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DNA Barcoding
Biodiversity studies represent the first step to provide a baseline for detecting the effect of climate change on marine
biota. A precise identification of all ecosystem components
will allow to analyze interspecific interactions and will
enable to determine factors, which influence its functioning.
Until recently, most of the biodiversity research has been
based on morphological analyses, which have many limitations, what might result in underestimation of diversity. In
the marine environment, cryptic speciation is common,
resulting in genetically differentiated lineages that are undistinguishable morphologically (Bickford et al. 2006).
Nonetheless, their recognition is important, as they can have
different functions in ecosystems (Fišer et al. 2015).
Similarly, the identification of very small organisms or early
life stages may be problematic, resulting in identification
restricted to the phylum or family level.
A promising auxiliary approach is the use of molecular
methods for identification and discrimination of species,
known as DNA barcoding, which enables not only the
assignment of unknown species, but it also enhances the discovery of new species (Bucklin et al. 2011), by matching
their genetic fingerprint to a known barcode reference. Its
development in recent years enabled more accurate species
identification (Hebert et al. 2003), and the effectiveness of
this approach has been established for several large groups of
organisms (Bucklin et al. 2011), due to contribution of big,
international projects, like Barcode of Life (www.barcodeoflife.org). Here, species identification is achieved by the
analysis of a short DNA sequence from a specific gene
region, called “the barcode”, by comparing it with the library
of reference barcode sequences derived from species of
known identity (Hajibabaei et al. 2007). The method is based
on the assumption that genetic differences between sequences
within a species (intraspecific variability) are smaller than
genetic differences among species (interspecific variability),
reflected in the so-called “barcoding gap” (a min. % difference between intra- and interspecific variability), can be
used to match the specimen’s barcode in the database, if an
appropriate reference sequence is available. The presence,
extent, and “position” of the barcoding gap differs between
species, and hence there is a need to use different markers for
different groups of organisms. One of the most commonly
used markers in animals is a 648-base fragment at the 5′ end
of mitochondrial gene cytochrome c oxidase I (COI), as it
has no introns (in some groups of animals), limited recombination and many copies per cell (Hajibabaei et al. 2007).
Other popular markers include the genomic ITS (internal
transcribed spacer I and II), 18S and the mitochondrial 16S
rDNA. The number of sequences in databases like GenBank
or BOLD are constantly increasing at a very fast rate.
Hajibabaei et al. (2007) summarized the number of available
sequences in public databases, and in only few years these
numbers have increased several times. Information on popular markers used for DNA barcoding and the corresponding
number of available sequences per organism group are presented in Table 2.
Like all identification methods, DNA barcoding has its
flaws, as it requires a reference sequence in the database
based on accurately identified organisms. Even though the
development of Gen Bank is very dynamic – new sequences
are submitted every day – sequences from many organisms
are lacking whilst other sequences may be present under a
wrongly identified species name. Nevertheless, molecular
methods may have advantages over morphological methods
in species identification as there is a lack of unique diagnostic morphological or morphometric characteristics separating species, but it can also be performed by a person without
specialized taxonomic knowledge. An integrative approach
using both molecular and morphological analyses, has been
shown to strengthen species identification in previous polar
taxonomic studies and provided the most reliable taxonomic
resolution (Heimeier et al. 2010) as compared to using either
method alone.
Indeed, identification of organisms based on nucleotide
sequences it is not always 100% accurate, which has led to
the use of the term Operational Taxonomic Unit (OTU) or –
in case of barcoding – Molecular Operational Taxonomic
Unit (MOTU), instead of “species”. Studies have been carried out where the function of particular organisms in the
ecosystem have been attributed to MOTUs (Ryberg 2015).
In the following sections we will provide examples to
illustrate the use of DNA barcoding in Arctic diversity
research and how can it be useful for detecting and monitoring of different processes in several important groups of
marine organisms.
Plankton
Plankton is a very diverse group, containing very small
organisms like viruses, heterotrophic single-cell organisms
(bacterioplankton), autotrophic organisms (phytoplankton)
and bigger animals (zooplankton). The diverse planktonic
communities encompass both the tiniest autotrophs, like unicellular algae Synechoccocus and Prochloroccocus, which
are responsible for the production of approximately 60% of
the atmospheric oxygen, as well as the siphonophores, which
can grow to about 40 m in length (Robison 1995). Yet another
important component of the plankton are pelagic copepod
crustaceans, which in many regions of the World’s Ocean are
the key species of the pelagic food webs, constituting up to
70% of the whole plankton biomass (Søreide et al. 2008).
Their relatively short life cycles, high reproductive outputs,
lack of direct antropogenic pressure and distributions depenArctic Ocean Biodiversity and DNA Barcoding – A Climate Change Perspective
DNA Barcoding
Biodiversity studies represent the first step to provide a baseline for detecting the effect of climate change on marine
biota. A precise identification of all ecosystem components
will allow to analyze interspecific interactions and will
enable to determine factors, which influence its functioning.
Until recently, most of the biodiversity research has been
based on morphological analyses, which have many limitations, what might result in underestimation of diversity. In
the marine environment, cryptic speciation is common,
resulting in genetically differentiated lineages that are undistinguishable morphologically (Bickford et al. 2006).
Nonetheless, their recognition is important, as they can have
different functions in ecosystems (Fišer et al. 2015).
Similarly, the identification of very small organisms or early
life stages may be problematic, resulting in identification
restricted to the phylum or family level.
A promising auxiliary approach is the use of molecular
methods for identification and discrimination of species,
known as DNA barcoding, which enables not only the
assignment of unknown species, but it also enhances the discovery of new species (Bucklin et al. 2011), by matching
their genetic fingerprint to a known barcode reference. Its
development in recent years enabled more accurate species
identification (Hebert et al. 2003), and the effectiveness of
this approach has been established for several large groups of
organisms (Bucklin et al. 2011), due to contribution of big,
international projects, like Barcode of Life (www.barcodeoflife.org). Here, species identification is achieved by the
analysis of a short DNA sequence from a specific gene
region, called “the barcode”, by comparing it with the library
of reference barcode sequences derived from species of
known identity (Hajibabaei et al. 2007). The method is based
on the assumption that genetic differences between sequences
within a species (intraspecific variability) are smaller than
genetic differences among species (interspecific variability),
reflected in the so-called “barcoding gap” (a min. % difference between intra- and interspecific variability), can be
used to match the specimen’s barcode in the database, if an
appropriate reference sequence is available. The presence,
extent, and “position” of the barcoding gap differs between
species, and hence there is a need to use different markers for
different groups of organisms. One of the most commonly
used markers in animals is a 648-base fragment at the 5′ end
of mitochondrial gene cytochrome c oxidase I (COI), as it
has no introns (in some groups of animals), limited recombination and many copies per cell (Hajibabaei et al. 2007).
Other popular markers include the genomic ITS (internal
transcribed spacer I and II), 18S and the mitochondrial 16S
rDNA. The number of sequences in databases like GenBank
or BOLD are constantly increasing at a very fast rate.
Hajibabaei et al. (2007) summarized the number of available
sequences in public databases, and in only few years these
numbers have increased several times. Information on popular markers used for DNA barcoding and the corresponding
number of available sequences per organism group are presented in Table 2.
Like all identification methods, DNA barcoding has its
flaws, as it requires a reference sequence in the database
based on accurately identified organisms. Even though the
development of Gen Bank is very dynamic – new sequences
are submitted every day – sequences from many organisms
are lacking whilst other sequences may be present under a
wrongly identified species name. Nevertheless, molecular
methods may have advantages over morphological methods
in species identification as there is a lack of unique diagnostic morphological or morphometric characteristics separating species, but it can also be performed by a person without
specialized taxonomic knowledge. An integrative approach
using both molecular and morphological analyses, has been
shown to strengthen species identification in previous polar
taxonomic studies and provided the most reliable taxonomic
resolution (Heimeier et al. 2010) as compared to using either
method alone.
Indeed, identification of organisms based on nucleotide
sequences it is not always 100% accurate, which has led to
the use of the term Operational Taxonomic Unit (OTU) or –
in case of barcoding – Molecular Operational Taxonomic
Unit (MOTU), instead of “species”. Studies have been carried out where the function of particular organisms in the
ecosystem have been attributed to MOTUs (Ryberg 2015).
In the following sections we will provide examples to
illustrate the use of DNA barcoding in Arctic diversity
research and how can it be useful for detecting and monitoring of different processes in several important groups of
marine organisms.
Plankton
Plankton is a very diverse group, containing very small
organisms like viruses, heterotrophic single-cell organisms
(bacterioplankton), autotrophic organisms (phytoplankton)
and bigger animals (zooplankton). The diverse planktonic
communities encompass both the tiniest autotrophs, like unicellular algae Synechoccocus and Prochloroccocus, which
are responsible for the production of approximately 60% of
the atmospheric oxygen, as well as the siphonophores, which
can grow to about 40 m in length (Robison 1995). Yet another
important component of the plankton are pelagic copepod
crustaceans, which in many regions of the World’s Ocean are
the key species of the pelagic food webs, constituting up to
70% of the whole plankton biomass (Søreide et al. 2008).
Their relatively short life cycles, high reproductive outputs,
lack of direct antropogenic pressure and distributions depenArctic Ocean Biodiversity and DNA Barcoding – A Climate Change Perspective