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

Mon Sep 4 06:05:47 CDT 2023

Dear Stephen,

normally, on all counts sequence data have to be analysed in context. If that is done properly, any problematic sequence would be identified and discarded. If your new spider species ate a fly and the sequence generated would be from the fly, no serious taxonomist would use this to describe a new spider. Also, ideally you have more than one sequence for a new taxon, either from different specimens or independently generated sequences from the same specimen.

There are, however, real scenarious that could cause problems. For instance, correct genome assembly is not trivial and much less so from mixed DNA. Thus, using entire genomes as types can be problematic, also because nobody has both the time and expertise to check these in a peer review process. Single markers are much easier to check and errors reveal themselves immediately. Another issue is describing new taxa from metabarcoding data, i.e. the DNA is known but no specimen associated with it. Imaging using an arthropod trap, homogenizing all the material and getting all the DNA out of it. You could rather easily separate the individual taxa based on their sequence data, but then you would only have DNA left, so no link to phenotype. In ecologically cryptic organisms, such as soild fungi or bacteria, this is a real and imminent problem very controversely discussed, also because quality control for such sequence data is limited.

Regards
Robert

Von: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
Gesendet: Montag, 4. September 2023 12:53
An: Lynn Raw <lynnrgraw at gmail.com>; Richard Pyle <deepreef at bishopmuseum.org>; Lücking, Robert <R.Luecking at bo.berlin>
Cc: Taxacom at mailman.nhm.ku.edu
Betreff: Re: Taxacom: building such a bridge (between DNA sequence and name) - was Minimalist revision of Mesochorus

I'm not up-to-date on how DNA sequences are actually generated, so maybe this worry no longer applies, but, it seems to me that any organism is itself an "ecosystem", with other organisms on and in it, including what it might have just eaten. So, what would happen if a new species was described based on a DNA sequence which was in fact a mixture of species? Another potential problematic scenario would be if there was some sort of error and the sequence specified in a description actually belonged to no organism.

Stephen

On Monday, 4 September 2023 at 10:44:33 pm NZST, Lücking, Robert via Taxacom <taxacom at lists.ku.edu> wrote:

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<mailto: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<mailto:deepreef at bishopmuseum.org>>
Cc: Taxacom at mailman.nhm.ku.edu<mailto: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<mailto: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<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.
>
>
>
> From: Andrew Whittington <awhittington at flyevidence.co.uk<mailto:awhittington at flyevidence.co.uk>>
> Sent: Friday, September 1, 2023 9:21 PM
> To: Richard Pyle <deepreef at bishopmuseum.org<mailto:deepreef at bishopmuseum.org>>; 'Derek Sikes'
> <dssikes at alaska.edu<mailto:dssikes at alaska.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
>
>
>
> 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%7C37074cf8324043201fea08dbad36e9f2%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638294223641252203%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=TdWuwjgzcz7dRHvYtRLrIajMn07ooPXvOr7FsvXAbbo%3D&reserved=0>
>
>  _____
>
> From: Taxacom <taxacom-bounces at lists.ku.edu<mailto: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> <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> <mailto:dssikes at alaska.edu> >;
> Taxacom at mailman.nhm.ku.edu<mailto: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> <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> <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>
>> <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> <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> <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%7C37074cf8324043201fea08dbad36e9f2%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638294223641252203%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=5WKU8SJ%2BnfAvEBUz3LE0aZDcHljkOPh7oJrpCk4aZL8%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%7C37074cf8324043201fea08dbad36e9f2%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638294223641252203%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=l4hUw0cfGPNg%2FBnxVxA573TQ4LZDeelE2nHDOpYBrso%3D&reserved=0>
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