[Taxacom] New species of the future

[Dan Lahr]

HI Jason,

I have to disagree with:

"The transcriptome though is superfluous. I understand that BGI wants to do
its 1000
transcriptome project but really, not useful in this specific case."

Deep phylogenetic reconstruction only needs a transcriptome, not a genome.
Especially on things where we have no idea what the genome is going to look
like, it is basically insanity to chase a genome.  TRasncriptomes are
relatively straight-forward pieces of data to generate, and very useful. If
it were to be done as species are described, it would be fantastic.

This is so much so that if you check back on the last 5 years, any relevant
microbial eukaryote that was described was described along with a
transcriptome.  I would also argue that people describing microbial
eukaryotes NEED to be describing them with lots of tools, this is the
nature of the game with the wee-beasties.

The following are only examples:

Pygsuia biforma (spectacular work)

http://rspb.royalsocietypublishing.org/content/280/1769/20131755

Collodictyon triciliatum

http://mbe.oxfordjournals.org/content/29/6/1557.full

best,

dan


__________________________________
Daniel J. G. Lahr
PhD, Assist. Prof.
Dept of Zoology, Univ. of Sao Paulo, Brazil
Office number: + 55 (11) 3091 0948
http://www.ib.usp.br/zoologia/lahr/



On Wed, Oct 30, 2013 at 1:06 PM, JF Mate <aphodiinaemate at gmail.com> wrote:

> To Dave Kirk and Lyubomir:
>
> We are discussing two separate things here. On the one hand we have the
> rise of digital, media-rich publications. To me multiple sources of
> information added to a description or any other paper for that matter is a
> plus. As an exercise or proof of concept I see the angle of the paper. But
> deep down it is a PR exercise, which no doubt is necessary in these days of
> shrinking budgets. But if this is the case, expensive descriptions are not
> going to enhance biodiversity inventorying.
>
> My argument is that a big portion of the cost is down to the cybertype
> and the transcriptome. I can see the applications of the CT scans, though I
> would argue that a cyber-type can also take other forms. The transcriptome
> though is superfluous. I understand that BGI wants to do its 1000
> transcriptome project but really, not useful in this specific case. Its use
> is more like a placeholder for a genome or as another bit of data added for
> sales purposes. Nothing wrong, simply rather pointless. Maybe if the paper
> had included several stages and both genders or done a comparison across
> several close species, then I could understand its inclusion.
>
> This brings me to the issue of expectations by "people" (not sure who you
> are referring to). People have multiple expectations but surely a common
> one should be the ability to successfully discriminate species X from all
> other previously described species. At its most basic, people just want a
> name. After that come the questions: what does it do; is it dangerous;
> rare, etc. But the first step is establishing that this group of organisms
> is different from the other groups we have previously defined, and it is
> identified for human purposes with this label.
>
> In this respect taxonomy is very economical, probably  the most economical
> aspect of biology, yet the argument here is that before spending a small
> amount of resources describing organisms we should spend a bunch to
> determine if they are worthy of description in the first place. Ignoring
> the problems with this economic model, who determines what is worthy?
> Chalara fraxinea or Agrilus planipennis were probably not very interesting
> when first described. You cannot determine a priori the value of a species,
> and often it requires decades to build a basic picture of the biology and
> ecology of each one. So how exactly is this model going to accelerate the
> output?
>
> When it comes to cost "(5) The effort was huge, the costs are there, but
> the project is not that
> expensive as one might think. It is surely cheaper if compared to the
> costs of
> an expedition to a tropical country to collect new species that will
> (probably)
> be never described." Yes, an expedition to the tropics to collect material
> is costly, probably more than a single description, but that is comparing
> apples and oranges. I am sure that spelunking for critters is costly as
> well, more so if we work out the cost per new species uncovered, but what
> we are discussing here is taxonomy. How Laputan taxonomy would improve
> access to funds is an open question, unless things have changed a lot
> lately and resources are infinite.
>
> So to me point 3 in Lyubomir´s list is the paper the aim of the paper, and
> there is nothing wrong with it, but the rest, including taxonomy, is at
> best incidental.
>
> Best
>
> Jason
>
> P.S. "tight adherence to the Old Ways is not going to ensure the survival
> of taxonomy" not the best sales pitch
> _______________________________________________
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
> The Taxacom Archive back to 1992 may be searched with either of these
> methods:
>
> (1) by visiting http://taxacom.markmail.org
>
> (2) a Google search specified as:  site:
> mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>
> Celebrating 26 years of Taxacom in 2013.
>