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

Fri Oct 10 07:14:47 CDT 2025

Dear all,

I think the solution is: species should be described using convincing evidence and a sound underlying concept, independent of the nature of the data. I prefer taxonomic expertise a hundred times over having to include molecular data. There are many scenarios where molecular data cannot be made available (old material, permits, Nagoya) or may not actually contribute to the matter. There are also scenarios where only DNA data are available (I am working on the topic of dark fungal taxa). For any of these, there is a suitable approach to draw meaningful, testable conclusions. Nowadays many labs start molecular analyses and they think they have a new species just because the sequences do not match anything in GenBank, forgetting about the actual homework: what species have been described in a genus and from where, how many of these have been sequenced, what are synonyms, are there potential names in other genera etc. Species are hypotheses that can, and should, be tested, then either supported or falsified. But it is better to have something formally described and turning out not to be a good species, than hesitating and subsumung potentially good species under existing names, "cf.", "sp.", "aff.", unless there is good reason to do so. Erroneous splitting can be easily corrected, erroneous lumping cannot.

Regards
Robert

-----Ursprüngliche Nachricht-----
Von: Taxacom <taxacom-bounces at lists.ku.edu> Im Auftrag von Kuoi Zhang via Taxacom
Gesendet: Freitag, 10. Oktober 2025 11:33
An: Alain Dubois <sapo421 at gmail.com>; Mikhail Daneliya <mdaneliya at gmail.com>
Cc: taxacom at lists.ku.edu
Betreff: Re: Taxacom: On describing new taxa without using phylogenetics: some suggestions

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%7Cd4adce3e882c4a83f8a708de07f69f66%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956953013601201%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=9KkQ4EHt5KbmuFUg42skpqQ8DzyLr8B1g7C0QtVNJDg%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%7Cd4adce3e882c4a83f8a708de07f69f66%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956953013625429%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=5l5sF%2BJQmzD5ycfZw0KeMiCz2Pehmm66SQL5hMCO%2FkE%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%7Cd4adce3e882c4a83f8a708de07f69f66%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956953013636604%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=XC2wRefD4EcqLSithsZPt7yYWEBF03CSxUXqWb%2FmsYI%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%7Cd4adce3e882c4a83f8a708de07f69f66%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956953013647590%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=dbbPqddsiJDwRqE3qp9F0OD8vRwiwMCQYbBa6ykkKWc%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
____________________________________

"La culture ce n'est pas avoir le cerveau farci de dates, de noms ou de chiffres, c'est la qualité du jugement, l'exigence logique, l'appétit de la preuve, la notion de la complexité des choses et de l'arduité des problèmes. C'est l'habitude du doute, le discernement dans la méfiance, la modestie d'opinion, la patience d'ignorer, la certitude qu'on n'a jamais tout le vrai en partage; c'est avoir l'esprit ferme sans l'avoir rigide, c'est être armé contre le flou et aussi contre la fausse précision, c'est refuser tous les fanatismes et jusqu'à ceux qui s'autorisent de la raison; c'est suspecter les dogmatismes officiels mais sans profit pour les charlatans, c'est révérer le génie mais sans en faire une idole, c'est toujours préférer ce qui est à ce qu'on préférerait qui fût." (Jean Rostand, *Le droit d'être naturaliste*, 1963).
___________________________________

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%7Cd4adce3e882c4a83f8a708de07f69f66%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956953013658781%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=JxPFrg4WdrLhgWSQ1X1u12LiF%2FRZpX4k0V5KH51lIL8%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_d&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cd4adce3e882c4a83f8a708de07f69f66%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956953013670224%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=l82Way58Z7kj%2F5Y2wQLUzXN9p%2FLAorsrJwmTPKmDzhQ%3D&reserved=0
> escribe_new_taxa_without_using_phylogenetics_Comment_on_Chen_et_al_202
> 5
> > <
> >
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.researchgate.net%2Fpublication%2F396239492_Why_we_should_not_d&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cd4adce3e882c4a83f8a708de07f69f66%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956953013681508%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=x7%2BpS3Hnp5MJPmqGEg51%2B73rYbc%2B3Lpss%2FC9%2B%2FTU56I%3D&reserved=0
> escribe_new_taxa_without_using_phylogenetics_Comment_on_Chen_et_al_202
> 5?_sg%5B0%5D=hqDEV92UeyWCOKjJ17ed1jbtmejHJ9MvHWGQaWxxhz91RNCiYocNZhGRj
> 2BRWUdscZ9UF6XUnkfkZoKRIVT8RXi0FUkNPb4Rchgejiww.9eeTE4s8-qcLQo1Mb6y-bv
> vUmMI_J0sUIayNKpVofl3fGnDJw9mz4G9HP665eLzB2opS-IMV26GiwEDPg5TCgA&_tp=e
> yJjb250ZXh0Ijp7ImZpcnN0UGFnZSI6InByb2ZpbGUiLCJwYWdlIjoicHJvZmlsZSIsInB
> vc2l0aW9uIjoicGFnZUNvbnRlbnQifX0
> > >
> >
> > 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%7Cd4adce3e882c4a83f8a708de07f69f66%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956953013694243%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=92mtO9ho0UqyM2Z%2BMluE3gEovx%2BIAITOxh76a9Wqhac%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%7Cd4adce3e882c4a83f8a708de07f69f66%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956953013709667%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=H4mhUzR1Jo3jYxXanli31B%2BlSo7OZVOmXEiKjw6KUCQ%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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