[Taxacom] Identification by what method?

[Richard Pyle]

Hi Doug,

> In the context of linking an unknown living specimen to a species name, the
> statement makes no sense. Over 99% of all species on the planet have never
> been sequenced AND had that sequence definitively matched to a name, so you
> can't effectively use gene sequencing to identify anything
> - at least, from among that 99% - to species. A tool that can give you a species
> name for less than 1% of extant biodiversity is a pretty sorry excuse for a "gold
> standard".

While I completely agree with where you are coming from, I'm not entirely sure that last statement is entirely fair.  The term "gold standard" to me implies the best possible solution, when circumstances allow for it.  That circumstances don't allow for it among 99% of species (probably more), doesn't mean it's not a reasonable "gold standard" to strive for.

Moreover, almost by definition, the 1% of species that meet the circumstances correspond to the 1% of species that are most conspicuous/obvious/impactful to humans.  As such, many of them involve species with important economic impact (pests, crops, etc., etc.), and as often these are the species that need to be identified, I don't think that a technique that applies to only 1% of species necessarily corresponds to applying in only 1% of situations where a species needs to be reliably identified.

> Traditional taxonomic tools can identify - by definition - essentially
> every single described species (somewhere between 1 and 2 million), which is
> about 10% of the existing diversity (there's debate over the actual figure), and
> can ALSO give you higher taxonomic ranks (above the species level) for
> increasingly higher percentages for every step up the hierarchy you go. 

Perhaps the techniques can, but the limitation is not the techniques -- the limitation is the number of people adequately trained to incorporate those techniques.  

Having said all that, I am still dubious about gene sequencing being represented as the "gold standard" for identification -- for reasons outlined in my previous post.

Aloha,
Rich