Taxacom: building such a bridge (between DNA sequence and name) - was Minimalist revision of Mesochorus

Mon Sep 4 16:13:59 CDT 2023

Dear Robert,

Many thanks for sharing this!  Yes, what you describe for (1) and (2) is similar to how it works in the ICZN Code as well.  As I noted previously, the context of my question wasn't about how the Codes currently operate, but how we might want to modify them to operate in a (near?) future world where DNA sequences are regarded as much more foundational to taxonomy and its associated nomenclature.

Your point about epitypes in (2) is exactly what I was getting at.  There have been proposals in the recent past (at least, within my tenure as a Commissioner) to introduce the concept of the epitype in the ICZN Code specifically to accommodate situations where a name-bearing type is still "extant", but is missing critical diagnostic characters (e.g., a patch of skin and scales from a fish, with nothing else left).  Obviously, the establishment of an epitype system in the zoological Code could be used (as I've suggested) as a mechanism to link a DNA sequence to a scientific name in a way that is Code-mandated.  Perhaps the best model for such language would be the ICNafp language for epitypes.

Again, many thanks for your input on this!

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
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.

> -----Original Message-----
> From: Lücking, Robert <R.Luecking at bo.berlin>
> Sent: Monday, September 4, 2023 12:44 AM
> To: Lynn Raw <lynnrgraw at gmail.com>; Richard Pyle
> <deepreef at bishopmuseum.org>
> Cc: Taxacom at mailman.nhm.ku.edu
> Subject: AW: Taxacom: building such a bridge (between DNA sequence and
> name) - was Minimalist revision of Mesochorus
> 
> Dear Richard,
> 
> all of what you describe works in the ICN for plants, algae and fungi. And there
> are known examples.
> 
> (1) Species described based on three specimens, one designated as holotype,
> the two other sequenced (why the only non-sequenced specimen was
> designated as type, who knows). The material is heterogeneous any may
> represent 2-3 different species. In that case, the name-bearing holotype defines
> the use of that name, whereas the other two, sequenced specimens belong to
> unnamed taxa. Straightforward (in such a case it would not make sense to link
> any of the two sequences to the name-bearing holotype).
> 
> (2) Holotype extant but too old to be sequenced: a sequenced epitype can be
> selected, but of course in a way that ideally there is no doubt that the epitype is
> conspecific with the holotype (e.g. a morphologically identical topotype from
> the same location).
> 
> (3) Turns out the taxonomic concept of a name is not in accordance with the
> original type but the wrong concept has been well-established in the literature.
> In that case the name can be conserved with a new, conserved type
> corresponding to the concept in use. The new, conserved type can have a DNA
> sequence attached to it. This would be a way to link a DNA sequence to a name
> that it was not originally linked to. But it needs a formal conservation proposal.
> 
> Regards
> Robert
> 
> 
> 
> 
> -----Ursprüngliche Nachricht-----
> Von: Taxacom <taxacom-bounces at lists.ku.edu> Im Auftrag von Lynn Raw via
> Taxacom
> Gesendet: Montag, 4. September 2023 12:17
> An: Richard Pyle <deepreef at bishopmuseum.org>
> Cc: Taxacom at mailman.nhm.ku.edu
> Betreff: Re: Taxacom: building such a bridge (between DNA sequence and name)
> - was Minimalist revision of Mesochorus
> 
> Hi Rich,
> Is there any need for such a DNA link to the type? You could say the same for
> blood plasma / serum proteins, sonagrams, etc. Surely any serious taxonomist
> will find whatever evidence is available from the literature and consider it along
> with the novel data from the new research.
> Regards,
> Lynn Raw
> 
> 
> > On 3 Sep 2023, at 21.53, Richard Pyle via Taxacom <taxacom at lists.ku.edu>
> wrote:
> >
> > Hi Andrew,
> >
> >
> >
> > The context of my post was in the hypothetical scenario where some sort of
> mechanism is established in the Code for accommodating a DNA sequence from
> a non-type specimen (Epitype?) to be nomenclaturally linked to the name.  This
> of course can already happen in cases where a Neotype is justified, but I agree
> that under the current rules, when no Neotype is involved, the scenario I
> describe would simply be treated as a misidentification.  The original thought
> experiment was how it might be possible to establish a more tangible
> nomenclatural link between a DNA sequence and a name, when the name-
> bearing type is unsequenceable.  I seriously doubt such a provision would be
> added to the fifth edition of the Code; but given the trajectory of the role of
> DNA in taxonomy, I could imagine something like this being incorporated into
> Code-6 (perhaps as part of a more comprehensive LAN-type approach).
> >
> >
> >
> > 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
> >
> > 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: Andrew Whittington <awhittington at flyevidence.co.uk>
> > Sent: Friday, September 1, 2023 9:21 PM
> > To: Richard Pyle <deepreef at bishopmuseum.org>; 'Derek Sikes'
> > <dssikes at alaska.edu>; taxacom at mailman.nhm.ku.edu
> > Subject: Re: Taxacom: building such a bridge (between DNA sequence and
> > name) - was Minimalist revision of Mesochorus
> >
> >
> >
> > Richard, I disagree - the DNA sequence is not associated with the
> > Type, so it is simply misidentification. Andrew
> >
> >
> >
> > Sent from Outlook for Android <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Faka.ms%2FAAb9ysg&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cb957d7e6e6ff4056237808dbad8bde31%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638294588485929289%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=PGxy%2BDZVp5EczjWCTNBfzeAnIpN7qgAGjOplRvT1bwI%3D&reserved=0>
> >
> >  _____
> >
> > From: Taxacom <taxacom-bounces at lists.ku.edu
> > <mailto:taxacom-bounces at lists.ku.edu> > on behalf of Richard Pyle via
> > Taxacom <taxacom at lists.ku.edu <mailto:taxacom at lists.ku.edu> >
> > Sent: Thursday, August 31, 2023 6:51:01 PM
> > To: 'Derek Sikes' <dssikes at alaska.edu <mailto:dssikes at alaska.edu> >;
> > Taxacom at mailman.nhm.ku.edu <mailto:Taxacom at mailman.nhm.ku.edu>
> > <Taxacom at mailman.nhm.ku.edu <mailto:Taxacom at mailman.nhm.ku.edu> >
> > Subject: Re: Taxacom: building such a bridge (between DNA sequence and
> > name) - was Minimalist revision of Mesochorus
> >
> >
> >
> > Thanks, Derek.
> >
> > This is the conundrum:  What happens when a DNA sequence, taken from a
> non-type specimen, is somehow formally/officially attached to the name, and
> then someone later declares that the two different specimens (the name-
> bearing type, and the specimen from which the DNA was extracted) are
> members of different species?
> >
> > An analogy in the Code is when there are Syntypes, and someone decides that
> the syntype series includes representatives of more than one species.  In such
> cases, a lectotype is selected from among the original syntype series, and the
> others become non-name-bearing paralectotypes.
> >
> > I imagine in such a situation with an "official" link between a non-type DNA
> sequence and a name where someone declares that they represent different
> taxa, the name remains linked to the original type specimen. In such cases, I
> would imagine a process for replacing the "official" DNA sequence with a "neo"
> DNA sequence.
> >
> > Bear in mind, this is a very tenuous proposal (to establish an official "genetic
> type" thing in the Code), and I seriously doubt it could be crafted with sufficient
> support for inclusion in Code 5, but it's not impossible (maybe Code-6?)  But I
> think that, given the direction things are going, there may indeed come a time
> when the broader taxonomic community will want some sort of formal link
> between a name and a DNA sequence.  Maybe not something as anemic as a
> barcode, but perhaps in a not-too-distant future where whole-genome
> sequences are commonplace, there could be real value in a provision of this
> sort.
> >
> > 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>
> > 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.
> >
> >> -----Original Message-----
> >> From: Taxacom <taxacom-bounces at lists.ku.edu
> >> <mailto:taxacom-bounces at lists.ku.edu> > On Behalf Of Derek Sikes via
> >> Taxacom
> >> Sent: Thursday, August 31, 2023 6:56 AM
> >> To: Taxacom at mailman.nhm.ku.edu
> <mailto:Taxacom at mailman.nhm.ku.edu>
> >> Subject: Taxacom: building such a bridge (between DNA sequence and
> >> name) - was Minimalist revision of Mesochorus
> >>
> >> Richard Pyle wrote "a mechanism for building such a bridge (between
> >> DNA sequence and name) in a Code-enforceable way,..."
> >>
> >> I would like to strongly endorse this notion!
> >>
> >> An issue those who deal with DNA barcodes often face is one species
> >> occurring in multiple 'BINs' (the Barcode of Life Datasystem (BOLD)
> >> algorithm-generated proxy or "best guess" for 'species'). There are
> >> many ways this can happen but the most interesting way is when
> >> multiple species are 'hiding' under one species name. In such cases the
> question then arises "OK, which one is the "real"
> >> species X?
> >>
> >> I've repeatedly suggested to those running BOLD that it would be VERY
> >> helpful to taxonomists if we could easily see in a BIN if there are
> >> any specimens from the Type Locality or if any specimens in the BIN
> >> are the primary type, etc. with some clear flagging or obvious
> >> declaration of some sort. Currently, there is nothing other than
> >> access to the collection localities via a map or data listing of the sequenced
> specimens.
> >>
> >> So I'll reiterate the incredible value to the future of taxonomy if
> >> there was some way to be much more certain than we normally are that
> >> THIS DNA sequence belongs to THIS species name.
> >>
> >> DNA-type specimens could be declared as a parallel typing system such
> >> that a taxonomist states "I have determined this DNA-sequenced
> >> specimen is the same species as that to which the primary type
> >> belongs, so I declare it the DNA- type of the species."
> >>
> >> If DNA can be obtained from the holotype then the holotype would be
> >> the DNA-type, but if that is not possible, then the DNA-type would be
> >> a different specimen.
> >>
> >> This would help reduce massive amounts of confusion and ambiguity
> >> over how to interpret DNA barcode data, which is growing at an enormous
> rate.
> >>
> >> Derek
> >>
> >>
> >>
> >>
> >> --
> >>
> >> +++++++++++++++++++++++++++++++++++
> >> *Derek S. Sikes*, Curator of Insects, Professor of Entomology
> >> University of Alaska Museum (UAM), University of Alaska Fairbanks
> >> 1962 Yukon Drive, Fairbanks, AK   99775-6960
> >> dssikes at alaska.edu <mailto:dssikes at alaska.edu>  phone: 907-474-6278
> >> he/him/his University of Alaska Museum
> >> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.uaf.edu%2Fmuseum%2Fcollections%2Fento%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cb957d7e6e6ff4056237808dbad8bde31%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638294588485929289%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=xVuHCJ%2F1Y18xmeRmx8n%2FWJs9KXyb%2BRNpveIbrZEoeR0%3D&reserved=0>
> >> -  search 393,654 digitized arthropod records
> >> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Farctos.database.museum%2Fuam_ento&data=05%7C01%7Ctaxacom%40lists.ku.edu%7Cb957d7e6e6ff4056237808dbad8bde31%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638294588485929289%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=GrDTIeyNRoylLA3B%2FxIoYcaBGL3THrjkMmFVXA4SwB4%3D&reserved=0>
> >> +++++++++++++++++++++++++++++++++++
> >>
> >> Interested in Alaskan Entomology? Join the Alaska Entomological
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> >>
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> 36 years, 1987-2023.
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> 36 years, 1987-2023.
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> 
> Nurturing nuance while assailing ambiguity and admiring alliteration for about
> 36 years, 1987-2023.