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Biologists have long sought new and
foolproof ways to tell one animal species from another. Since Darwin,
scientists have used appearance
or reproductive compatibility to tell species apart.
But the ability to make iron-clad identifications has alluded them for
centuries.
For marine biologists, the quest for precision has been a special challenge
because of the strong physical similarities
that exist among many fish species. Now, scientists at Scripps Institution of
Oceanography at UC San Diego
are pioneering a technique that is taking the mystery out of fish
species identification. Scripps marine biology professors Ron Burton
and Phil Hastings are combining DNA identification with bar coding
technology,
the same idea behind retail checkout stands everywhere.
But instead of ringing up prices for milk or bread, biological barcoding
compares animal DNA in tissue samples with stored genetic information about a
specific species,
creating the genetic equivalent of a fingerprint match.
Burton and Hastings fish bar-coding project is in the midst of building a
database library one species at a time,
a reference that promises to become a trove of information about evolutionary
developments as it expands.
More immediately, it could assist in the conservation of fish populations,
including species threatened by extinction.
Well, fish bar-coding is a technique that we use to,
by using molecular sequence data to identify
either products or samples of certain species
by matching the genetic sequence in that sample
to a known genetic sequence taken from an organism that has been identified
properly. It's analogous to a supermarket bar-code in that
it's a very simple way to make identification but it's different in
that it's unique to each
species and each species has a unique sequence for certain gene
of choice. The project here at Scripps Institution of Oceanography was
funded by California Sea Grant in order to build an archive of known
genetic sequences from known specimens of
species for the all fishes in California. These marine vertebrates
collection at Scripps has been involved in this project
largely as an archive of the materials that we've been collecting.
So we archive here in the collection the specimen that the known, that the
tissue sample was taken from again, it's here
basically to serve as a voucher for confirming identifications in the
future.
We also archive the tissue samples here in the collection and those are used for a
variety of
genetic studies by researchers around the world. What we do in this lab is the
actual DNA sequencing.
Out of all of the DNA we just amplify a short sequence, about seven hundred base
pairs,
and make millions of copies of that
and those copies then are the results of that reaction
are then cleaned up, removing the
reactants, just keeping the DNA sequence of interest
and that DNA sequence is then put into a
DNA sequencing reaction and
automated sequencing follows and so the end result is
from each specimen we get a DNA sequence that's approximately
five to seven hundred base pairs long and that is in fact the DNA bar-code.
Establishing a database of California fish species
is giving researchers a level of understanding of fish evolution and
relationships between
fish that was not possible before fish bar codes.
Okay, there are a number of scientific applications for this barcode
and among them are identification of early life-history stages
of fishes. It's actually very difficult to identify
a fish larva to species and that's especially true for fish eggs
which more or less all look alike but using this genetic sequence we can
actually take
something that has no morphologically distinct characters on identified to
species.
The application of that is that by
being able to monitor the abundance of eggs and larvae
for instance at a marine reserve area, we give you some
insight into how effective the marine reserve is, serving for a haven for
reproduction and
in fishes that the refuge is protecting so we can identify say the
production of eggs from a certain area
using this technique. The California Fish Barcode project based at Scripps
is contributing to broad barcoding efforts hoping to apply barcodes to
every fish species on the planet. DNA barcoding is already been applied in
several cases to
monitor what's being sold in fish markets
and to make sure that labeling is in fact
indicative of what the species composition is in a market
it also is important for the public to
to make sure they're getting what they think they're getting and the reason for
this is
in some cases species in a market
like red snapper we could be seeing red snapper
at many fish markets and that would lead someone to believe that the fish is
actually very common
when in fact what's being sold is a diversity of different species,
some of which are common some of which aren't and so it can lead to a false
impression about the abundances of species to the public and so you can
see where you would say you know
red snapper is in a decline
yet someone going to fish markets would say how can it be in decline every
market I go to has tons of red snapper to sell.
Well in fact a lot of those fish have been shown not to actually be
red snapper but to be others sometimes related, sometimes
less related species. Not only are fish being bar-coded
but scientists around the world have undertaken the ambitious task of
classifying every organism on the planet envisioning
future devices capable of tapping into databases full of information,
scientists involved in the International Barcode of Life Project
are hoping to put the natural world at our fingertips.
Our project was actually conceived several years ago
to serve as a resource for the fishes of California. That's only one
of several ongoing projects to create similar databases for other lineages
of organisms. For example, there's a group in England that's assembling a bar
code for all mosquito species
in the world and that's actually is very important for disease,
monitoring disease factors, etc. Well,
a former colleague of mine, Dan Jansen has suggested that
you know what we ought to work towards is a small hand-held unit
that we could basically plug into any little piece of tissue and it would read
back
from the DNA barcode database.
It would tell you what the sequence is, compare it to all existing sequences and
instantly inform us
preferably not only what the species is but give you a full
range of information about that species. Where it's
found, what it does, and so on and
we're getting to the point given changes in technology all the time
where it's not too far reaching to think that a little hand-held device
could give us a DNA sequence in a matter of
a couple minutes.
This has been a presentation
of Scripps Institution of Oceanography at UC San Diego.