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

Thu Oct 9 10:56:48 CDT 2025

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>
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
> Personal Web<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmalacology.net%2F&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C753e7a4710884233d37608de074c7e9f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956222278905995%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=tVjh75dhzzG3O2qX%2FjnSkj3W%2F0ATUS%2Fp%2B34X5xeuR3U%3D&reserved=0> | ORCID<
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F0000-0002-3426-9273&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C753e7a4710884233d37608de074c7e9f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956222278925652%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=k52JXnIhFjKEZbtDWVoVRQ0fABlgB8HjMGGXs%2FX2kXs%3D&reserved=0>
> School of Biological, Earth and Environmental Sciences
> University of New South Wales
> Australian Museum Research Institute
> Australian Museum
>
> ________________________________
> From: Richard Zander <Richard.Zander at mobot.org>
> Sent: Friday, October 10, 2025 1:19:50 am
> To: Taxacom (taxacom at lists.ku.edu) <taxacom at lists.ku.edu>; Kuoi Zhang <
> 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.
> ________________________________
> From: Taxacom <taxacom-bounces at lists.ku.edu> on behalf of Kuoi Zhang via
> Taxacom <taxacom at lists.ku.edu>
> Sent: Monday, October 6, 2025 8:52 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%7C753e7a4710884233d37608de074c7e9f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956222278940129%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=u7awCV1ji45xY7CElNppx25qGLcllqpPrdfnp%2BKSwaE%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%7C753e7a4710884233d37608de074c7e9f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956222278954847%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=zCa%2F%2BpdlcIV4nQu0YASngdjJsPNojpD3yPdgVi6HG3U%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%7C753e7a4710884233d37608de074c7e9f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956222278970587%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=cB6776jRyy6mqlikHU%2BVnE6jcEnwgFOG1NDKHyiwK70%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%7C753e7a4710884233d37608de074c7e9f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956222278985044%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=MsnA6d%2Fij42%2FZg2IVTD7jGTW%2FXmPWh6xlg2oqyHzvA4%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%7C753e7a4710884233d37608de074c7e9f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956222278999586%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=gOngNON4DXBT7Z0KngyZYIS6FJchS5nnspRGVgCzw5A%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%7C753e7a4710884233d37608de074c7e9f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956222279014402%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=WGMPXr7ObDKHBjr4n4vq2XtDhEN1Fh%2B%2F%2FPm36Ccgvgw%3D&reserved=0<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmalacology.net%2F&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C753e7a4710884233d37608de074c7e9f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956222279028843%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=CS88CYQZrg4QLmgXe6shF%2FzTDj1hQAvHgftGUm4xNGk%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%7C753e7a4710884233d37608de074c7e9f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956222279046880%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=uEd38F0%2F1AHmIjlQURfhWO6WTL1fkbfu12n4WxJ0DjE%3D&reserved=0<
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F0000-0002-3426-9273&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C753e7a4710884233d37608de074c7e9f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956222279061206%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=KvOeAevtsZeWfWPk7mVJiZKJ2Ovp6xeT6mEShjJsbGg%3D&reserved=0>>
> School of Biological, Earth and Environmental Sciences
> University of New South Wales
> Australian Museum Research Institute
> Australian Museum
>
> _______________________________________________
> Taxacom Mailing List
>
> Nurturing nuance while assailing ambiguity for 38 years, 1987-2025.
>
> Send Taxacom mailing list submissions to: taxacom at lists.ku.edu
> For list information; to subscribe or unsubscribe, visit:
> https://lists.ku.edu/listinfo/taxacom<
> https://lists.ku.edu/listinfo/taxacom>
> You can reach the person managing the list at: taxacom-owner at lists.ku.edu
>
>
> _____________________________ SECURITY WARNING: This email originated from
> outside of Missouri Botanical Garden. Please be careful when you click
> links/attachments or enter login credentials. If in doubt, please contact
> IT Support by opening a ticket at itsupport at mobot.org or call
> 314-577-0895.
>
> _______________________________________________
> Taxacom Mailing List
>
> Nurturing nuance while assailing ambiguity for 38 years, 1987-2025.
>
> Send Taxacom mailing list submissions to: taxacom at lists.ku.edu
> For list information; to subscribe or unsubscribe, visit:
> https://lists.ku.edu/listinfo/taxacom
> You can reach the person managing the list at: taxacom-owner at lists.ku.edu
>
>
>

-- 
Scott Thomson

Centro de Estudos dos Quelônios da Amazônia - CEQUA
Petrópolis, Manaus
State of Amazonas, 69055-010
Brasil

https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.carettochelys.com%2F&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C753e7a4710884233d37608de074c7e9f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956222279075583%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=%2FMtfx%2BpmeUJjPL2sziIEIFtdQNFZeAGyeLrK80Khzqo%3D&reserved=0
ORCID: https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Forcid.org%2F0000-0003-1279-2722&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C753e7a4710884233d37608de074c7e9f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956222279089890%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=qZ19WlI1mwz%2FYRUpo5h9d4BX1jIT%2B0gsQHWZBqK7bGY%3D&reserved=0
Lattes: *https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flattes.cnpq.br%2F0323517916624728*&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C753e7a4710884233d37608de074c7e9f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956222279104883%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ooi%2FGIHqnNqxVtm2CJiWF2hy9esIrM%2FY4KKYGsqjAr0%3D&reserved=0
<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwwws.cnpq.br%2Fcvlattesweb%2FPKG_MENU.menu%3Ff_cod%3D1E409F4BF37BFC4AD13FD58CDB7AA5FD%23&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C753e7a4710884233d37608de074c7e9f%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956222279119861%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=rE7aEbZXEZDjUSstk5bbxjltHZUoH6z%2Ff2aVeagyl1g%3D&reserved=0>
Skype: Faendalimas
Mobile Phone Brasil: +55 11 98178 7270
Whatsapp: +55 11 98178 7270