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

Mon Sep 4 16:07:16 CDT 2023

> Is there any need for such a DNA link to the type?

I don't know.  Some people are suggesting there is (or ultimately will be), as DNA sequences become ever more foundational to the process of taxonomy.  I can imagine a world in the not-too-distant future (perhaps even within my own lifetime) when the personal computer everyone carries with them wherever they go (currently known as a "smart phone", but probably by some other name in the future) can extract full-genome sequences from the air or soil or water or actual organism (if any are left in this future world), and compare them against a database of millions (billions?) of other full-genome sequences using algorithms honed by thousands of taxonomists with actual hands-on understandings of organisms in their natural environments (call them old-school "Naturalists"). These algorithms would be calibrated against centuries of historical taxonomy to extract taxonomically relevant information from the full genome and to estimate whether communication among biologists is enhanced or muddled depending on if one treats a given organism (based on its full-genome) as conspecific with an existing name-bearing type of an existing scientific name, vs. establishing a new name-bearing type with its own new scientific name.

In this imaginary (but not implausible) future world, it sure would be nice if the massive database included full-genome sequences for all name-bearing types of all scientific names going back to Linnaeus.  And this, of course, would require a provision of the Code to "anchor" scientific names to DNA sequences among the many, many existing names that lack sequenceable name-bearing types.

Coming back to your question of whether there is a "need" for this kind of Code-governed linkage.  My answer is:  Right now?  No.  Especially if we're talking DNA sequences that fall short of full-genome, and where we're not even close to developing the necessary well-calibrated algorithms.  But in the future world?  Maybe -- especially if things play out along the lines of what I described above.  Maybe it's too soon to be thinking about it ('though comments on this list would suggest otherwise).  Maybe Linnean-style nomenclature (and the associated Codes) will have been abandoned by the time this future world exists (probably?). But among the topics I've seen grace this email list over the years, I find this one somewhat more intellectually stimulating than some of the others I've witnessed.

Anyway, that's the basic rationale behind why I thought it was interesting to discuss -- at least as a hypothetical concept.

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: Lynn Raw <lynnrgraw at gmail.com>
> Sent: Monday, September 4, 2023 12:17 AM
> To: Richard Pyle <deepreef at bishopmuseum.org>
> Cc: Andrew Whittington <awhittington at flyevidence.co.uk>; 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
> 
> 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%7C456d3ee3834946d5150208dbad8aef77%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638294584461280427%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Zy6YPLexT4nVn2J51AMy9NEZ7%2BPFhs0o3CBwjMrbp08%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%7C456d3ee3834946d5150208dbad8aef77%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638294584461280427%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=7ZstYo4ehs66p47bY7oII%2BKBAvs8KL0yS%2BD7i%2FJkc6Q%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%7C456d3ee3834946d5150208dbad8aef77%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638294584461280427%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=yzvYxzSX0F7l3LMU7ThNtJQyIzw5pbWeBZmpqno8W58%3D&reserved=0>
> >> +++++++++++++++++++++++++++++++++++
> >>
> >> Interested in Alaskan Entomology? Join the Alaska Entomological
> >> Society and / or sign up for the email listserv "Alaska Entomological
> >> Network" at https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.akentsoc.org%2Fcontact_us&data=05%7C01%7Ctaxacom%40lists.ku.edu%7C456d3ee3834946d5150208dbad8aef77%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638294584461280427%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=QAFs51UReLw4sxOBOoeQSEQlJpkYeraLq9EmchMBsb4%3D&reserved=0
> >> _______________________________________________
> >> Taxacom Mailing List
> >>
> >> Send Taxacom mailing list submissions to: taxacom at lists.ku.edu
> >> <mailto:taxacom at lists.ku.edu>  For list information; to subscribe or
> unsubscribe, visit:
> >> https://lists.ku.edu/listinfo/taxacom
> >> You can reach the person managing the list at:
> >> taxacom-owner at lists.ku.edu <mailto:taxacom-owner at lists.ku.edu>  The
> Taxacom email archive back to 1992 can be searched at:
> >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftaxacom.markmail.org%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7C456d3ee3834946d5150208dbad8aef77%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638294584461280427%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LdTy7z7GmtMFJCy%2BFhlfYG3hX8olRHV9ckma0J0pATI%3D&reserved=0
> >>
> >> Nurturing nuance while assailing ambiguity and admiring alliteration
> >> for about
> >> 36 years, 1987-2023.
> >
> > _______________________________________________
> > Taxacom Mailing List
> >
> > Send Taxacom mailing list submissions to: taxacom at lists.ku.edu
> > <mailto:taxacom at lists.ku.edu> For list information; to subscribe or
> > unsubscribe, visit: https://lists.ku.edu/listinfo/taxacom
> > You can reach the person managing the list at:
> > taxacom-owner at lists.ku.edu <mailto:taxacom-owner at lists.ku.edu>
> > The Taxacom email archive back to 1992 can be searched at:
> > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftaxacom.markmail.org%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7C456d3ee3834946d5150208dbad8aef77%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638294584461280427%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LdTy7z7GmtMFJCy%2BFhlfYG3hX8olRHV9ckma0J0pATI%3D&reserved=0
> >
> > Nurturing nuance while assailing ambiguity and admiring alliteration for about
> 36 years, 1987-2023.
> >
> > _______________________________________________
> > Taxacom Mailing List
> >
> > Send Taxacom mailing list submissions to: taxacom at lists.ku.edu For
> > list information; to subscribe or unsubscribe, visit:
> > https://lists.ku.edu/listinfo/taxacom
> > You can reach the person managing the list at:
> > taxacom-owner at lists.ku.edu The Taxacom email archive back to 1992 can
> > be searched at: https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftaxacom.markmail.org%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7C456d3ee3834946d5150208dbad8aef77%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638294584461280427%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LdTy7z7GmtMFJCy%2BFhlfYG3hX8olRHV9ckma0J0pATI%3D&reserved=0
> >
> > Nurturing nuance while assailing ambiguity and admiring alliteration
> > for about 36 years, 1987-2023.