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

Daniel Whitmore whitmore.daniel at gmail.com
Fri Jul 26 00:16:09 CDT 2019


These last comments from David and Stephen hit the nail on the head.

A brief morphological diagnosis would have been desirable (and possibly required by the Code?), but how can you reliably provide a morphological diagnosis if you haven't studied the rest of the described diversity in the group? The paper is based on the assumption that any molecularly-identified species collected in ACG is new, which is possible but not adequately discussed by the authors in context with the previously known diversity.

Daniel

Sent from my iPhone

> On 26 Jul 2019, at 06:18, David Redei via Taxacom <taxacom at mailman.nhm.ku.edu> wrote:
> 
> This paper is a complete mystery for me.
> 
> The authors claim that Zelomorpha had 50+ described species prior to this
> study, distributed from S USA to Argentina, but predominantly Neotropical.
> Now they collected 336 specimens from Costa Rica, they sequenced all of
> them, grouped into 15 genetic-distance-based species, and describe each of
> those as new.
> 
> Apparently the genus is fairly unrevised, at least in the present paper I
> did not find any reference to previous revisions or comprehensive taxonomic
> works which the authors used for identification. In their paper I did not
> find a single remark about the previously described 50+ spp. of Zelomorpha,
> except one species, Z. arizonensis, of which they possessed some molecular
> material, therefore they provided p-distances between Z. arizonensis and
> some of their new species. The new species are not placed into taxonomic
> context, simply defined one by one with brief sequences, and the paper does
> not give any arguments why did the authors think that each of their 15 new
> species is different at species level from the 50+ already described
> Zelomorpha..
> 
> The study gives me the impression that the authors simply went to a
> tropical place, collected many specimens of a given group, sorted to
> species following some criteria (p-distance), and described everything as
> new, with completely omitting the very significant already-described
> diversity of the group in the region. I did not find any justification in
> the paper why they felt this procedure as justified. There was no
> Zelomorpha previously described from Costa Rica? Even if it is true (not
> discussed in the paper), all other species described from other Neotropical
> countries can be a priority excluded, do the authors really think that
> there is no need to compare any of the Costa Rican species with any other
> Neotropical already-described Zelomorpha? Why? At least some justification
> should have been given for this in the paper, I did not find any.
> 
> Such a protocol of course speeds up taxon naming significantly, because it
> is of course fairly easy to describe a big number of "new species" from any
> place of the world if one ignores all previously described species, and
> leaves the painstaking work of compasons with the previously described
> species for others. But it seems a fairly trivial procedure and I do not
> really understand the point for doing so, in my opinion it *increases *rather
> than decreases confusion within the given taxon. I am not a Hymenoptera
> specialist, but judging merely from this paper it seems to me that now we
> have 50+ spp. of Zelomorpha defined exclusively on a morphological basis,
> 15 spp. defined on a molecular basis, and only one of of them (Z.
> arizonensis) has both morphological and molecular definition. (I do not
> consider providing a single lateral habitus photo as a meaningful
> morphological definition and a valid comparison with other taxa.) With
> other words, nomenclature of the genus is now split into two: there are
> "molecular species" and "morphological species" of Zelomorpha, with almost
> no connection between the two groups, therefore identification of any
> specimen now is probably more difficult than before, in lack of a uniform
> taxonomic framework.
> 
> Sorry if I completely misunderstood the paper and I misinterpret its
> content, but based on reading the paper quite carefully this was my
> impression. If my impression is correct, then it is difficult to call this
> work as "taxonomy".
> 
> With best regards,
> 
> David Redei
> 
> 
> On Fri, 26 Jul 2019 at 10:34, 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!
>>>>> _______________________________________________
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>>>>> 
>>>>> 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
>>>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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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.
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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.
>>>> 
>>>> 
>>>> 
>>>> --
>>>> 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>
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>> 
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>> |  | Virus-free. www.avast.com  |
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