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

Wed Oct 8 10:38:24 CDT 2025

" rue, that's the point. But many of the new taxa are not proposed by
monophyly and characters."

Interested in an example, but even so, such entities may be falsifiable in
the sense that subsequent analysis could show them to not be monophyletic,
or that some such characters are insufficient to meet those standards.

"I think molecule-based or morphology-based is not fundamentally different;
they are all characters."

In that sense one might say that cladistics and phenetics (overall
similarity) are not all that different either. Might as well say that
cladistically crocodile/alligator sister group with birds is not all that
different from phenetically being sister group of lizards or some other
extant reptile group.

"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."

Interested to know the context of the distinction being 'dubious' Agree
that in general sense DNA molecules and developmental genetics (morphology)
are both 'morphology, but they can generate very different conflicting
results - e.g. the human-chimp clade (supported by molecules) vs the
human-orangutan clade (supported by morphology). At present there is no
objective way to chose between them.

Cheers, John

On Tue, Oct 7, 2025 at 10:24 PM Kuoi Zhang <zhang.guo-yi at outlook.com> wrote:

> "disagree with the statement....all new taxa that are proposed are
> hypotheses that can be refuted and falsified" If a taxon is proposed based
> on evidence of monophyly then it would seem that the monophyly claim is
> potentially open to refutation and falsification.
>
>
> True, that's the point. But many of the new taxa are not proposed by
> monophyly and characters.
>
> "cladistics” is now often understood as referring specifically to
> parsimony-based approaches" I believe this is a misunderstanding.
> Cladistics, in its original form, was about grouping taxa according to
> uniquely shared features. Parisony was just one of many potential
> algorithms for making a judgement about how to balance out conflicting
> relationships indicated by different uniquely shared features. I know of
> some cladists who are not enamoured with standard parsimony methods (e.g.
> PAUP). I am not sure that molecular methods are 'cladistic' in the original
> sense, especially if uniquely shared molecular characters are only defined
> after the tree is selected.
>
>
> I remember there was a discussion on a blog, but anyway, it's a language
> philosophy. I followed the common usage, especially after the "parsimony
> gate", which is a choice by the "previous" Cladistics journal, Willi Hennig
> Society, and Ernst Mayr's comments to people who supported the opinion of
> Willi Hennig. I think molecule-based or morphology-based is not
> fundamentally different; they are all characters.
>
> "as fossil taxa can indeed be placed within a phylogenetic framework using
> morphological characters." Problem occurs when clades are supported by
> molecular features that are not known for fossils. For example, molecular
> folk argue for a human-chimp sister group, in which case there is no
> evidence for fossils such as Australopiths being placed within a
>  human-chimp clade. Ironically there is evidence to place them in a
> human-orangutan clade. In another irony, there was a prominent
> paleoanthropologist, Pilbeam, who dismissed morphology in favor of
> molecules because he made a mistake with one of his fossil assignments, but
> then later went on to present himself as an authority on what fossils were
> hominids (i.e. within the human lineage). He had his cake and ate it too.
>
>
> Thanks for sharing these dramas. Paleoanthropology always has quite a lot
> of dramas. You may miss the point. The point is that someone thinks fossils
> can't be placed in phylogenetics because most of them have no molecules
> available. It's not about conflicts between morphology and molecule.
>
> As for having a phylogeny, whether morphological or molecular, not always
> possible.  For example, in my group of study (Hepialidae), there are two
> genera in S Africa, Eudalaca and Gorgopis, for which neither have any
> identifiable autapomorphy. Probably they are a mix, and maybe in the future
> prove to be a single taxon, or two or more taxa under a different
> arrangement. It is possible to find new species and see that they fall
> within one or other genus as currently circumscribed by currently named
> species, and in one of them, to compare with the type species as a
> reference point. Under this circumstance I will make the best argument
> possible for assigning a new species to one or other genus and leave it to
> future research to conform or falsify my current choice. To me this is
> better than not describing and naming these entities at all just because
> there is no resolved phylogeny.
>
>
>  I may disagree with you on describing species. We wrote the last
> paragraph on describing new taxa and open nomenclature, including the
> morphological code widely used in Australia.
>
> 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%7Cd3288433769f46e4d64508de0680ce70%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955347453882286%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=0ZLH9PmFsWT%2FKwkxomMuJvUF0XLhl3zUa5O4Wfmhmr8%3D&reserved=0> | OCRID
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> School of Biological, Earth and Environmental Sciences
> University of New South Wales
> Australian Museum Research Institute
> Australian Museum
>
> ------------------------------
> *From:* John Grehan <calabar.john at gmail.com>
> *Sent:* Wednesday, 8 October 2025 12:49
> *To:* Lücking, Robert <R.Luecking at bo.berlin>
> *Cc:* Kuoi Zhang <zhang.guo-yi at outlook.com>; taxacom at lists.ku.edu <
> taxacom at lists.ku.edu>
> *Subject:* Re: Taxacom: On describing new taxa without using
> phylogenetics: some suggestions
>
> Hi Guyoi,
>
> Just a couple of off the cuff remarks as I have not read the paper in the
> link and am not deep into the metaphysics of taxonomy or systematics (I
> leave that to those who are).
>
> "disagree with the statement....all new taxa that are proposed are
> hypotheses that can be refuted and falsified" If a taxon is proposed based
> on evidence of monophyly then it would seem that the monophyly claim is
> potentially open to refutation and falsification.
>
> "cladistics” is now often understood as referring specifically to
> parsimony-based approaches" I believe this is a misunderstanding.
> Cladistics, in its original form, was about grouping taxa according to
> uniquely shared features. Parisony was just one of many potential
> algorithms for making a judgement about how to balance out conflicting
> relationships indicated by different uniquely shared features. I know of
> some cladists who are not enamoured with standard parsimony methods (e.g.
> PAUP). I am not sure that molecular methods are 'cladistic' in the original
> sense, especially if uniquely shared molecular characters are only defined
> after the tree is selected.
>
> "as fossil taxa can indeed be placed within a phylogenetic framework using
> morphological characters." Problem occurs when clades are supported by
> molecular features that are not known for fossils. For example,
> molecular folk argue for a human-chimp sister group, in which case there is
> no evidence for fossils such as Australopiths being placed within a
> human-chimp clade. Ironically there is evidence to place them in a
> human-orangutan clade. In another irony, there was a prominent
> paleoanthropologist, Pilbeam, who dismissed morphology in favor of
> molecules because he made a mistake with one of his fossil assignments, but
> then later went on to present himself as an authority on what fossils were
> hominids (i.e. within the human lineage). He had his cake and ate it too.
>
> As for having a phylogeny, whether morphological or molecular, not always
> possible.  For example, in my group of study (Hepialidae), there are two
> genera in S Africa, Eudalaca and Gorgopis, for which neither have any
> identifiable autapomorphy. Probably they are a mix, and maybe in the future
> prove to be a single taxon, or two or more taxa under a different
> arrangement. It is possible to find new species and see that they fall
> within one or other genus as currently circumscribed by currently named
> species, and in one of them, to compare with the type species as a
> reference point. Under this circumstance I will make the best argument
> possible for assigning a new species to one or other genus and leave it to
> future research to conform or falsify my current choice. To me this is
> better than not describing and naming these entities at all just because
> there is no resolved phylogeny.
>
> Just my two cents worth, and mostly out of ignorance no doubt.
>
> Cheers, John
>
> On Tue, Oct 7, 2025 at 1:53 AM Lücking, Robert via Taxacom <
> taxacom at lists.ku.edu> wrote:
>
> Dear Guoyi,
>
> your point is well founded. The confusion may be in the term
> "phylogenetics". This term relates to the establishment of genealogies,
> regardless of the methods used. What you refer to is the use of
> quantitative methods, even when only morphological data are available. I
> believe the term is then "cladistics", which came long after the use of
> "phylogenetics". There are also other quantitative methods, including an
> array of multivariate analyses and phenotype-based phylogenetic binning
> (which was precisely designed for fossils but can be used for any kind of
> phenotype data).
>
> Regards
> Robert
>
>
> -----Ursprüngliche Nachricht-----
> Von: Taxacom <taxacom-bounces at lists.ku.edu> Im Auftrag von Kuoi Zhang via
> Taxacom
> Gesendet: Dienstag, 7. Oktober 2025 03:52
> An: Taxacom (taxacom at lists.ku.edu) <taxacom at lists.ku.edu>
> Betreff: 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%7Cd3288433769f46e4d64508de0680ce70%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955347453931629%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=skxaLvgU5RvWK3cIaFyHMSukiKL99u8HcAt%2BiIcESeU%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_describe_new_taxa_without_using_phylogenetics_Comment_on_Chen_et_al_2025&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cd3288433769f46e4d64508de0680ce70%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955347453947692%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=lMhNkP2kqrRiLrEetKCURE7AwsDvdwIi4eP7eZgzHsM%3D&reserved=0
> <
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.researchgate.net%2Fpublication%2F396239492_Why_we_should_not_describe_new_taxa_without_using_phylogenetics_Comment_on_Chen_et_al_2025%3F_sg%255B0%255D%3DhqDEV92UeyWCOKjJ17ed1jbtmejHJ9MvHWGQaWxxhz91RNCiYocNZhGRj2BRWUdscZ9UF6XUnkfkZoKRIVT8RXi0FUkNPb4Rchgejiww.9eeTE4s8-qcLQo1Mb6y-bvvUmMI_J0sUIayNKpVofl3fGnDJw9mz4G9HP665eLzB2opS-IMV26GiwEDPg5TCgA%26_tp%3DeyJjb250ZXh0Ijp7ImZpcnN0UGFnZSI6InByb2ZpbGUiLCJwYWdlIjoicHJvZmlsZSIsInBvc2l0aW9uIjoicGFnZUNvbnRlbnQifX0&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cd3288433769f46e4d64508de0680ce70%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955347453962982%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=nzU46C4XhojUPleQrC7p8vqdF1sNsTvlW4Hqfsr9gYA%3D&reserved=0
> >
>
> 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<
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> South Wales Australian Museum Research Institute Australian Museum
>
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