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

Sun Sep 3 14:52:58 CDT 2023

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%7Cc1dfcb59f8d7409d674e08dbacb7630e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638293675879907669%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=TJ0M9TGZ0JKZuQtueQjGQQ5Cb3jQpEu8sQmnblTmZxE%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%7Cc1dfcb59f8d7409d674e08dbacb7630e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638293675879907669%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=fWDPSsAj%2F3NQ7iJCFX6ew5KeWluhzs0MtTeXAI8FKek%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%7Cc1dfcb59f8d7409d674e08dbacb7630e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638293675879907669%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=FyVB3waRySeQE1Z4jJ811h1qpkaj0wuIUIg8vzVltXw%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%7Cc1dfcb59f8d7409d674e08dbacb7630e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638293675879907669%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=j3TnRT%2BKQ5wTlCLmU6tGl5DWm8MGkleG%2BIeThZF4c4w%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%7Cc1dfcb59f8d7409d674e08dbacb7630e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638293675879907669%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=jGazsw9TtBg35x9JM6l1jsDQmM%2Fif5J4LtTEsIO5h9g%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%7Cc1dfcb59f8d7409d674e08dbacb7630e%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638293675879907669%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=jGazsw9TtBg35x9JM6l1jsDQmM%2Fif5J4LtTEsIO5h9g%3D&reserved=0

Nurturing nuance while assailing ambiguity and admiring alliteration for about 36 years, 1987-2023.