Ann Bucklin, University of Conneticut
Listen Now Download as mp3 from the show The Census of Marine Life - Celebrating a decade of discoveries
With many millions of specimens collected by scientists from the Census of Marine Life over the last decade, the task of identifying them all to species level is still a long way out of reach. But powerful genetic tools have been developed that help catalogue ocean diversity much more quickly than is possible with traditional taxonomy.
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Ann - We would love to name everything in the ocean. We have a team of expert taxonomists in every team whose job it is to name species. Weíve found hundreds of new species, weíre in the process of naming them, we think itís the right thing to do.
The problem is that naming species with formal taxonomic descriptions is a very slow process. And so many of us feel that we just donít have the time. So the next best thing that we can offer is some kind of objective, reliable, valid indicator of what a species is.
What the Census has done is say that we have a reliable marker of species that we call a DNA barcode. And thatís a short sequence and we know that it doesnít contain all the information that we know morphologists would like us to have. But we also know that itís a really good indicator of what a species is and is not.
And so the goal of the Census barcoders is to provide a set of data which can be translated eventually, when we get to it, into species. The wonder of barcodes Ė there are some dynamics of DNA sequences that are quite remarkable and extremely helpful in this endeavour. One of them, in all cases the DNA sequence variation is less within a species than between a species. Thatís called a barcode gap. Barcodes are good to identify species.
Another one is that barcodes do a very good job of clustering major groups of animals. You may not know what species it is but you know which group it belongs to. And so with barcodes you can get a kind of an index of biodiversity. It isnít the same as naming species but it actually is going to help us conserve them.
Sarah - Ann, how do you go about barcoding? Do you take a scoop of sediment and work out, right, thereís this many types of nematode worm, thereís this many types of mollusc in this sample.
Ann - The way the Census has started barcoding is what we call ďgold standard barcodingĒ. And so we work from an identified specimen. A taxonomist says this is the species and that taxonomist gives the specimen to the barcoders and we determine a sequence. And so now we have a gold standard. We have a DNA sequence with a name on it. And so overall, 35,000 species of marine organisms, marine animals, have been barcoded.
Now, what weíre starting to do is to take that scoop of animals, whether itís a net sample of plankton, a scoop of sediment, any type of habitat that you could name and weíre doing deep sequencing with a new high through-put sequencing.
What we do then is a very complicated analytical task, which is done for us by bioinformatics, to tell us how many species we think are in that sample. Some of those will match our library of gold standard barcodes, some will not. But some will be close enough so that we can classify. So we can say, we donít know what copepod that is but we know itís a copepod. So thatís the power of what we call environmental barcoding.
Sarah - So how important do you think barcoding has been within the Census. How important a role has it played within it?
Ann - The Census has embraced barcoding across all the 14 field projects. Thereís a partner program to the Census thatís called the Consortium of the Barcode of Life. And the Consortium of the Barcode of Life has a campaign for marine species that started in 2004 and weíve worked very closely together. Some of the Census projects have partnered with the Consortium of the Barcode of Life, some of them have done it themselves.
But very early on in the Census, all of the projects were asked to designate a person, a laboratory, to learn the standardized techniques of the Consortium of the Barcode of Life, all of the data quality requirements.
So what we have now, of course, is a situation where the sum is great, much greater, than itís parts because we actually have data from all the Census projects that are entirely comparable, carried out using the same protocol, the same approach, the same gene, so we are looking at a library of barcodes now that is going to be a baseline for us to both to continue the gold standard barcoding effort and also use environmental barcoding to do this kind of index. We call it a genomic signature, a genomic fingerprint so that each ocean realm can have a different genomic fingerprint characterised by barcode diversity. Itís not the same as knowing species diversity, but itís close.