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

Kuoi Zhang zhang.guo-yi at outlook.com
Thu Oct 9 11:38:09 CDT 2025 

Hello Scott

Thanks for your correction, I was thinking about period but wrote point.

For the genera, history obviously influenced, then the conclusion is not trying best to keep rationale. Unfortunately, that's the stupidity of taxonomy.

Best regards
Guoyi

Guoyi Zhang
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Australian Museum Research Institute
Australian Museum
________________________________
From: Scott Thomson <scott.thomson321 at gmail.com>
Sent: Friday, October 10, 2025 3:06:03 AM
To: Kuoi Zhang <zhang.guo-yi at outlook.com>
Cc: Richard Zander <Richard.Zander at mobot.org>; Taxacom (taxacom at lists.ku.edu) <taxacom at lists.ku.edu>
Subject: Re: Taxacom: On describing new taxa without using phylogenetics: some suggestions

Sorry also have to comment on this one:

>Third, any classification or phylogenetic analysis is inherently tied to a specific temporal slice; trees are constructed based on observed taxa at a given point in time.

Well if you do a combined analysis of living and fossil taxa thats not quite true, though you would often portray the fossils in a way that shows this, depending on how you draw the tree. IN my paper on Elseya lavackorum I had taxa ranging from recent to 106 million years old.

Cheers Scott

On Thu, Oct 9, 2025 at 12:56 PM Scott Thomson <scott.thomson321 at gmail.com<mailto:scott.thomson321 at gmail.com>> wrote:
Just a brief comment on one point you make here.

>Fourth, the patterns you describe regarding microgenera depend on existing nomenclature. Without these historical naming conventions, it is unclear why so many taxa would not later be synonymized, so these patterns cannot be considered purely emergent from evolutionary processes.

Unfortunately in some groups the history of discovery (whether it should or should not) does have an impact on the eventual splitting or lumping of groups. There are massive genera that have had multiple proposals published to split them up. Not groups I have worked on but on the face of it they seemed reasonable arguments (Anolis for example) yet the major reason that has not been accepted is historical. Basically people like the way things are.

Further to this the history, or order of discovery, can have a big impact on the lumping of genera, again arguments are raised, sometimes successfully to override proposals to lump and again it is based on preference or convenience, particularly if legislation is involved.

What basically happens is that depending on the group the level of evidence to make a change differs, often depending on non taxonomic arguments.

Cheers Scott

On Thu, Oct 9, 2025 at 12:42 PM Kuoi Zhang via Taxacom <taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu>> wrote:
Hello Richard

Thank you for sharing your points. I usually had not noticed some publications published by certain publishers. We would like to offer some clarifications and considerations from our perspective:

First, in modern phylogenetic practice, ancestral taxa can indeed be represented as tips when extant or sampled; therefore, the restriction of placing ancestors only at internal nodes is not necessary.

Second, the approach of dividing taxa into paraphyletic units at the earliest possible point—essentially naming new genera or microgenera while the ancestor is still extant—risks artificially inflating taxonomic units and may not reflect distinctions that are practically or evolutionarily meaningful. Phylogenetics noticed that instead of ignoring that as what you said. Based on your ideas, it's also true "Given that about half of all extant species are immediate progenitors of one or more other species", you can't predict what will happen in the future, why do you want describe new species before its ancestor absent?

Third, any classification or phylogenetic analysis is inherently tied to a specific temporal slice; trees are constructed based on observed taxa at a given point in time.

Fourth, the patterns you describe regarding microgenera depend on existing nomenclature. Without these historical naming conventions, it is unclear why so many taxa would not later be synonymized, so these patterns cannot be considered purely emergent from evolutionary processes.

Finally, we wish to emphasize that, for sufficiently large phylogenetic trees, the number of possible monophyletic groupings is already extremely large, but the number of corresponding paraphyletic groupings is even greater due to combinatorial possibilities.

We hope these points clarify our perspective. I understand that some advanced theories are always met with difficulties. Many can accept phylogenetic networks, but perhaps not the “rule of four”? I actually also heard little about high-resolution phylogenetics. It might refer to the genomic study. In any case, as our paper states, “Regardless of the framework, taxonomic conclusions must be testable and falsifiable.”

Best regards,

Guoyi

Guoyi Zhang
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________________________________
From: Richard Zander <Richard.Zander at mobot.org<mailto:Richard.Zander at mobot.org>>
Sent: Friday, October 10, 2025 1:19:50 am
To: Taxacom (taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu>) <taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu>>; Kuoi Zhang <zhang.guo-yi at outlook.com<mailto:zhang.guo-yi at outlook.com>>
Subject: Re: Taxacom: On describing new taxa without using phylogenetics: some suggestions

Oh, my, I just got into this thread. The present author states:
"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.:

I have pointed out in several papers that cladistics-oriented phylogenetics is based on determining shared ancestry. Given that about half of all extant species are immediate progenitors of one or more other species, and given that cladistic methods, molecular or morphological, ignore this fact, the present phylogenetic methods produce very low resolution dendrograms. This leads to massive lumping of perfectly acceptable classical taxa into bloated clades.

Luckily, evolution is so powerful that the overall patterns are somewhat preserved in cladistics. This is no excuse for hammering away at taxonomic names with the equivalent of 1970's cluster analysis.

What I call high-resolution phylogenetics uses descent with modification, and places inferred species at dendrogram nodes. Check my recent material on ResearchGate or Academia.edu for examples. The only caveat is that you need to learn how to do classical taxonomy using morphological traits, something perhaps overwhelming to many cladists.

There is yet hope for taxonomy.

Richard H. Zander - Missouri Botanical Garden - 4344 Shaw Blvd. - St. Louis, MO 63110 U.S.A.
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From: Taxacom <taxacom-bounces at lists.ku.edu<mailto:taxacom-bounces at lists.ku.edu>> on behalf of Kuoi Zhang via Taxacom <taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu>>
Sent: Monday, October 6, 2025 8:52 PM
To: Taxacom (taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu>) <taxacom at lists.ku.edu<mailto: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%7Ca2436be0ce914413f1a508de07523dee%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956246969044360%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=MEZon5B4H3USV8fVY%2B%2FQoRNZPWmX12UCRPX0KSftqmM%3D&reserved=0<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1080%2F00222933.2025.2564347&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Ca2436be0ce914413f1a508de07523dee%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956246969059124%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=a9Wyq9WjjhZXcnbEkblN5OcWcIQyCCRXvxPe0ZouGdo%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%7Ca2436be0ce914413f1a508de07523dee%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956246969073067%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=PFiitYoEZq6pgOcduzQcT3pu4gujR3lVLj3Y3btsb%2Fg%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%7Ca2436be0ce914413f1a508de07523dee%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956246969089273%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=oZKoEO8uc67muynSayzz6%2FCWMcUvmq%2FRmio9CY6tXZA%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&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Ca2436be0ce914413f1a508de07523dee%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956246969105360%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=YjjYLuQnAAHAg%2BDCTF3G%2BNXe%2FF4dRcmIhoM11en7Qp4%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
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