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

Wed Oct 8 14:02:25 CDT 2025

Dear Robert, all,

I agree with you. Morphological evolution is indeed fascinating, but it should be studied in the context of DNA-based phylogenies rather than by continuing to infer evolutionary relationships solely from morphology, which is highly prone to homoplasy. Of course, when dealing with fossils, we must still rely on morphological data, but this inevitably introduces substantial uncertainty into the taxonomy of extinct taxa - likely persisting indefinitely.

Sincerely,

Marko M. 

-----Original Message-----
From: Taxacom <taxacom-bounces at lists.ku.edu> On Behalf Of Lücking, Robert via Taxacom
Sent: keskiviikko 8. lokakuuta 2025 18.51
To: John Grehan <calabar.john at gmail.com>; Kuoi Zhang <zhang.guo-yi at outlook.com>
Cc: taxacom at lists.ku.edu
Subject: Re: Taxacom: On describing new taxa without using phylogenetics: some suggestions

Dear John,

homoplasy in phenotype is much more frequent than homoplasy in DNA sequence data. Also, the number of characters in sequence data is larger by up to several orders in magnitude. So yes, I would say that there are substantial differences between these types of data and molecular data cannot be considered equal to phenotype data. That said, DNA sequence data are not the answer to everything and often provide conflicting results between different markers or for example multimarker vs. phylogenomic data. One always has to remain critical but unless DNA sequence data can be proved erroneous, I would go with the hypothesis that in case of conflict between molecular and morphological data, the molecular data are objectively more likely to show the correct relationships. E.g. crocodiles with birds and humans with chimps. If you get such constellations repeatedly with different kinds of molecular data using different analytical tools, it becomes really difficult to doubt or reject them.

Regards
Robert

Von: John Grehan <calabar.john at gmail.com>
Gesendet: Mittwoch, 8. Oktober 2025 17:38
An: Kuoi Zhang <zhang.guo-yi at outlook.com>
Cc: Lücking, Robert <R.Luecking at bo.berlin>; taxacom at lists.ku.edu
Betreff: Re: Taxacom: On describing new taxa without using phylogenetics: some suggestions

" 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<mailto: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%7Ce9283f7028f5473826e408de069d3cc8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955469563077519%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=K0V37rVYfhGuPwyn5%2F3ZaRzRLkCoTcheD%2Bb%2BzQFnaNk%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%7Ce9283f7028f5473826e408de069d3cc8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955469563096202%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=fdlBQv%2B7sIHVhR4ExHOXYlidPI1Fix7n4EGvHLeZysk%3D&reserved=0>
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<mailto: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<mailto:zhang.guo-yi at outlook.com>>; taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu> <taxacom at lists.ku.edu<mailto: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<mailto: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<mailto: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<mailto:taxacom at lists.ku.edu>) <taxacom at lists.ku.edu<mailto: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%7Ce9283f7028f5473826e408de069d3cc8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955469563114149%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=htbbf0RoKopGPV9dyF5vcX5YMlWd9kswq04VTfZDue8%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%7Ce9283f7028f5473826e408de069d3cc8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955469563126307%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=wfETdgsmB%2B5OWivjxvjb8wEKCvZKZQ1vyyruYOCCVK4%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%7Ce9283f7028f5473826e408de069d3cc8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955469563142539%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=eT%2Fc4sMcYaVuWRzAE8ixztora01wT3uM5gJqeNZYu0Y%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<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmalacology.net%2F&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Ce9283f7028f5473826e408de069d3cc8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955469563153132%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=zcELcc2x20BO%2BUzkypMJDe6Q%2FGfEz3gRsUFxXN8gaTk%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%7Ce9283f7028f5473826e408de069d3cc8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955469563163548%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=sYpFODuwTq3MRGo8rEkuACTV8jEzGF9%2FqG48ArggESI%3D&reserved=0>
School of Biological, Earth and Environmental Sciences University of New South Wales Australian Museum Research Institute Australian Museum

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