[Taxacom] OMG! DNA only descriptions (with one habitus photo)!

Donald Hobern dhobern at gbif.org
Thu Jul 25 19:24:10 CDT 2019


We're drifting somewhat from the original topic, but I would argue that the kind of community mapping I described may be the perfect tool to enable any leaders who actually care to factor real understanding of biodiversity patterns and values into land-use and sustainability planning.

Biodiversity is important within the framework of the Sustainable Development Goals, for example, but today can only be factored into landscape models via a few proxy groups. We can change this for the better. If we can retain, and indeed boost, the value of taxonomic research, as we do so, then we get multiplier effects for both taxonomy and conservation.

The only aspect that drives me to defeatism is my growing doubt that many of us have leaders who care.

Donald


----------------------------------------------------------------------
Donald Hobern - dhobern at gbif.org<mailto:dhobern at gbif.org>
Global Biodiversity Information Facility http://www.gbif.org/
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________________________________
From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
Sent: Friday, July 26, 2019 2:01 AM
To: Michael Heads <m.j.heads at gmail.com>; Donald Hobern <dhobern at gbif.org>
Cc: taxacom <taxacom at mailman.nhm.ku.edu>
Subject: Re: [Taxacom] OMG! DNA only descriptions (with one habitus photo)!

Donald,
No offence, but I view that as somewhat of a defeatist attitude!
"I mean simply that, within the next few years, the tooling and practice underpinning the majority of biodiversity survey work for such groups will be based on high-throughput sequencing"
In some areas maybe, like mycology where fungi have fruiting bodies only some of the time and there is no way to ID hyphae morphologically, but I don't see any signs of that happening in general botany, for example. None of the botanists I know are about to give up doing field surveys by way of traditional methods! If local councils etc. want to know what plants are in an area up for development or whatever, they are not turning to DNA sequencing.
Unless we keep shouting loudly that sequencing relies on a taxonomic foundation (rather than the other way round), we are going to help taxonomy on the road to extinction.
Just knowing DNA sequences of species before they become extinct due to "climate change" (or whatever your doomsday scenario of choice is) is essentially no different to not knowing anything about them!
Cheers, Stephen

On Thursday, 25 July 2019, 11:44:45 pm UTC, Donald Hobern <dhobern at gbif.org> wrote:


I mean simply that, within the next few years, the tooling and practice underpinning the majority of biodiversity survey work for such groups will be based on high-throughput sequencing. We will be mapping community composition, species distribution and species interactions via DNA. Increasingly, this information will be all, or almost all, we have for large swathes of species.

As organismal enthusiasts, I think we would both want this information to be more than a cloud of anonymous clusters. If we tell the world to pay us to find morphological criteria for separating all of these clusters, we will rightly be told to do it on our own time. If however, we keep these clusters as low-information, but potentially very well mapped, components in an evolution of our current taxonomic models, we will be able to apply more effort to study and describe in more detail those species that actually matter from a functional, conservation or human-relevance aspect.

I see this as a sensible strategy for triaging taxonomic effort in a planet that is on fire.

Donald


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Donald Hobern - dhobern at gbif.org<mailto:dhobern at gbif.org>
Global Biodiversity Information Facility http://www.gbif.org/
----------------------------------------------------------------------

________________________________
From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of Michael Heads via Taxacom <taxacom at mailman.nhm.ku.edu>
Sent: Friday, July 26, 2019 1:33 AM
To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
Cc: taxacom <taxacom at mailman.nhm.ku.edu>
Subject: Re: [Taxacom] OMG! DNA only descriptions (with one habitus photo)!

that only matters if you have an absolutist, neodarwinian view of species.
If you have a darwinian or molecular, 'relative' view of 'the species', the
question (whether single species or many) isn't important. The focus is on
'natural' or 'monophyletic groups.

On Fri, Jul 26, 2019 at 11:03 AM Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
wrote:

> Michael,
> That may be convenient from one among infinite possible perspectives, but
> having a formal name for a superficially cobbled together species concept
> is arguably not a good thing! Parasitoids (unlike herbivores) are rarely
> host specific to that extent (1:1), so how are we suppose to know if it is
> several species each with a different single host, or one polyphagous
> species?
> Stephen
>
> On Thursday, 25 July 2019, 10:33:35 pm UTC, Michael Heads <
> m.j.heads at gmail.com> wrote:
>
>
> Stephen: you say 'all we have is one very superficial habitus photo and a
> DNA sequence'. A DNA sequence is pretty important.
> The paper is a valuable contribution in insect-plant relations, and the
> nomenclature is useful. if I want to discuss, say, restriction to legumes,
> I can cite all these new standardised, binomial names easily, e.g.
> Zelomorpha willsflowersi Meierotto,  known from three species of Erebidae
> feeding on young leaves of Fabaceae.... In most molecular papers, you don't
> get any new formal names, so if you want to discuss their amazing results
> you often have to refer to 'the molecular clade including samples 2, 31 and
> 14'. (or species 2, 31 and 14).
>
> Kirk: you say 'This is just another instance of technology driving science
> at the expense of the established principles upon which science is supposed
> to be based'. Which established principles?
>
>
> On Fri, Jul 26, 2019 at 10:16 AM Stephen Thorpe via Taxacom <
> taxacom at mailman.nhm.ku.edu> wrote:
>
>  The specimens may not last forever (Brazil Museum fire, etc.), then all
> we have is one very superficial habitus photo and a DNA sequence for an
> individual! Don't get me wrong, I'm all in favour of photos in taxonomy, as
> you know, but they have to be a good set of diagnostic photos, and I'm
> picking that if the authors didn't have time to write down a verbal
> morphological diagnosis for each proposed new species, then they didn't
> have time to examine the specimens very closely either to determine which
> characters were important to photograph! This isn't taxonomy!
> Stephen
>
>     On Thursday, 25 July 2019, 10:04:16 pm UTC, Thomas Pape via Taxacom <
> taxacom at mailman.nhm.ku.edu> wrote:
>
>  >>> all we have here is one photo of possibly limited diagnostic value
> and a DNA sequence for that same individual
>
> This is by itself very useful. And the specimen can be consulted for
> further documentation.
> For many of the new species there are several specimens considered to be
> conspecific, although these are not documented with neither barcode nor
> photo. Great baseline data.
>
> Neal quoted Andy Brower for "... simply because species can be identified
> and publicized on the basis of a few nucleotide differences it does not
> mean that they should be".
> The question is how much (and which kind of) data we think is sufficient
> to justify the proposal of a scientific species-group name.
> No straight answer.
>
> /Thomas Pape
>
>
> -----Original Message-----
> From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> On Behalf Of Stephen
> Thorpe via Taxacom
> Sent: 25. juli 2019 23:28
> To: taxacom at mailman.nhm.ku.edu; Kirk Fitzhugh <kfitzhugh at nhm.org>
> Subject: Re: [Taxacom] OMG! DNA only descriptions (with one habitus photo)!
>
>  One of my main worries with this approach is that it seems pretty obvious
> that they are basing their judgements of species distinctions on a cursory
> and superficial morphological examination and then assuming that the
> associated DNA profiles define species! Obviously, however, every
> individual organism has a different DNA profile, and I doubt that any
> categorical genetic genetic distance between species applies across the
> board, so, when all said and done, all we have here is one photo of
> possibly limited diagnostic value and a DNA sequence for that same
> individual! This is not taxonomy as we know it! They should have known that
> DNA really stands for Do Not Attempt!
> Stephen
>     On Thursday, 25 July 2019, 08:19:46 pm UTC, Kirk Fitzhugh via Taxacom <
> taxacom at mailman.nhm.ku.edu> wrote:
>
>  Revolutionary? Not at all. Especially given the largely toothless
> opinions regarding species and taxa overall that permeate biology. This is
> just another instance of technology driving science at the expense of the
> established principles upon which science is supposed to be based.
>
>
> On Thu, Jul 25, 2019 at 12:51 PM Stephen Thorpe via Taxacom <
> taxacom at mailman.nhm.ku.edu> wrote:
>
> > https://dez.pensoft.net/article/34683/
> >
> > Yikes!
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> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> J. Kirk Fitzhugh, Ph.D.
> Curator of Polychaetes
> Invertebrate Zoology Section
> Research & Collections Branch
> Natural History Museum of Los Angeles County
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> Los Angeles CA 90007
> Phone: 213-763-3233
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> --
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>
> My books:
>
> *Biogeography and evolution in New Zealand. *Taylor and Francis/CRC, Boca
> Raton FL. 2017.
> https://www.routledge.com/Biogeography-and-Evolution-in-New-Zealand/Heads/p/book/9781498751872
>
>
> *Biogeography of Australasia:  A molecular analysis*. Cambridge
> University Press, Cambridge. 2014. www.cambridge.org/9781107041028<http://www.cambridge.org/9781107041028>
>
>
> *Molecular panbiogeography of the tropics. *University of California
> Press, Berkeley. 2012. www.ucpress.edu/book.php?isbn=9780520271968<http://www.ucpress.edu/book.php?isbn=9780520271968>
>
>
> *Panbiogeography: Tracking the history of life*. Oxford University Press,
> New York. 1999. (With R. Craw and J. Grehan).
> http://books.google.co.nz/books?id=Bm0_QQ3Z6GUC
> <http://books.google.co.nz/books?id=Bm0_QQ3Z6GUC&dq=panbiogeography&source=gbs_navlinks_s>
>
>
>
>
>
>
>
>
>
>
>

--
Dunedin, New Zealand.

My books:

*Biogeography and evolution in New Zealand. *Taylor and Francis/CRC, Boca
Raton FL. 2017.
https://www.routledge.com/Biogeography-and-Evolution-in-New-Zealand/Heads/p/book/9781498751872


*Biogeography of Australasia:  A molecular analysis*. Cambridge University
Press, Cambridge. 2014. www.cambridge.org/9781107041028<http://www.cambridge.org/9781107041028>


*Molecular panbiogeography of the tropics. *University of California Press,
Berkeley. 2012. www.ucpress.edu/book.php?isbn=9780520271968<http://www.ucpress.edu/book.php?isbn=9780520271968>


*Panbiogeography: Tracking the history of life*. Oxford University Press,
New York. 1999. (With R. Craw and J. Grehan).
http://books.google.co.nz/books?id=Bm0_QQ3Z6GUC
<http://books.google.co.nz/books?id=Bm0_QQ3Z6GUC&dq=panbiogeography&source=gbs_navlinks_s>

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