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

Soowon Cho chosoowon at gmail.com
Fri Jul 26 00:57:23 CDT 2019


Dear Stephen,
-----
Are these "words"?? 43–45 TTA, 54–57 CTTT, 75 G~
-----
What other ways of wording can you think of in describing DNA, a part of
the species, specific for the species other than what they did? Do you
think those "words" they used do not satisfy the ICZN?

Sincerely,

On Fri, Jul 26, 2019 at 11:34 AM Stephen Thorpe via Taxacom <
taxacom at mailman.nhm.ku.edu> wrote:

>  To be available, every new name published after 1930 must satisfy the
> provisions of Article 11 and must13.1.1. be accompanied by a description or
> definition that states in WORDS characters that are purported to
> differentiate the taxon
> Are these "words"?? 43–45 TTA, 54–57 CTTT, 75 G, 136–138 GTG, 165 T, 321
> G, 417 G, 462 G, 477 C, 561 G, 684 G
>     On Friday, 26 July 2019, 12:59:54 am UTC, Stephen Thorpe via Taxacom <
> taxacom at mailman.nhm.ku.edu> wrote:
>
>   Robert,I must disagree. Unlike specialist herbivores, insect parasitoids
> rarely if ever have a single host species. You can't just assume different
> host => different parasitoid, and use this as a basis for the taxonomy!
> Some species will have wide host ranges, and others less so. It would take
> a great deal more time and effort to sort that out than it would to simply
> look at traditional morphological characters used to separate species in
> the group and offer this in the form of a brief diagnosis.Cheers, Stephen
>     On Friday, 26 July 2019, 12:55:55 am UTC, Robert Zuparko <
> rz at berkeley.edu> wrote:
>
>  I am by no means in favor of the DNA approach, but I would like to point
> out that the characterization of  "... 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!" is not correct. In the paper, the authors
> note that biological associations of parasitoids with their hosts made up a
> big part of their determinations, a key factor that is very useful in
> distinguishing parasitoid species.
>
>
> Robert Zuparko
> Essig Museum of Entomology
> 1101 Valley Life Sciences Building, #4780
> University of California
> Berkeley, CA 94720-3112
> (510) 643-0804
>
>
>
>
> |  | Virus-free. www.avast.com  |
>
>
> On Thu, Jul 25, 2019 at 5:33 PM John Longino via Taxacom <
> taxacom at mailman.nhm.ku.edu> wrote:
>
> We need to shout loudly about taxonomic underpinning: agreed. The DNA
> barcode enthusiasts could dial down the hubris a bit. We generally do not
> do environmental sampling for all sequences in a soup, the way microbial
> ecologists do. We use experience with a group (field surveys,
> morphological examination) to select which individuals to sequence, among
> the infinite biomass one could select. A highly efficient means of
> learning about macroorganismal diversity. I sometimes feel that people
> forget how much taxonomic knowledge goes into deciding which specimens to
> sequence.
>
> Botanists giving up field surveys: disagree. One doesn't follow from the
> other. Most botanists I know find their field surveys even more rewarding
> when they can complement morphological results with sequence results,
> greatly enhancing what they learn and guiding new expeditions to new
> places.
>
> Local councils: disagree. Highly trained botanist cannot be in all places
> at all times. When sequence-based identification is easy and accessible, a
> local enthusiast can look around, get to know the local flora, query a
> sequence database to get the identification, look at taxonomic info and
> learn about the species. I predict this capability will increase
> opportunities for professional taxonomists, because people will want web
> resources with abundant info on the species they have found.
>
> What I find disagreeable about dna barcoding evangelists is their
> dismissing of taxonomy as too slow or too old fashioned. That always
> smacks of hucksterism, like selling "new and improved" versions of
> something by smearing some competing or older brand. From my perspective
> the most advanced taxonomists have always kept abreast of the latest
> technological developments that improve understanding of diversity. To me,
> the paper that sparked this conversation is a nice collaboration of
> sophisticated taxonomists, field naturalists, and dna barcoders. It is too
> bad they "sell" their work by juxtaposing it to "that bad, old, slow
> taxonomy." They could just say "DNA barcoding has allowed us to advance
> taxonomy, building on the large knowledge of morphological divisions among
> clades, to further differentiate species differences within
> morphologically uniform groups."
> ________________________________________
>
> John T. (Jack) Longino
> Department of Biology
> 257 S 1400 E, University of Utah
> Salt Lake City, UT 84112 USA
>
>
>
> Longino Ant Lab at https://sites.google.com/site/longinoantlab/
> Project ADMAC at https://sites.google.com/site/admacsite/home
>
>
>
>
>
>
> On 7/25/19, 6:01 PM, "Taxacom on behalf of Stephen Thorpe via Taxacom"
> <taxacom-bounces at mailman.nhm.ku.edu on behalf of
> taxacom at mailman.nhm.ku.edu> wrote:
>
> > 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:
> >
> > #yiv3499115493 P {margin-top:0;margin-bottom:0;}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
> >
> >
> >----------------------------------------------------------------------Dona
> >ld Hobern - dhobern at gbif.orgGlobal 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!
> >> > _______________________________________________
> >> > Taxacom Mailing List
> >> >
> >> > Send Taxacom mailing list submissions to: taxacom at mailman.nhm.ku.edu
> >> > For list information; to subscribe or unsubscribe, visit:
> >> > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> >> > You can reach the person managing the list at:
> >> > taxacom-owner at mailman.nhm.ku.edu
> >> > The Taxacom email archive back to 1992 can be searched at:
> >> > http://taxacom.markmail.org
> >> >
> >> > Nurturing nuance while assaulting ambiguity for 32 some years,
> >>1987-2019.
> >> >
> >> --
> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >> J. Kirk Fitzhugh, Ph.D.
> >> Curator of Polychaetes
> >> Invertebrate Zoology Section
> >> Research & Collections Branch
> >> Natural History Museum of Los Angeles County
> >> 900 Exposition Blvd
> >> Los Angeles CA 90007
> >> Phone: 213-763-3233
> >> FAX: 213-746-2999
> >> e-mail: kfitzhug at nhm.org
> >> http://www.nhm.org/site/research-collections/polychaetous-annelids
> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >> _______________________________________________
> >> Taxacom Mailing List
> >>
> >> Send Taxacom mailing list submissions to: taxacom at mailman.nhm.ku.edu
> For
> >> list information; to subscribe or unsubscribe, visit:
> >> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> >> You can reach the person managing the list at:
> >> taxacom-owner at mailman.nhm.ku.edu The Taxacom email archive back to 1992
> >> can be searched at: http://taxacom.markmail.org
> >>
> >> Nurturing nuance while assaulting ambiguity for 32 some years,
> >>1987-2019.
> >>
> >> _______________________________________________
> >> Taxacom Mailing List
> >>
> >> Send Taxacom mailing list submissions to: taxacom at mailman.nhm.ku.edu
> For
> >> list information; to subscribe or unsubscribe, visit:
> >> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> >> You can reach the person managing the list at:
> >> taxacom-owner at mailman.nhm.ku.edu The Taxacom email archive back to 1992
> >> can be searched at: http://taxacom.markmail.org
> >>
> >> Nurturing nuance while assaulting ambiguity for 32 some years,
> >>1987-2019.
> >> _______________________________________________
> >> Taxacom Mailing List
> >>
> >> Send Taxacom mailing list submissions to: taxacom at mailman.nhm.ku.edu
> >> For list information; to subscribe or unsubscribe, visit:
> >> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> >> You can reach the person managing the list at:
> >> taxacom-owner at mailman.nhm.ku.edu
> >> The Taxacom email archive back to 1992 can be searched at:
> >> http://taxacom.markmail.org
> >>
> >> Nurturing nuance while assaulting ambiguity for 32 some years,
> >>1987-2019.
> >>
> >> _______________________________________________
> >> Taxacom Mailing List
> >>
> >> Send Taxacom mailing list submissions to: taxacom at mailman.nhm.ku.edu
> >> For list information; to subscribe or unsubscribe, visit:
> >> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> >> You can reach the person managing the list at:
> >> taxacom-owner at mailman.nhm.ku.edu
> >> The Taxacom email archive back to 1992 can be searched at:
> >> http://taxacom.markmail.org
> >>
> >> Nurturing nuance while assaulting ambiguity for 32 some years,
> >>1987-2019.
> >>
> >>
> >>
> >> --
> >> 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
> >>
> >>
> >> *Molecular panbiogeography of the tropics. *University of California
> >> Press, Berkeley. 2012. 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&sourc
> >>e=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
> >
> >
> >*Molecular panbiogeography of the tropics. *University of California
> >Press,
> >Berkeley. 2012. 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>
> >_______________________________________________
> >Taxacom Mailing List
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> >taxacom-owner at mailman.nhm.ku.edu
> >The Taxacom email archive back to 1992 can be searched at:
> >http://taxacom.markmail.org
> >
> >Nurturing nuance while assaulting ambiguity for 32 some years, 1987-2019.
> >
> >_______________________________________________
> >Taxacom Mailing List
> >
> >Send Taxacom mailing list submissions to: taxacom at mailman.nhm.ku.edu
> >For list information; to subscribe or unsubscribe, visit:
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> >taxacom-owner at mailman.nhm.ku.edu
> >The Taxacom email archive back to 1992 can be searched at:
> >http://taxacom.markmail.org
> >
> >Nurturing nuance while assaulting ambiguity for 32 some years, 1987-2019.
>
>
> _______________________________________________
> Taxacom Mailing List
>
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>
> Nurturing nuance while assaulting ambiguity for 32 some years, 1987-2019.
>
>
>
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>
>
> _______________________________________________
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> The Taxacom email archive back to 1992 can be searched at:
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> Nurturing nuance while assaulting ambiguity for 32 some years, 1987-2019.
>
> _______________________________________________
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> Nurturing nuance while assaulting ambiguity for 32 some years, 1987-2019.
>


-- 
Soowon Cho
chosoowon at gmail.com
Dept Plant Medicine
Chungbuk Nat'l Univ
Cheongju, 361-763
KOREA


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