Taxacom: On describing new taxa without using phylogenetics: some suggestions

[Kuoi Zhang]

Hello Rich

To clarify, I don't think our approach is limited to cladistics. Part of my email was actually a rebuttal to the article “Should we describe genera without molecular phylogenies?” (Páll-Gergely, 2017), though our paper itself only mentioned that point briefly.

“Taxonomy CAN BE a science, and all new taxa that are proposed CAN BE THOUGHT OF AS hypotheses that can be refuted and falsified IN THE CONTEXT OF AN EXPLICIT CONCEPTUAL FRAMEWORK FOR DELINEATING TAXA.”

Thank you for allowing me to elaborate on this. If Páll-Gergely’s statement were rephrased in this way, I would completely agree.

I also understand the fuzziness among different species concepts; indeed, each reflects a different philosophical or ideological standpoint. That is not the focus of our paper. In the discussion section, we wrote that “Regardless of the framework, taxonomic conclusions must be testable and falsifiable.” I fully understand your point about the limits of strict falsifiability; still, we believe that partial progress in that direction is better than none at all.

However, I think most would agree that we should not return to merely listing morphological patterns to describe additional taxa. As we noted, “It is regrettable that recent efforts have, in some instances, regressed to pre-1900s practices by neglecting established phylogenetic methodologies.”

I also agree with your remark that “our field can improve if we better understand where we all agree and disagree on conceptual principles, rather than debate because we don’t actually understand each other.” Our paper does not advocate any particular species concept; instead, it argues that whatever concept one adopts should be testable and falsifiable, even if not in a fully strict sense.

Finally, thanks for your explanation and long email.

Best regards
Guoyi



Guoyi Zhang (she/her), MRes, PhD candidate
Personal Web<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmalacology.net%2F&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Ca835a227a19c4bf0762708de061a4f34%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638954907255115078%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=59DpVr6RcflP0%2FOFInNPlg7JIgTzGOVRVU8ubE%2BmlAg%3D&reserved=0> | OCRID<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F0000-0002-3426-9273&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Ca835a227a19c4bf0762708de061a4f34%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638954907255134850%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=7xkEtvAdi%2F%2BaJlybFsU2JLqhoCsqTmh7oVc1%2B8tNF70%3D&reserved=0>
School of Biological, Earth and Environmental Sciences
University of New South Wales
Australian Museum Research Institute
Australian Museum

________________________________
From: Richard Pyle <Deepreef at bishopmuseum.org>
Sent: Wednesday, 8 October 2025 13:19
To: Kuoi Zhang <zhang.guo-yi at outlook.com>; Taxacom (taxacom at lists.ku.edu) <taxacom at lists.ku.edu>
Subject: RE: Taxacom: On describing new taxa without using phylogenetics: some suggestions

Dear Guoyi,

Thank you for sharing this to the list.  Somewhat like Robert Lücking, I interpret your argument to be in support of using more rigorous forms of analyses for inferring phylogenetic patterns among organisms (though I'm not sure you were specifically limiting your argument to the cladistic method per se).

I confess I have not had time to read your paper in full (I chose instead to respond specifically to the comments in your email by writing this long email, taking more time to do so than it would have taken to read the paper...sorry...).  Perhaps after I have time to read the paper (I did download it), I'll understand better what your point is.

> This paper briefly summarizes why taxonomy is a science, how taxonomy can
> be a science, how the ideas and methods of Kant, Darwin, Hennig, and
> Popper have influenced modern taxonomy, and why contemporary
> taxonomic research should not be separated from phylogenetics, both from
> the perspectives of history and the philosophy of science.

I don't have any problems with the above-quoted text.  But the title of the Article ("Why we should not describe new taxa without using phylogenetics") refers specifically to "describing new taxa".  Taken literally, "taxa" is a word that refers to a circumscribed set of organisms (alive, recently dead, and yet-to-be-born), and the word "describing" can be understood to mean something along the lines of "providing evidence in support of some sort of [phylogenetic] basis for defining the boundaries of the circumscription" (in this case, "[phylogenetic] basis" essentially implies a reference to some sort of conceptual framework for delineating taxa on certain biological or evolutionary principles, such as the BSC, PSC, etc.).  Adding in the word "new" would allow for a literal interpretation of "describing new taxa" that would work out to something like "providing evidence to support a circumscribed set of organisms that has not been previously asserted".  Examples of this might include cases where two populations of organisms consistently referred to as distinct species should instead be regarded as conspecific.

However, most practicing taxonomists would likely interpret the expression "describing new taxa" more explicitly as something like "proposing a new scientific name to represent a particular circumscribed set of organisms that hitherto fore had previously not been recognized as such at a particular taxonomic rank".  For example, "describing a new species".

Whether or not I agree or disagree with the statement expressed in the title of your paper depends on which of these two things you mean. If your arguments are referring to the former context (i.e., debating the phylogenetic affinities and clusterings of circumscribed taxa independently of whether or not they already have scientific names to represent them), then I don't disagree.  But if this latter interpretation is what you are focused on, then I do have some comments (as follows).

Having already established that I agree that Taxonomy can certainly be framed as "science", following the scientific method, etc., I'll start by taking a closer look at this assertion:

> I personally disagree with the statement “taxonomy
> is a science, and all new taxa that are proposed are hypotheses that can be
> refuted and falsified.”

As written in the text as you quote it, I also disagree with the statement.  However, I would agree with a slightly altered version of this statement written as “taxonomy CAN BE a science, and all new taxa that are proposed CAN BE THOUGHT OF AS hypotheses that can be refuted and falsified IN THE CONTEXT OF AN EXPLICIT CONCEPTUAL FRAMEWORK FOR DELINEATING TAXA.”
[My additions in ALL CAPS.]

For example, IN THE CONTEXT of a strict interpretation of the BSC, the notion that population A and population B are different species can be "falsified" if a viable offspring resulting from the cross-breeding of one individual from each of the two populations can be shown to exist in nature.

The problem with the BSC -- and pretty-much all "species concepts" -- is that none of them can be rigorously applied. I don't just mean "impractical", I mean that pretty-much all of them necessitate some sort of fuzziness at the margins. For the BSC example, if viable hybrids between two populations that have ample opportunity to interbreed with each other are extremely rare (maybe only one or two cases out of millions of sympatric non-hybrid), then adherents of the BSC would "let it slide" and continue to recognize them as distinct species (despite being explicitly falsified). This is what I mean by "fuzziness".

If this were NOT the case (i.e., "fuzziness" was not tolerated), then every "species" that has ever existed on Earth must have first come into existence as the offspring of a distinct species (i.e., the F1 offspring is a different species from the biological parent[s]).  However, because it IS the case (i.e., that "fuzziness" is necessary for each of the various "species concepts"), then applying strict "falsifiability" is difficult or impossible.

Indeed, I think this core conundrum lies at the heart of why there is still no consensus on which of the various "species concepts" is the one to use (certainly many people have argued that one or another has "won out", but these are the proclamations of partisans).  In other words, I think one of the main reasons why there is no consensus on a "species concept", is because each one has its own flavor of "fuzziness", and different taxonomic practitioners find these different flavors to be more or less distasteful.  My (strong) suspicion is that this will never be resolved, and that the reason it will never be resolved is that the better we understand the process of evolution, the more obvious it becomes that it does not result in "taxa" (not at the rank of species, and certainly not at higher ranks).  Rather, we humans, in an effort to make sense of the diversity of life, and especially in order to facilitate communication with each other about what we perceive to be "units of biodiversity", have adopted a system of naming and classifying biodiversity into such perceived units.

And this is what brings me to the main point (disagreement?) I have on this topic, which has to do with the intersection between "taxonomy" (which certainly CAN be practiced as a science in particular circumstances), and "nomenclature" (which is a standardized protocol -- perhaps the longest-standing and widely adopted such standards in all of science).

Too often in these sorts of debates, people conflate these two things (taxonomy and nomenclature).  This is why I began this long-winded and rambling email with the parsing of meaning of the phrase "describing new taxa".  In the latter context ("proposing a new scientific name to represent a particular circumscribed set of organisms that hithertofore had previously not been recognized as such at a particular taxonomic rank"), we are very-much in the realm of nomenclature. In this realm, the use of a scientific name (e.g., a species name) is proposed as a label applied to an implied circumscribed set of organisms.  The Linnean system of nomenclature (as governed by the various Codes) is based on "name-bearing types" (i.e., holotype, lectotype, neotype, syntypes, etc.). This means that the only objective link between a particular Linnean-style scientific name and actual biodiversity is the name-bearing type specimen(s). The broader circumscribed set of non-type organisms (e.g., a "clade") to which any particular scientific name label is applied is entirely within the realm of "Taxonomy", and not nomenclature per se. (Note that efforts such as PhyloCode attempt to resolve this gap between taxonomy and nomenclature, but have yet to gain wide-spread adoption across the majority of practicing taxonomists.)

I think the reason the Taxonomy issues get conflated with nomenclature is that we use these Linnean-style scientific names as proxies for circumscribed taxa (as they were intended to be used), but we're notoriously sloppy about how we do this (i.e., we're not often explicit as to what specific circumscribed set of organisms -- taxon -- we mean when we use a scientific name as a proxy in this way).  As a result of that pervasive historical "sloppiness", the de-facto definition for "species" continues to be what it always has for the last couple of centuries:  "a species is what a taxonomist (or community of taxonomists) says it is".  Such a definition is not "falsifiable" in a biological/evolutionary sense (of course), so in this context of "species", the notion that "a species is a hypothesis" only makes sense in a sociological context (e.g., "I hypothesize that proposing this new scientific name linked to this name-bearing type will improve the effectiveness/efficiency of communication between and among people").

So... why did I waste so much of my time writing this (and waste the time of everyone who might be foolish enough to read it all)?  I guess my answer is that I believe our field (biological taxonomy) can improve if we better understand where we all agree and disagree on conceptual principles, vs. simply debate because we don't actually understand each other. This is my attempt to clarify exactly what you are proposing in your assertions about "[w]hy we should not describe new taxa without using phylogenetics".

Aloha,
Rich

P.S. Note, in my comments above I have avoided any reference to "molecular" vs. "morphological" characters as the basis for taxonomic analysis.  My comments above are all independent of this (somewhat dubious) distinction.

Richard L. Pyle, PhD
Director of EXCORE | Senior Curator of Ichthyology | Database Coordinator for Natural Sciences
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 Kuoi Zhang
> via Taxacom
> Sent: Monday, October 6, 2025 3:52 PM
> To: Taxacom (taxacom at lists.ku.edu) <taxacom at lists.ku.edu>
> Subject: Taxacom: On describing new taxa without using phylogenetics: some
> suggestions
>
> Zhang G, Feng Q. 2025. Why we should not describe new taxa without using
> phylogenetics. Comment on Chen et al. (2025). Journal of Natural History
> 59(37–40): 2355–2359.
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1080%2F00222933.2025.2564347&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Ca835a227a19c4bf0762708de061a4f34%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638954907255149775%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=KLztlkXHv17kfDA7eCIWs71Uuvq9u7o4Xmn8ksiCv7c%3D&reserved=0
>
> pdf available at
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.researchgate.net%2Fpublication%2F396239492_Why_we_should_not&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Ca835a227a19c4bf0762708de061a4f34%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638954907255164143%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=fvJ84T8SSA1ttAif5duX6ZrQWICPoXD2ue8atgi1%2Bkw%3D&reserved=0
> _describe_new_taxa_without_using_phylogenetics_Comment_on_Chen_et_
> al_2025<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.researchgate.net%2Fpublication%2F396239492_Why_we_sh&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Ca835a227a19c4bf0762708de061a4f34%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638954907255179959%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=mKA0YLscZGH7IDrdH1CGMBzaoDpbWNPJbkQRXoIgC3E%3D&reserved=0
> ould_not_describe_new_taxa_without_using_phylogenetics_Comment_on_
> Chen_et_al_2025?_sg%5B0%5D=hqDEV92UeyWCOKjJ17ed1jbtmejHJ9MvHW
> GQaWxxhz91RNCiYocNZhGRj2BRWUdscZ9UF6XUnkfkZoKRIVT8RXi0FUkNPb4
> Rchgejiww.9eeTE4s8-qcLQo1Mb6y-
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>
> Under the pressure of an overwhelming number of problematic new taxa, we
> call for taxonomists to incorporate phylogenetic methods and reasoning into
> their taxonomic work. I understand that many may disagree, but please allow
> me to explain.
>
> This paper briefly summarizes why taxonomy is a science, how taxonomy can
> be a science, how the ideas and methods of Kant, Darwin, Hennig, and
> Popper have influenced modern taxonomy, and why contemporary
> taxonomic research should not be separated from phylogenetics, both from
> the perspectives of history and the philosophy of science.
>
> To reach readers who may be new to phylogenetics, we must emphasize that
> phylogenetics is not limited to molecular data. Although I belong to
> Generation Z, I am aware that phylogenetics was first widely applied to
> morphological characters long before molecular sequencing became
> common. While morphology-based phylogenetics may suffer from
> homoplasy, something is still better than nothing. Simply describing
> morphological patterns without an explicit phylogenetic framework is less
> informative and less scientific than conducting morphology-based
> phylogenetic analyses.
>
> I am aware of previous arguments presented in the paper “Should we
> describe genera without molecular phylogenies?”, whose author strongly
> opposed our views and directly criticized our commentary during the review
> process. That paper lacked a clear understanding of phylogenetics based on
> morphological data, as also revealed during the review process of our own
> manuscript. The author wrote, “not to mention fossil taxa, which also need to
> be placed in the system obviously without molecular support.” I believe most
> paleontologists would disagree with this statement, as fossil taxa can indeed
> be placed within a phylogenetic framework using morphological characters.
>
> In response to claims such as “we should invest more trust in the taxonomic
> evaluations of the decreasing number of taxonomists and allow more
> freedom for morphology-based grouping,” I would say: “Taxonomy should
> not become theology, where people are expected to believe without
> evidence.” Furthermore, I personally disagree with the statement “taxonomy
> is a science, and all new taxa that are proposed are hypotheses that can be
> refuted and falsified.” A taxon described solely by a fixed morphological
> pattern, as the author often does, cannot truly be falsified, since any
> additional variation can easily be reinterpreted as representing a new taxon.
> Such direct assertions are not falsifiable, much like religious doctrines. When
> synonyms or new taxonomic acts are later proposed, it merely reflects a
> redefinition of original taxa using new assertions or occasionally falsifiable
> methods.
>
> Ultimately, this commentary only represents our perspective on taxonomic
> practice. We are also happy to receive any constructive feedback.
>
> Best regards
> Guoyi
>
> Guoyi Zhang (she/her), MRes, PhD candidate Personal
> Web<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmalacology.net%2F&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Ca835a227a19c4bf0762708de061a4f34%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638954907255194231%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=AZVs2yphDxk%2B6Xd2Ua7qh%2FyTqi%2FzqidpFeJwWyJjWe0%3D&reserved=0> | OCRID<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F0000-0002-3426-&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Ca835a227a19c4bf0762708de061a4f34%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638954907255208796%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=QmAAO8PWOW49cTUKwb7zvM2SFueQuAN%2F4bCC4ju99Nw%3D&reserved=0
> 9273>
> School of Biological, Earth and Environmental Sciences University of New
> South Wales Australian Museum Research Institute Australian Museum
>
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