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

Fri Oct 10 04:33:16 CDT 2025

Hello

I would like to clarify some points regarding species description. The idea that one can describe a species “without knowing its phylogenetic position” implicitly assumes prior knowledge of its higher-level identity. You said "I am interested more in differences, which are crucial in establishing sp.n., rather than similarities" For example, calling a new bird a “sparrow” already presupposes what a sparrow is, a definition that is itself grounded in shared evolutionary history or "similarity", or else in pure arbitrariness. If so, why make this approach black box?

Species delimitation of course rely on species concept, that's what we said. However, any species concept that ignores relationships becomes circular or vacuous.

As for the argument about urgency and conservation, we fully agree that rapid documentation of biodiversity is important. However, this does not justify abandoning rigorous species delimitation. Our paper’s final paragraph already anticipated such claims and offered constructive solutions. Otherwise, one might as well follow the so-called ridiculous “dark taxonomy” approach, relying on DNA barcodes and even AI-generated description, which would indeed be much faster, as seen in papers claiming to describe over 200 “new species” based on barcoding. If extinction is the concern, does it actually prevent specimen collection? And if the specimens already exist in collections, why is there such a rush?

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%7Ced8137689cd349b6391c08de07e00df8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956856112944694%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=3FmNxrsAVd9ckuHLSFDnx%2BtBJjHZLZmVnfs364dDH%2FE%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%7Ced8137689cd349b6391c08de07e00df8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956856112963761%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=GHUKjsrIBu%2FThe7zuo9Ht37ckP%2BfThM5jEpLrUGzLXE%3D&reserved=0>
School of Biological, Earth and Environmental Sciences
University of New South Wales
Australian Museum Research Institute
Australian Museum

From: Taxacom <taxacom-bounces at lists.ku.edu> on behalf of Alain Dubois via Taxacom <taxacom at lists.ku.edu>
Sent: Friday, October 10, 2025 4:56:10 PM
To: Mikhail Daneliya <mdaneliya at gmail.com>
Cc: taxacom at lists.ku.edu <taxacom at lists.ku.edu>
Subject: Re: Taxacom: On describing new taxa without using phylogenetics: some suggestions

Thanks Mikhail!

Happy to see at least a post dealing with species, and an opinion on which
I agree.

Most of the previous posts, although claiming to write about "taxa", were
dealing only with supraspecific taxa.

But species also are taxa, and the most important to discover and
characterised, in my opinion, in our century of extinctions, because many
of them will turn irremediably extinct in the coming decades.

Phylogenetic relationships are only rarely useful to distinguish species.

Classifying species into higher taxa (genus and above) will be possible
when they are extinct, and is not as urgent as collecting, naming and
keeping specimens in permanent collections.

https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.researchgate.net%2Fpublication%2F391684504_Zootaxonomy_in_the_Century_of_Extinctions&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Ced8137689cd349b6391c08de07e00df8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956856112975880%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=hnZyzHV5nFlykeuwtt5ohSTdS8yxqDQdimHuTt%2F7%2BLM%3D&reserved=0

https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.researchgate.net%2Fpublication%2F370546256_Is_it_still_acceptable_to_describe_a_taxon_or_synonymise_a_nomen_without_molecular_data_The_Rana_Paa_barmoachensis_case_Dicroglossidae_Painae&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Ced8137689cd349b6391c08de07e00df8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956856112988201%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=5%2B5V7Ybo0D%2BgYWXbJ%2FEC9mdFr%2F4TuJcdapCJ2BMoZpo%3D&reserved=0

Best wishes,

Alain
____________________________________

Professeur retraité Alain Dubois
Muséum National d'Histoire Naturelle
Institut Systématique, Evolution, Biodiversité (ISYEB) - UMR 7205
75005 Paris
France

E-mail: <sapo421 at gmail.com>
Phone: (33).6.62.52.04.21
____________________________________

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___________________________________

Le ven. 10 oct. 2025 à 07:18, Mikhail Daneliya via Taxacom <
taxacom at lists.ku.edu> a écrit :

> Thank you!
>
> As a practicing taxonomist, for describing a new species I am interested
> more in differences, which are crucial in establishing sp.n., rather than
> similarities. I need to provide firstly evidence that it is a separate
> taxon, and only the next stage would be to find out its origin. I typically
> have no issues placing it in a genus. You do not need phylogeny to prove
> that a new species of sparrow is a sparrow. Although, of course, there are
> exceptions of difficult taxa with unclear position. A diagnosis is more
> important than affinities. In other words, I describe a new species even
> without clear understanding of its position, but I would not be able to do
> so, if I do not see that a species is significantly different from its
> congeners. To be more theoretical, establishment of new species is about a
> species concept rather than its relations.
>
> On the other hand, phylogenetic component definitely makes a study more
> comprehensive. And I published also works with stronger phylogenetic
> component. But should it dictated? Does not look so.
>
> Sincerely,
>
> Mikhail Daneliya
>
> On Tue, 7 Oct 2025, 04:52 Kuoi Zhang via Taxacom, <taxacom at lists.ku.edu>
> wrote:
>
> > 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%7Ced8137689cd349b6391c08de07e00df8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956856113003399%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=TjgZJK%2FRL%2FY%2BGAH%2FmNTv47R5EgThCJ5mKCKAu%2F468l8%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%7Ced8137689cd349b6391c08de07e00df8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956856113023767%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=th45FZL5Kw7xP2e7TcXPXWVg4rTBclujExlm285%2BwTY%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%7Ced8137689cd349b6391c08de07e00df8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956856113042020%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=xzioTCRKy%2Br5trWh3FPBvE%2BV7J6BDe%2Bc8JmF7CN857w%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%7Ced8137689cd349b6391c08de07e00df8%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956856113056421%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=RqEWpfq8M56RXxjsSvis0%2FYWINAn4PTkrvvOc2qEEFc%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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