingly important to develop rapid and robust ways of describing and cataloguing marine biodiversity. Molecular tools of universal implementation, such as
the recently proposed DNA barcodes (“a rigorously standardized sequence of a minimum length and quality from an agreed-upon gene, deposited in a major sequence
database, and attached to a voucher specimen whose origins and current status are
recorded”) can counter conventional limitations, providing a simple, yet robust system to unambiguously identify not only whole individuals, but eggs, larvae and body
fragments. Such approaches necessarily include a range of molecular identification
strategies based on the analysis of homologous gene regions (e.g. COI, 16S, 18S and
ITS) for delimiting species boundaries and in their discovery, as well as associated
“genome screens” for the identification of functional capacity.
Hebert et al. (2003) introduced the concept of a DNA barcode, and proposed
a new global approach to species identification, which offered great promise to
counter many limitations of the classical taxonomic approach. The new approach
was based on the premise that the sequence analysis of a short fragment of a single
gene (eg, cytochrome c oxidase subunit 1, CO1), enables unequivocal identification
of many animal species. Hence, the DNA barcode would provide a standardised tool
for fast, simple, robust and precise species identification. The rationale and approach
of DNA barcoding are essentially the same whichever region of the genome is
selected. The basic premise is that for each currently known species an unequivocal match can be established with the DNA barcode obtained by comparing the
same DNA regions. The resultant “matching hypothesis” underpins the rationale
for implementing the new molecular bioidentification system, which importantly
also extends and incorporates, rather than substitutes, the classical Linnaean system (Costa and Carvalho 2007). It is also assumed that a low between- versus
within-species divergence represents reproductively isolated entities according to
the biological species concept, thereby conforming to the Linnaean binomial system (Goméz et al. 2007). Reference barcoded specimens of each species that have
been identified by experts are deposited in a museum and therefore available for
double-checking and for long-term study. Once this reference database is complete,
it can be used to assign an unknown sample to a known species.
Whilst COI-based molecular barcoding is gaining momentum, COI does not
work effectively for the molecular identification of all eukaryotic taxa and different markers are used for bacteria, Archaea and viruses (see below). This is
predominantly because in some eukaryotes, such as the nematoda, the COI gene is
characterised by unusual molecular evolutionary rates and processes. In nematodes,
COI has high mutational rates and is very A+T rich with biased substitution patterns
(Blouin et al. 1998, Blouin 2000) making it rather unsuitable for DNA taxonomy
studies (Hajibabaei et al. 2007). Such challenges are demanding the acknowledgement of alternative markers for certain taxa and attempts are being made to
accommodate suites of markers into the DNA barcoding movement. Examples of
alternative markers include ribosomal genes that have been used for decades to identify multiple suites of microbial eukaryotes. It was first demonstrated in the 1960s
that ribosomal genes (rDNA) and their gene products (rRNA) could be used for the
9
marine species from on-going environmental change and habitat disturbance make
it increasingly important to develop rapid and robust ways of describing and cataloguing marine biodiversity. Molecular tools of universal implementation, such as
the recently proposed DNA barcodes (“a rigorously standardized sequence of a minimum length and quality from an agreed-upon gene, deposited in a major sequence
database, and attached to a voucher specimen whose origins and current status are
recorded”) can counter conventional limitations, providing a simple, yet robust system to unambiguously identify not only whole individuals, but eggs, larvae and body
fragments. Such approaches necessarily include a range of molecular identification
strategies based on the analysis of homologous gene regions (e.g. COI, 16S, 18S and
ITS) for delimiting species boundaries and in their discovery, as well as associated
“genome screens” for the identification of functional capacity.
Hebert et al. (2003) introduced the concept of a DNA barcode, and proposed
a new global approach to species identification, which offered great promise to
counter many limitations of the classical taxonomic approach. The new approach
was based on the premise that the sequence analysis of a short fragment of a single
gene (eg, cytochrome c oxidase subunit 1, CO1), enables unequivocal identification
of many animal species. Hence, the DNA barcode would provide a standardised tool
for fast, simple, robust and precise species identification. The rationale and approach
of DNA barcoding are essentially the same whichever region of the genome is
selected. The basic premise is that for each currently known species an unequivocal match can be established with the DNA barcode obtained by comparing the
same DNA regions. The resultant “matching hypothesis” underpins the rationale
for implementing the new molecular bioidentification system, which importantly
also extends and incorporates, rather than substitutes, the classical Linnaean system (Costa and Carvalho 2007). It is also assumed that a low between- versus
within-species divergence represents reproductively isolated entities according to
the biological species concept, thereby conforming to the Linnaean binomial system (Goméz et al. 2007). Reference barcoded specimens of each species that have
been identified by experts are deposited in a museum and therefore available for
double-checking and for long-term study. Once this reference database is complete,
it can be used to assign an unknown sample to a known species.
Whilst COI-based molecular barcoding is gaining momentum, COI does not
work effectively for the molecular identification of all eukaryotic taxa and different markers are used for bacteria, Archaea and viruses (see below). This is
predominantly because in some eukaryotes, such as the nematoda, the COI gene is
characterised by unusual molecular evolutionary rates and processes. In nematodes,
COI has high mutational rates and is very A+T rich with biased substitution patterns
(Blouin et al. 1998, Blouin 2000) making it rather unsuitable for DNA taxonomy
studies (Hajibabaei et al. 2007). Such challenges are demanding the acknowledgement of alternative markers for certain taxa and attempts are being made to
accommodate suites of markers into the DNA barcoding movement. Examples of
alternative markers include ribosomal genes that have been used for decades to identify multiple suites of microbial eukaryotes. It was first demonstrated in the 1960s
that ribosomal genes (rDNA) and their gene products (rRNA) could be used for the