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

Fri Aug 25 23:02:24 CDT 2023

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
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> -----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
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