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

[Richard Pyle]

James has already addressed the error in Stephen’s previous message equating DNA sequences to “single specimen”.  In summary, both morphological and genetic characters are recorded from individual specimens.  They are then aggregated from multiple specimens to reflect patterns from which we infer/define taxa.  Trying to separate genetic characters from morphological characters on this basis is fallacy.

 

My question for Stephen is this:  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?

 

In any case, there are several different positions here, and I see them being mixed up in this discussion:

 

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.

 

I’m sure there are other variants of these as well. Note that all of them are in the context of using *only* DNA characters to define/infer taxa.  I suspect almost all of us would agree that DNA characters are at least somewhat valuable for augmenting morphology-based taxonomy, but I wanted to focus explicitly on taxa based entirely on DNA characters.

 

My own position (currently) is #3, but I could potentially be persuaded to shift to #4 if the benefits are clear.   I also temper my position with an understanding that we’re rapidly progressing towards better understanding how to interpret DNA characters, and more ubiquitous/cheap/easy access to them; and also the realization that there are more un-named taxa that still needed to be named and catalogued than what we have named & catalogued over the past ~2.5 centuries.  In other words, unless we very dramatically lose the race against extinction, there will ultimately be far more taxa named in the future than there have been named already.

 

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: Sunday, February 14, 2021 3:37 PM
To: Mallet, James <jmallet at oeb.harvard.edu>
Cc: iczn-list at afriherp.org; Richard Pyle <deepreef at bishopmuseum.org>; Taxacom <taxacom at mailman.nhm.ku.edu>
Subject: Re: [iczn-list] [Taxacom] GENERAL CALL TO BATTLE

 

At any rate, matters are unclear (as alluded to by your use, James, of "I think"). I am more concerned with the general issues than any particular paper. I think that sequences might provide useful evidence in support of morphological taxonomy in some problem cases, but I do not think that the role of sequences in taxonomy should be primary, nor do I think sequences should be used in cases where morphology alone is clear and unproblematic. A morphologically based taxonomy should come first, wherever possible, and then sequencing can be used, if required, to help identify larval stages, undiagnostic sexes (e.g. females, where the taxonomy is based on male genitalia) or sterile individuals of plants.

Cheers,

Stephen

 

On Monday, 15 February 2021, 02:01:18 pm NZDT, Mallet, James <jmallet at oeb.harvard.edu <mailto:jmallet at oeb.harvard.edu> > wrote: 

 

 

Perhaps I was not clear, but these ambiguity codes imply that they do not just record single sequences, but variable sequences of groups of individuals they believe are species that do better to provide diagnosis.

 

I'm not a fan of species description based only on barcoding, myself, or at least I see it has flaws when used to decide the taxonomic decision of what a species is. However, the authors are not doing this, I think.

 

The mtDNA barcodes are useful characters, and therefore are not an inherently worse diagnostic tool than, say, morphological characters or ecology (such as host range in a parasitoid). And the authors of this article were clearly interested in the biology (host range, location) and provided types with some discussion of differences in morphology from other species. It would be preferable if they'd also expanded their diagnosis beyond what they called "minimalist", but they didn't, and so some of their species names will probably be difficult to apply later on; but I don't think that they thereby violate the ICZN Code.

 

J

 

 

From: iczn-list <iczn-list-bounces at afriherp.org <mailto:iczn-list-bounces at afriherp.org> > On Behalf Of Mallet, James
Sent: Sunday, February 14, 2021 6:47 PM
To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz <mailto:stephen_thorpe at yahoo.co.nz> >
Cc: iczn-list at afriherp.org <mailto:iczn-list at afriherp.org> ; Richard Pyle <deepreef at bishopmuseum.org <mailto:deepreef at bishopmuseum.org> >; Taxacom <taxacom at mailman.nhm.ku.edu <mailto:taxacom at mailman.nhm.ku.edu> >
Subject: Re: [iczn-list] [Taxacom] GENERAL CALL TO BATTLE

 

If I understand correctly the authors were at pains to  provide a CONSENSUS sequence that may have included some ambiguity codes (not just A, G, C, and T, but also other IUPAC codes - such as Y - for ambiguity among different individuals) . J

 

On Feb 14, 2021, at 5:23 PM, Stephen Thorpe <stephen_thorpe at yahoo.co.nz <mailto:stephen_thorpe at yahoo.co.nz> > wrote:

 

Rich,

 

There is a big and important difference between DNA-only and morphology-only descriptions which you seem to be overlooking: 

There is no obvious way to circumscribe a taxon (species) from a single DNA-sequence (i.e. a single individual). We both seem to doubt that you can say, across the board, that anything within 4% (or whatever) difference is the same species. Additionally, but importantly, if you define a species by DNA only that can be recognised morphologically (but you ignore the morphology), then you alienate taxonomy end users who do not work with sequencing. All other things being equal, this is a bad thing to do!

 

By contrast, it is very rare bad taxonomy to simply base a new species on a morphological description of the holotype, without giving an explicit or implied circumscription of the new species. Admittedly, the circumscription is often implied rather than explicit. For example, if someone describes a new species of beetle belonging to a group for which the taxonomy is based on male genitalia, and provides an illustration of the male genitalia of the unique holotype (i.e. the new species is based on a single individual), then it is implicit that to be the same species, the male genitalia has to be essentially identical (i.e. disregarding very minor individual differences). The practical application of this for identification from the description relies on the identifier having sufficient experience to be able to judge "essentially identical", but in practice this is almost always unproblematic. Nothing is perfect, but such morphological identification works pretty darn well in practice, but I don't see an equivalence with DNA-only identification. The latter might work in practice for INDIVIDUALS, e.g. the police find your DNA at the crime scene and identify you accordingly! But I don't see that it works for species, except perhaps in a few easy cases where the taxonomy is already resolved on morphological grounds and the DNA is just a secondary way to identify the species.

 

Cheers,

 

Stephen

 

On Monday, 15 February 2021, 10:24:48 am NZDT, Richard Pyle via Taxacom <taxacom at mailman.nhm.ku.edu <mailto:taxacom at mailman.nhm.ku.edu> > wrote: 

 

 

I dunno, Stephen:



> I'm just applying it to the particular case of 

> DNA-only descriptions to illustrate that no taxonomy 

> is involved, it is just someone saying "hey taxonomists, 

> I'm giving whatever taxonomic entity includes this DNA 

> sequence the name Aus bus, so you are going to have 

> to take it into account if you do any future taxonomic 

> work on the group". 



On what basis are you attributing this to DNA-only descriptions, and not morphology-based descriptions?  What if I wrote:



“I'm just applying it to the particular case of morphology-only descriptions to illustrate that no taxonomy is involved, it is just someone saying ‘hey taxonomists, I'm giving whatever taxonomic entity includes this morphological character the name Aus bus, so you are going to have to take it into account if you do any future taxonomic work on the group’.” 



How is that different, exactly?  You might reply, “Because I can see morphological characters with my eyes”.  And then I would reply, “Yeah, but lots of those characters – especially in insects -- require special technology (e.g., microscopes) to see”.  And then you might say, “No, no, everyone has access to a microscope, but not everyone has the ability to extract DNA sequences.”  And then I would come back with “Yeah, but how much longer will that be true?” And then we’d probably go back and forth a few more times, then one of us would eventually give up and go back to doing other work.



Or something like that.



> It leaves the taxonomist with no morphological 

> clues as to the species so named, so I suggest 

> that it is nothing but big problem for taxonomy! 



So… I’ve been actively involved with this debate going back to the very early days of PCR.  The basic argument is this:  “Almost nothing of value for taxonomic or phylogenetic research exists in morphology that does not also exist *somewhere* in the genome.”  For two and a half centuries, taxonomists were (and still are) using morphological characters as proxies for genetic information (whether they knew/know it or not).  By this I mean that, as taxonomists, we work with characters that are inherited across many generations of the taxa we study, and try to ignore characters that depend on environmental factors or ontogenetic factors or other life-history-related stuff (e.g., males vs. females, etc.).  I can imagine 10 or 20 or 50 years from now taxonomists looking back at this era and being impressed with how good we were at using these crude proxies (phenotypes) as metrics for elucidating evolutionary relationships, despite our handicap of not having access to full genomes within seconds using our iTricorders.



I’ve said this before, and I’ll reiterate here:  Some of my posturing on this debate is very-much playing the role of devil’s advocate.  I actually consider myself “old-school” when it comes to my own taxonomic practice – relying almost exclusively on morphological characters for my new species, and adding in DNA information (usually barcodes) only as one more line of evidence supporting my taxonomic decisions.  But here’s the thing:  I feel this way not because I don’t believe that DNA will ultimately prove to be *the* basis of future taxonomy (it inevitably will). Rather, at this particular point in history I don’t think we’re quite “there yet” in our ability to interpret DNA evidence for anchoring our taxonomy as effectively as we are/have been with morphology.  This is obviously changing (rapidly), but that change as applied to taxonomic practice will need to be graceful (not abrupt) to transition the 250+ year legacy of morphology-based taxonomy to DNA-based taxonomy.



> This problem could be avoided if the Code 

> were to prohibit DNA-only descriptions.



No, not really.  More the opposite, I think.



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 <mailto:deepreef at bishopmuseum.org> 

<http://hbs.bishopmuseum.org/staff/pylerichard.html <https://urldefense.proofpoint.com/v2/url?u=http-3A__hbs.bishopmuseum.org_staff_pylerichard.html&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=3uOEnwhjH4qUqTLCy4GIX0xRsO-0ln3kGqNCAL1DzmY&m=fV8h7KdqauzLREFqRl9bfb9D8bH0oRolcaEDeLuYrl8&s=E7iNiPMPDYbuymU4yJleXnbrP_Av5f2X6f7vkA1JcJA&e=> > 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 <mailto:stephen_thorpe at yahoo.co.nz> > 
Sent: Sunday, February 14, 2021 10:04 AM
To: 'Francisco Welter-Schultes' <fwelter at gwdg.de <mailto:fwelter at gwdg.de> >; iczn-list at afriherp.org <mailto:iczn-list at afriherp.org> ; Richard Pyle <deepreef at bishopmuseum.org <mailto:deepreef at bishopmuseum.org> >
Cc: 'Taxacom' <taxacom at mailman.nhm.ku.edu <mailto:taxacom at mailman.nhm.ku.edu> >
Subject: Re: [iczn-list] GENERAL CALL TO BATTLE



Rich,



"This is how the Code works for *all* names, going back to Linnaeus, and long before DNA was even known to exist.  This is what typification is all about"



Yes, I know that! I'm just applying it to the particular case of DNA-only descriptions to illustrate that no taxonomy is involved, it is just someone saying "hey taxonomists, I'm giving whatever taxonomic entity includes this DNA sequence the name Aus bus, so you are going to have to take it into account if you do any future taxonomic work on the group". It leaves the taxonomist with no morphological clues as to the species so named, so I suggest that it is nothing but big problem for taxonomy! This problem could be avoided if the Code were to prohibit DNA-only descriptions. The Code would not thereby be meddling in taxonomy because there is no taxonomy involved in DNA-only descriptions! The Code would simply be prohibiting one process by which names can be proposed in a way that can negatively impact on taxonomy.



Cheers, Stephen



On Monday, 15 February 2021, 08:50:43 am NZDT, Richard Pyle <deepreef at bishopmuseum.org <mailto:deepreef at bishopmuseum.org>  <mailto:deepreef at bishopmuseum.org <mailto:deepreef at bishopmuseum.org> > > wrote: 



_______________________________________________
Taxacom Mailing List

Send Taxacom mailing list submissions to: taxacom at mailman.nhm.ku.edu <mailto:taxacom at mailman.nhm.ku.edu> 
For list information; to subscribe or unsubscribe, visit: http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom <https://urldefense.proofpoint.com/v2/url?u=http-3A__mailman.nhm.ku.edu_cgi-2Dbin_mailman_listinfo_taxacom&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=3uOEnwhjH4qUqTLCy4GIX0xRsO-0ln3kGqNCAL1DzmY&m=fV8h7KdqauzLREFqRl9bfb9D8bH0oRolcaEDeLuYrl8&s=6CnaPtpfam8T1_aWGtmx7YPOYet3lOBfeWCMoQXmCv8&e=> 
You can reach the person managing the list at: taxacom-owner at mailman.nhm.ku.edu <mailto:taxacom-owner at mailman.nhm.ku.edu> 
The Taxacom email archive back to 1992 can be searched at: http://taxacom.markmail.org <https://urldefense.proofpoint.com/v2/url?u=http-3A__taxacom.markmail.org&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=3uOEnwhjH4qUqTLCy4GIX0xRsO-0ln3kGqNCAL1DzmY&m=fV8h7KdqauzLREFqRl9bfb9D8bH0oRolcaEDeLuYrl8&s=XmEsEN5BTbYHopiO6YjoSOvRsFq6p68M3RkjRHcFeDQ&e=> 

Nurturing nuance while assaulting ambiguity for about 34 years, 1987-2021.

_______________________________________________
iczn-list mailing list
iczn-list at afriherp.org <mailto:iczn-list at afriherp.org> 
http://list.afriherp.org/mailman/listinfo/iczn-list