Going GaGa for DNA Barcodes?

Aleiodes gaga (Braconidae).  From Butcher, Smith, Sharkey and Quicke (2012), ZooTaxa 3457: 1-232.

As I said in a recent New to Nature column in The Observer perhaps the best part of a recent paper by Butcher et al. in which nearly 180 new species of Braconidae of the genus Aleiodes are described from Thailand is that it ends the charade that advocates of DNA barcoding see it only as a new species identification tool and not a process for discovering new species.  Of course the web page banner for the Canadian Centre for DNA Barcoding already blew their cover with its proud slogan: "Advancing species identification and discovery."  One would think that they seriously believe that species are just sitting there waiting to be recognized, that species are nothing more than arbitrary bits of more or less continuous variation, and that species do not require any cerebral effort, just technology.  That traditionally discovered and described species are carefully worded hypotheses based on the comparison of many specimens, often hundreds or thousands, that make generalizations about the distributions of characters that are explicitly and rigorously testable seems not to deter the DNA barcoders from discovering "species" based on slight differences in a fragment of COI.

I do give thanks and credit to Butcher et al. for being explicit and for creating a large dataset that can become a test bed for just how well DNA barcodes do at detecting new species.  Even more, they had the good sense and decency to treat their sequence data as characters, naming names as it were and specifying the nucleic acids at particular bases rather than the Canadian Chaos method that just measures distances.

Among their species is one that they named in honour of Lady GaGa.  This was a shrewd move and there were thousands of sites returned on a Google search less than 24 hours after my column was printed in London.  The authors may have gone gaga for DNA, but at least they have a sense of humor.  The GaGa species differs from its nearest relative by just four nucleobases... G-A-G-A.

Dear Carl,


Your legacy continues.  You will be delighted to read the latest State of Observed Species (SOS) Report from the International Institute for Species Exploration.  It documents that 19,232 new species were named in calendar year 2009... about twice as many species as you knew in your lifetime!  You will not be surprised that the largest number were insects, and of those, beetles.  Some things never change.  Your life's work continues apace and there is no end in sight.  Frontiers are opening on every front.  The Russians will probably break through the ice shield of Antarctica this week to tap the third largest freshwater lake on earth, its first connection with the surface through thousands of metres of ice for hundreds of thousands of years.  Like one of your blushing flowers, Vostok will soon yield its biodiversity for our exploration and amazement.  And the IISE is on the threshold of a demonstration project that will show how museums and their collections can be catapulted into center stage for biodiversity research and exploration in the 21st century.

Your humble disciple,


QDW

Dear Caroli,

I have long struggled to comprehend why taxonomy is so misunderstood, particularly by non-taxonomic biologists.  At least part of the confusion is that taxonomy is many things to many people.  To a field biologist who simply wants to identify a plant or animal at a study site, the whole of his exposure to taxonomy may progress no farther than a diagnostic key and a bewildering list of synonyms.  To him, synonyms are a nuisance inasmuch as he just wants to know what name to use.  And once identified and known by name, he may not see further need of taxonomy.  It is to this almost trivial aspect of taxonomy that things like DNA barcoding is directed.  It assumes that species are just arbitrary bits of a genetic continuum carved out and named for convenience and to avoid biodiversity chaos.  Were this true, DNA barcoding would be as good an option as any.  Fortunately, it is not.

To the comparative biologist, taxonomy is the source of hypotheses about phylogenetic relationship and an incredibly useful vocabulary by which to indicate which monophyletic clade is being discussed.  This phylogenetic systematic division of taxonomy begins to get at the depth, complexity, and intellectual richness of taxonomy.

A growing user community are the biomimicry pioneers who would use evolutionary adaptations as a source of entrepreneurship and problem-solving.  To this community, taxonomy is not merely an identification and a name.  The phylogenetic classification is the key to predicting where to look to find an attribute of an organism of interest.  Moreover, it is in the detailed description of species --- the attention to anatomical detail --- that many of the most important adapations are to be found.  This community appreciates that there is deep value in descriptions that can never be approached by molecular data alone, even if barcodes are aligned with libraries of known species (something both claimed and demonstrably violated by some of its luminaries who say that barcodes are identification and not species discovery tools at the same time that they promote them as species discovery tools).  Integrity, it would seem, takes a back seat to profits.

And finally, there is the taxonomy of taxonomists.  To the taxonomist his science is the ultimate expression of evolutionary biology.  In the course of his revision or monograph, he combines the adventure of boots-on-the-ground exploration, the scholarship involved in studying all descriptions and type specimens since 1758, the exciting discovery associated with deep thought about and interpretation of homology, and the intellectual satisfaction of understanding the origin and entire evolutionary history of not only a monophyletic group of species but also of the transmutation of numerous suites of characters.  This intellectual exercise knows none of the normal bounds of space or time, taking as a limitation only the boundaries of synapomorphy and energetic search for characters.

Those who trivialize taxonomy as an identification service have failed to grasp the significance of those identifications and names.  They are reliable only because they reflect rigorous theories about characters, species, and clades and that is no trivial scientific accomplishment.

Your Apostle,

Quentin

The Oldest Profession

Dear Carl,

I once wrote in a book review that taxonomy is the oldest profession practiced with our clothes on which is, I believe, truthful. It occurred to me that, thanks to your keen fashion sense, it is also one of few professions ever practiced in Lapland threads. Thanks for being a trendsetter.

Your Apostle,

Quentin

The humble science

Dear Carl,

In February, 1676, Sir Isaac Newton wrote to Robert Hooke that "If I have seen further it is only by standing on the shoulders of giants." Thanks to your system of names, as now codified in the International Code of Zoological Nomenclature, this kind of humility is imposed upon every taxon expert.

In order to master a single genus, a taxonomist must read and understand every theory of a species proposed since your own masterpiece in 1758, including each theory of homology contained in each description, grasp their implications for variations and character distributions, and then assess those predictions by comparing tens of thousands of accumulated specimens. No other field of biology has such deep scholarship as a standard mode of practice.

Naming a species in your system is one of very few sure paths to immortality. While a paper published in other biological disciplines is effectively ignored after a few years, taxonomic papers will remain mandatory reading for students of taxa who will not be born for centuries to come. The upside of course is the exhilaration of knowing that your good work will exist in perpetuity. The downside is that your mistakes will last just as long. Taxonomists alone bear the burden of signing their work, since author names follow the genus and specific epithet in your binomial system and will forever be there for adoration or cursing.

Apostolically yours,

Quentin

Kära Prof. von Linné,

Thought you might enjoy seeing my latest specimen of Canis lupus L., "Maddie," en galen hund.
Hon är en mun paus som en phylocodeer.

Din apostle,

Quentin

Conspiracy Theory

Avena sativa L., the cultivated oat, was named by Linnaeus.

"In the magical Universe there are no coincidences and there are no accidents. Nothing happens unless someone wills it to happen." --- William S. Burroughs