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

Thu Oct 9 11:06:03 CDT 2025

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>
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> 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%7Cb49633e46fd749f97bd008de074dc8a4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956227839839131%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ZQIAj0V%2B2xGTe7HjMvMLgETo82I%2FJ6CDEt6ZiykqorE%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%7Cb49633e46fd749f97bd008de074dc8a4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956227839919796%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ubr0MyF%2BuGh0CWSMfuAi2Q9IiMqrVw3eqikvkg0Km5w%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%7Cb49633e46fd749f97bd008de074dc8a4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956227839960538%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=pcB%2FJwU41P5p8nXpuqY1lz1M%2BlUi59qZBRw0VodX690%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%7Cb49633e46fd749f97bd008de074dc8a4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956227840723569%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Dunt%2B1UVCahRsw5n7E%2BcLDG8BgzpwKta68%2F337dRSu4%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%7Cb49633e46fd749f97bd008de074dc8a4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956227840772327%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=3TM5QaHLhfh4S8Fbzp7UnH1APxuSWBTvtuIxlzRFWOk%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%7Cb49633e46fd749f97bd008de074dc8a4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956227840792342%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=BqdT3ns5oYXTcOcaTkCzLSz%2F8khzbvbI1M928VJbhQM%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%7Cb49633e46fd749f97bd008de074dc8a4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956227840816880%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ytMmLz5FybT4r7Pt1laLtvlVdeiWMoVfn7bxAuOdUFg%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%7Cb49633e46fd749f97bd008de074dc8a4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956227840836883%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=qIweQnNzArcxK%2FKppUOx5DguQzZWrGhIfF6iKwo3OhQ%3D&reserved=0<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmalacology.net%2F&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cb49633e46fd749f97bd008de074dc8a4%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956227840856349%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=r2SscuperSuR43PObI4o4Ppmn3FD01b%2FgYkoEIaEiqY%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
>>
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> --
> Scott Thomson
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-- 
Scott Thomson

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

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