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

[Stephen Thorpe]

 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> wrote:  
 
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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> On Behalf OfMallet, James
Sent: Sunday, February 14, 2021 6:47 PM
To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
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
 
  
 
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> 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> 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

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From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
Sent: Sunday, February 14, 2021 10:04 AM
To: 'Francisco Welter-Schultes' <fwelter at gwdg.de>;iczn-list at afriherp.org; Richard Pyle <deepreef at bishopmuseum.org>
Cc: 'Taxacom' <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> > wrote:
 


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