[Taxacom] New species of the future

Tue Oct 29 17:09:51 CDT 2013

Dear Jason,

taxonomists really need to move beyond the tight limits of our discipline.  Diagnostic is not sufficient for the rest of the world.  People, reasonably, want to know what this new taxon is doing differently from other things.  If nothing, then why do we need to name it?  We should be looking towards a time where we place taxa into a functional landscape (i.e. predictive modelling <http://h2020.myspecies.info/content/conference-summary>).  Tight adherence to the Old Ways is not going to ensure the survival of taxonomy. .

So really, what is the problem with presenting the transcriptome, if possible?

For the cyber-type, this is surely a mechanism better suited to some taxa (typically small and soft-bodied) than others.  OK this is an arthropod, but its a proof of principle.  It still makes a workable facsimile accessible essentially everywhere.  Is that not better than just a corpse in a jar on a shelf somewhere?

Cheers, Dave
Declaration: co-author on this paper.
--
On 29 Oct 2013, at 22:22, JF Mate <aphodiinaemate at gmail.com> wrote:

> I´m with Stephen on this one, but I would go further and ask if it´s really
> the future. I like the CT 3D type although I just don´t see it becoming
> mainstream in the medium term. My biggest doubt though is, why the
> transcriptome? It is quite expensive to do (unless you happen to have next
> gen equipment, but still not cheap) and it is not really diagnostic, not in
> the same way as a genome probably is (not many around to tell really), and
> since BGI has proposed the million genome project, wouldn´t it have made
> more sense to wait and do the full genome? I have checked the BGI website
> and there is no Myriapod listed (though there are two Chilopods). The
> sampling a bit off too but I am somewhat befuddled Eupolybothrus is not
> there (or at least another Myriapod).
> 
> Jason
> 
> 
> On 29 October 2013 11:42, Lyubomir Penev <lyubo.penev at gmail.com> wrote:
> 
>> *Eupolybothrus cavernicolus*, a cave-dwelling centipede discovered in a
>> remote karst region of Croatia, has become the first new eukaryotic species
>> described with fully sequenced transcriptomic profile, DNA barcoding ,
>> detailed anatomical X-ray micro-tomography (micro-CT), and a movie of the
>> living specimen, all this in addition to the conventional morphological
>> description, photos and SEM images.
>> This, most data-rich species description, represents also the first
>> biodiversity project that joins the ISA (Investigation-Study-Assay)
>> Commons, that is an approach created by the genomic and molecular biology
>> communities to store and describe different data types collected in the
>> course of a multidisciplinary study.
>> 
>> Details are available through the following links:
>> 
>> Original article:*Eupolybothrus cavernicolus* Komerički & Stoev sp. n.
>> (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species
>> description combining transcriptomic, DNA barcoding and micro-CT imaging
>> data <http://biodiversitydatajournal.com/articles.php?id=1013>
>> 
>> GigaScience editorial: Biodiversity research in the "big data" era: *
>> GigaScience* and Pensoft work together to publish the most data-rich
>> species description <http://www.gigasciencejournal.com/content/2/1/14>
>> 
>> Press release: The cyber-centipede: From Linnaeus to big
>> data<http://www.eurekalert.org/pub_releases/2013-10/pp-tcf102513.php>
>> 
>> More on the ISA approach:Toward interoperable bioscience
>> data<http://www.nature.com/ng/journal/v44/n2/full/ng.1054.html>
>> 
>> Cheers,
>> Lyubomir
>> --
>> Dr. Lyubomir Penev
>> Managing Director
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