Taxacom: On species diagnoses and DNA-based descriptions in taxonomic practice

Fri Aug 25 23:26:23 CDT 2023

Hi Thomas and thanks Rich and Stephen for your responses. I wanted to
clarify one thing here. You say you're a physician with an interest in
taxonomy so I am not sure exactly how detailed your understanding of
taxonomy and nomenclature are. These are two different things. Rich has
discussed it from a nomenclatural position that is looking at the
application of names to biological entities. I guess I was trying to speak
more from a taxonomic position. Remember that as a taxonomist I identify
that a population of some organism is a species, using a variety of
methodologies and my assumption set would be based on a species concept.
Then I use code to determine if there is already a name for that entity
(its rules help me which names are available and applicable to this
entity), and if not provide the rules for naming it.

Stephen pointed out one issue that has become apparent, which really harks
back to funding. Taxonomy in a way has moved from the Museum to the
University with the advent of DNA technology. I think this is unfortunate.
Universities need high turnover fast paced grants that work well with the
time frames of post graduate student programs. DNA is perfect for that,
morphology is harder. Hence many Universities that are doing taxonomy are
largely churning out high volume rapid turnover student projects with
guaranteed results (i do not mean a guarantee of a new species just a good
result i.e. a phylogeny). Morphology requires years of dedicated practice
usually restricted to groups that are practical in size. Ok for tenure but
not so easy for post grads. Unfortunately Universities are very good at
getting funding for this. Stephen hinted it was laziness, I think a fairer
summary is its a practical approach to the realities of scientific funding.
I agree with Stephen, I too prefer morphology, I use DNA as well but by far
I spend more time pouring over skeletons than I ever would in a DNA lab,
it's taken me 30 years to develop some 600 skeletal characters and I can
get 1.5 million base pairs in a few weeks.

Last thing to remember here the Codes do not dictate the taxonomy. A
species is a species due to the evidence presented about it, the Code just
helps determine what to call it, one way or another. Therefore the codes
will never attempt to control what is or is not a species, just what to
call it.

Cheers Scott

On Sat, Aug 26, 2023 at 1:02 AM Richard Pyle via Taxacom <
taxacom at lists.ku.edu> wrote:

> I see Scott Thomson and Stephen Thorpe have already replied, but I will
> give you my own thoughts before I read their messages:
>
> > First, a question about using a genome-wide DNA sequence as sole
> diagnosis
> > for a taxonomic species. Suppose technology advances so that a
> description
> > of the complete sequence of all the nucleic acid macromolecules making up
> > the genetic complement of each potential specimen supposedly representing
> > a newly-discovered taxonomic species is attainable. Then, if each living
> being
> > has a unique genetic complement (at least one single nucleotide
> > polymorphism or indel making one of its DNA sequences unique among
> > those of other living beings), what will prevent a seeker of cryptic
> species
> > from using every specimen as a type for a separate taxonomic species?
>
> You touch on a very critical point here, and is really at the crux of the
> issue behind the recently published paper, as well as more generally with
> respect to how the next Edition of the Code is crafted.  I will try to
> diagram the issue as concisely as possible.
>
> When we use the term "species" in the sense of a taxon, we are referring
> to a circumscribed set of organisms. I will refer to this as a "taxon".
>
> When we use the term "species" in the sense of nomenclature (e.g., ICZN
> Code), we are referring to a text-string label used to represent a
> "species" in the sense of a taxon.  I will refer to this as a "taxon-name".
>
> The ICZN Code establishes a set of standard rules for proposing
> taxon-names, and for determining which taxon-name has priority in cases
> where more than one proposed taxon-name is deemed to apply to the same
> taxon.
>
> The ICZN Code goes to some lengths to limit its scope to rules associated
> with taxon-names, without imposing any constraints on how taxonomists
> determine what circumscribed sets of organisms represent distinct/unique
> taxa (including "species" in the sense of a taxon).
>
> Among the rules in the ICZN Code is that newly proposed names must include
> the designation of a name-bearing type specimen for each species-group
> taxon-name.  This represents the only tangible/objective link between a
> taxon-name and the associated taxon.
>
> Another rule in the ICZN Code is Article 13.1.1, which stipulates that
> "...every new name published after 1930 must... be accompanied by a
> description or definition that states in words characters that are
> purported to differentiate the taxon..."
>
> There is a fair bit of disagreement among practicing taxonomists how,
> exactly to determine whether a published paper proposing a new taxon-name
> either does, or does not, fulfill this requirement. However, most
> taxonomists (including most Commissioners) seem to agree that:
> - The "description or definition" that accompanies the proposal of a new
> name does not need to apply to the name-bearing type specimen
> - The "description or definition" that accompanies the proposal of a new
> name does not need to be accurate or correct
> - When the "description or definition" is not consistent with the
> name-bearing type, the name-bearing type still remains the reference point
> for the taxon-name, and the only objective link between the taxon-name and
> the associated taxon.
>
> The logical problem with the requirement of Art. 13.1.1, is that it
> challenges the intention of the ICZN Code to limit its scope to
> nomenclature, rather than taxonomy.
>
> The question I have posed on several occasions is: What *nomenclatural*
> value does Art 13.1.1 provide?  There are many reasons why " a description
> or definition that states in words characters that are purported to
> differentiate the taxon" is very helpful for taxonomists, but there are
> MANY things that are very helpful to taxonomists that are nevertheless
> outside the scope of the ICZN Code.  The only semi-plausible benefits to
> nomenclature for maintaining the requirement of Art 13.1.1, that I can
> think of, are things like:
> - When the name-bearing type is lost of no longer extant, the "description
> or definition" allows the definition of the associated taxon-name to have a
> subjective relationship to a taxon.
> - In cases where a Neotype is to be designated, the "description or
> definition" helps narrow the scope of potential organisms that should be
> serve as a Neotype.
>
> Beyond that, the main argument for maintaining this requirement within the
> Code essentially boils down to: "Because that's how taxonomists have always
> done it."  I agree this is a compelling reason to maintain this rule, but
> the logical flaw in this rule nevertheless remains.
>
> Now, to tie all of this back to your question:  The purpose of the
> recently published article is (at least in my mind) to spark discussions
> such as this one, to get taxonomists thinking carefully about how the next
> edition of the Code should be modified to strengthened the relevant
> requirements in the Code (represented in the Current Code by Art. 13.1.1).
> There is near-universal agreement that the existing requirement (and
> wording thereof) is ambiguous and open to too much interpretation, so it
> absolutely needs to change.  But there are various options for implementing
> that change. One of these options is to abandon the requirement entirely.
> Another option is to refine the requirement such that the "description or
> definition" accompanying a new taxon-name proposal explicitly describes or
> defines the name-bearing type specimen (rather than the taxon as a whole).
> Just to be clear:  I am NOT talking about what makes a "good" new-species
> description for purposes of taxonomy.  Obviously, there are all kinds of
> information that a good new-species description should include, and we
> should all strongly support best practices.  What I am talking about is
> much narrower in scope, which is the specific subset of elements included
> within a new species description that play a role in fulfilling
> requirements for new taxon-names.
>
> Your specific question is: "... what will prevent a seeker of cryptic
> species from using every specimen as a type for a separate taxonomic
> species?"  The answer is: Nothing.  There has never been a rule that
> prevents anyone from doing exactly this, and there likely never will be
> such a rule.  The main reason nobody has done it, and likely won't do it,
> is that most people care about their scientific reputation.  As such, they
> generally (though not always) limit their proposals for new scientific
> names to entities that will not be immediately disregarded by the broader
> taxonomic community.  Nothing in the ICZN Code (past, present, or likely
> future) prevents me from describing four new species in the Genus Homo, one
> designating myself as the name-bearing type, one designating my wife as the
> name-bearing type, and one each designating each of my two children as the
> name-bearing type.  Indeed, nothing in the ICZN Code prevents me from
> proposing billions of new species-group names within the genus Homo.  It is
> not the job of the Code to do this.  And the point of the
> recently-published paper was not to do this either (nor to encourage it).
>
> We, as a broader community of Taxonomists, need to think carefully about
> how we want the next Code to refine the requirements currently represented
> in Art. 13.1.1, which potentially straddle the boundary between
> nomenclature and taxonomy.
>
> > Second, and related to the first question, if each natural species is a
> lineage-
> > segment, why is each taxonomic species diagnosis drawn from one or more
> > unrelated specimens instead of from a directly observed lineage-segment
> of
> > specimens?
>
> The basis of Linnean nomenclature is to provide a consistent method for
> establishing unique text-string labels to serve as proxies to represent
> circumscribed sets of organisms.  It's pretty remarkable that this system
> -- one of the longest-standing and most universally adopted standards in
> all of science -- was actually first established by a Creationist (and a
> century before Darwin's "Origin of Species"). My point here is that the
> system of nomenclature is not tied to any particular notion of "natural"
> species, lineage-segment-based or otherwise.  In spite of this, and for all
> its flaws, the system continues to work remarkably well (if it had not, it
> wouldn't continue to survive after a quarter of a millennium).
>
> > That is, cannot biological taxonomy be an experimental, as well
> > as a descriptive, science?
>
> It certainly can be, in a narrowly-defined context.  But for various
> reasons, it has not been.  One of those reasons, which sparks spirited
> debates (including here on Taxacom), is the philosophical distinction of
> "species as natural entities that taxonomists discover", vs. "species as
> artificial constructs meant to improve the efficiency of communication
> among humans".  Each side has its ardent supporters, and as far as I can
> tell, each side believes it's winning the debate.
>
> And with that, it's time I head home for dinner.
>
> 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: Taxacom <taxacom-bounces at lists.ku.edu> On Behalf Of Thomas
> > McCabe via Taxacom
> > Sent: Friday, August 25, 2023 3:21 PM
> > To: taxacom at lists.ku.edu
> > Subject: Taxacom: On species diagnoses and DNA-based descriptions in
> > taxonomic practice
> >
> > Hello. I am a physician biologist with an interest in biological
> taxonomy and
> > the discussions at Taxacom. May I add a comment and questions about the
> > journal article referenced by Thomas Pape ("Tightening the requirements
> for
> > species diagnoses would help integrate DNA-based descriptions in
> taxonomic
> > practice", *PLoS* Biol 21(8): e3002251)? The authors of this paper go
> beyond
> > nomenclature to advocate for taxonomic species diagnoses that are both
> > contrastive and state-specific. The authors also attend to the
> interesting
> > possibility and problems of defining species solely with genome-wide DNA
> > sequences.
> >
> > Regarding defining species, I request thoughts on two questions, the
> first
> > skeptical, the second leading.
> >
> > First, a question about using a genome-wide DNA sequence as sole
> diagnosis
> > for a taxonomic species. Suppose technology advances so that a
> description
> > of the complete sequence of all the nucleic acid macromolecules making up
> > the genetic complement of each potential specimen supposedly representing
> > a newly-discovered taxonomic species is attainable. Then, if each living
> being
> > has a unique genetic complement (at least one single nucleotide
> > polymorphism or indel making one of its DNA sequences unique among
> > those of other living beings), what will prevent a seeker of cryptic
> species
> > from using every specimen as a type for a separate taxonomic species?
> >
> > Second, and related to the first question, if each natural species is a
> lineage-
> > segment, why is each taxonomic species diagnosis drawn from one or more
> > unrelated specimens instead of from a directly observed lineage-segment
> of
> > specimens? That is, cannot biological taxonomy be an experimental, as
> well
> > as a descriptive, science?
> >
> > Respectfully,
> >
> > Thomas McCabe, M.D., M.P.H.
> >
> > Independent Scholar
> > _______________________________________________
> > 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%7C01d62fe45064424f6e6308dba5eca2c6%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638286208005781759%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=dfYPfX1edU2OTSmSmNsDT2GRvAsh%2Fy4JabkCTgEC79A%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%7C01d62fe45064424f6e6308dba5eca2c6%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638286208005781759%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=dfYPfX1edU2OTSmSmNsDT2GRvAsh%2Fy4JabkCTgEC79A%3D&reserved=0
>
> Nurturing nuance while assailing ambiguity and admiring alliteration for
> about 36 years, 1987-2023.
>

-- 
Scott Thomson

Centro de Estudos dos Quelônios da Amazônia - CEQUA
Petrópolis, Manaus
State of Amazonas, 69055-010
Brasil

https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.carettochelys.com%2F&data=05%7C01%7Ctaxacom%40lists.ku.edu%7C01d62fe45064424f6e6308dba5eca2c6%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638286208005781759%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RgrklC06xKVDhzRbuTovQ95h0ScBT7l1nsoPRFmyM7E%3D&reserved=0
ORCID: https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Forcid.org%2F0000-0003-1279-2722&data=05%7C01%7Ctaxacom%40lists.ku.edu%7C01d62fe45064424f6e6308dba5eca2c6%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638286208005781759%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=EwdM6J0akAdDxwtCKfJdSTruxA0uDWWTepj%2BaOuqpkI%3D&reserved=0
Lattes: *https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flattes.cnpq.br%2F0323517916624728*&data=05%7C01%7Ctaxacom%40lists.ku.edu%7C01d62fe45064424f6e6308dba5eca2c6%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638286208005781759%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=EP6vWiKK0C8ZCDtf4eylT1ZaBFW%2BAGkllzraL3Cik9U%3D&reserved=0
<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwwws.cnpq.br%2Fcvlattesweb%2FPKG_MENU.menu%3Ff_cod%3D1E409F4BF37BFC4AD13FD58CDB7AA5FD%23&data=05%7C01%7Ctaxacom%40lists.ku.edu%7C01d62fe45064424f6e6308dba5eca2c6%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638286208005781759%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=tVG%2FVOPeF8QijTa95RqaSU3t9GX8YVJuoBOrLofFGLA%3D&reserved=0>
Skype: Faendalimas
Mobile Phone Brasil: +55 11 98178 7270
Whatsapp: +55 11 98178 7270