[Taxacom] [iczn-list] GENERAL CALL TO BATTLE

Mon Feb 15 18:23:52 CST 2021

Hi Richard,

I could certainly live with  3. as you have listed however I have
tendencies towards 2. I certainly believe DNA analysis is useful; it has
certainly demonstrated its capacity for instance to identify types that are
effectively nomen dubium, or just simple misidentified types. They also, in
a total evidence approach, add confidence to trees. As I am both a
taxonomist and a paleontologist I do look at the perspective of usability
of characters and DNA has limited usefulness for fossil taxa, and hence I
certainly appreciate a more complete taxonomic analysis that includes
morphology for crossover to the fossils.

This works both ways as in molecular analysis it is common practice to date
lineages using fossils and the placement of the fossil taxa should be on
the basis of an apomorphic analysis and hence this also requires
morphology. I fully acknowledge however that all these issues are taxonomic
not nomenclatural but I am concerned that if taxa are named based only on
DNA that the necessary morphological analysis does not get done as without
the prospect of naming taxa doing the morphology for DNA only species feels
somewhat like cleaning up a mess left by others. It can also be difficult
to fund.

Cheers Scott

On Mon, Feb 15, 2021 at 8:12 PM Richard Pyle via Taxacom <
taxacom at mailman.nhm.ku.edu> wrote:

> Thanks, Stephen.  But you didn’t answer my questions.  I’ll repeat them
> here:
>
>
>
> Do you object to taxa based only on DNA characters because the idea is
> fundamentally flawed (i.e., it will never be justifiable)?  Or, like me, do
> you object to it simply because we do not *yet* understand DNA characters
> well enough to use them to infer/define taxa in a way that is consistent
> with how taxa have been defined for the past couple of centuries?  If the
> former, then can you give me examples of morphological characters useful to
> inferring/defining taxa that are not controlled by information stored in
> the DNA?
>
>
>
> Or better yet, maybe you could indicate which of the following 5
> perspectives most represents your own:
>
>
>
> 1.      DNA characters are fundamentally flawed. DNA evidence is not (and
> never will be) legitimate as the only basis for inferring/defining taxa
> because it doesn’t contain the same information that morphology does and/or
> fails to accurately reflect what the essence of “taxa” should be.
>
>
>
> 2.      DNA characters are limited because they are hard to access. DNA
> evidence may be useful as the only basis for inferring/defining taxa, but
> it’s only useful to people who have access to sequencing technology, and
> therefore should be avoided as the only type of character to base taxa on.
>
>
>
> 3.      DNA characters are limited because we don’t yet know how to
> interpret them. DNA evidence may be useful as the only basis for
> inferring/defining taxa, but even with access to sequencing technology we
> don’t really understand it well enough (yet) to infer/define taxa in ways
> that are consistent with the long history of morphologically-based taxa,
> and we shouldn’t rely on it entirely until we can ensure continuity of
> general taxonomic practice.
>
>
>
> 4.      We should prepare for a new way of defining/inferring taxa.
> Because DNA evidence has the potential to be extremely useful as the only
> basis for inferring/defining taxa once we understand it a bit better, we
> should start transitioning to a new way of inferring/defining taxa now and
> facilitate this transition to happen gracefully.
>
>
>
> 5.      We should embrace a new way of defining/inferring taxa *now*. We
> already understand DNA evidence well enough, and we should embrace a new
> way of inferring/defining taxa now, even if it is disharmonious with the
> “old ways” of inferring/defining taxa based on morphological characters.
>
>
>
> Or feel free to define a new one that represents your perspective.  I
> invite John (and anyone else) to do the same.
>
>
>
> Aloha,
> Rich
>
>
>
>
>
>
>
> Richard L. Pyle, PhD
> Senior Curator of Ichthyology | Director of XCoRE
>
> Bernice Pauahi Bishop Museum
>
> 1525 Bernice Street, Honolulu, HI 96817-2704
>
> Office: (808) 848-4115;  Fax: (808) 847-8252
>
> eMail: deepreef at bishopmuseum.org
>
>  <http://hbs.bishopmuseum.org/staff/pylerichard.html> BishopMuseum.org
>
> Our Mission: Bishop Museum inspires our community and visitors through the
> exploration and celebration of the extraordinary history, culture, and
> environment of Hawaiʻi and the Pacific.
>
>
>
> From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
> Sent: Monday, February 15, 2021 9:54 AM
> To: Richard Pyle <deepreef at bishopmuseum.org>; John Grehan <
> calabar.john at gmail.com>
> Cc: iczn-list at afriherp.org; Taxacom <taxacom at mailman.nhm.ku.edu>
> Subject: Re: [Taxacom] [iczn-list] GENERAL CALL TO BATTLE
>
>
>
> Rich,
>
> James may have proposed a putative answer to my comment, but that doesn't
> mean my view was an "error", not yet anyway. I still maintain (to answer
> your question) that DNA sequencing isn't taxonomy, but may however have a
> secondary support role for taxonomy. Taxonomy is not simply about attaching
> names to species via type specimens. That is nomenclature. Taxonomy is
> about circumscribing species. There is an obvious (imperfect, but
> nevertheless obvious) correlation between morphology and species (=more or
> less: groups of individuals who freely interbreed and have the same basic
> interactions with other species and the abiotic environment). If all
> individuals of all species looked the same, then taxonomy would be
> pointless. The whole point of taxonomy is to be able to infer interactions
> from morphology. Sometimes there are problem cases that may benefit from
> DNA sequencing in a supporting role. However, if you define species by DNA
> sequence, you provide no link between morphology and interactions. You
> simply leave the hard work for someone else down the track to try to find
> that link, putting many potential hurdles in their way, such as the
> difficulty in obtaining usable DNA for many rare or inaccessible species.
>
> I am not convinced that simply claiming that this or that base in a
> sequence can vary within the same species ("consensus sequences"), based on
> a limited sample, amounts to a meaningful circumscription of the species.
> How do they (a hypothetical "they") know the different sequences are the
> same species?? Because they are judging by morphology! They are just not
> sharing with the reader the details of this all important morphology! They
> are withholding these details because they cannot be bothered taking the
> time to present them! Instead they just churn out the sequences ... thanks,
> but no thanks!
>
> Cheers, Stephen
>
>
>
> On Tuesday, 16 February 2021, 08:25:20 am NZDT, John Grehan via Taxacom <
> taxacom at mailman.nhm.ku.edu <mailto:taxacom at mailman.nhm.ku.edu> > wrote:
>
>
>
>
>
> Some misplaced 'humor' - Is it a cat or a dog I have as a pet? Looks like a
> cat, but I can't trust that. It could be a cryptic elephant. Wait.... I'll
> just get my DNA tricorder and we will know for sure (and which pet food to
> buy).
>
> cheers, John Grehan
>
>
>
>
> >
> >
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