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

Thu Oct 9 11:23:27 CDT 2025

Regarding Robert's observation that " Going back to the humans vs.
orang-utan vs. chimp problem: what about when one uses behaviour as
classification criterion? If you compare behaviour vs. morphology/anatomy,
then you obtain a conflict, as each set of characters results in a
different classification. There is no objective way to sort this out, other
than using an unrelated set of characters, DNA sequence data. These tell us
that behaviour is a better predictor of relationships in this case than
morphology/anatomy."

I would view behaviour as an expression of morphology/anatomy in the sense
that all of this represents characteristics of developmental pathways. I
contrast that to base pair alignment or base pair counting. I sometimes
wonder whether divergence is best estimated by unique divergence in
developmental pathways or some overall measure of base pair similarity. I
don't know whether that is resolvable. For the most part molecular trees
give credible results (in terms of morphology) but quite a few cases of
glaring inconsistency and not involving antiquated notions of the
morphology. I look at the human sister group question as the ultimate
example of the challenge. While I have my own opinion favoring the
orangutan, it is really just my opinioni. Interestingly for me, when I
approached varous molecular systematists about the issue I was met with
silence or outright hostility. If the morphology could be objectively
refuted they could have shown that. But declined. And the hominid
systematics world continues to do so, even to the point of ensuring no
reference to the orangutan evidence (especially by the paleontologists
involved).

On behaviour, when some human characteristic shows up in chimps it gets a
huge amount of publicity. When it is an orangutan, nothing. Just a 'chance'
anomaly. It is a possibility that the chimp-human clade is true (and
converse of course), and all the uniquely shared human-orangutan features
are plesiomorphies that were lost in the African apes (including reversion
to more primitive states such as external estrus changes, monkey external
ear etc.), along with pretty much any morphological evidence of derived
human-chimp features. It sometimes seems as if God is laughing at us. Make
it look like we have an orangutan ancestor, when we don't. The literature
is filled with an amazing amount of contortions trying to make a human out
of a chimpanzee. All very entertaining if nothing else.

I was informed by one orangutan biologist that when chimpanzee biologists
visited an orangutan field site, they would sometimes whisper to her that
'orangutans are smarter than chimps'. Whispered, because of course it did
not fit the evolutionary scheme. And what does not fit is never said aloud.

Cheers, John

On Thu, Oct 9, 2025 at 10:43?AM Richard Zander <Richard.Zander at mobot.org>
wrote:

> In descent with modification analysis, inference ofdirect  descent can be
> from ancestor to descendant, in morphology by second-order Markov chain (1.
> generalist to ingroup, 2. similarity to outgroup) in a minimally
> monophyletic group, AND by the bracketing of a descendant species with
> ancestral molecular variants on a molecular cladogram (apophyly-paraphyly
> pairs). This integrates both molecular and morphological methods. See my
> paper on integrated analysis on ResearchGate and Academia.edu for an
> example.
>
>
> 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 Marko Mutanen
> via Taxacom <taxacom at lists.ku.edu>
> *Sent:* Wednesday, October 8, 2025 2:02 PM
> *To:* L?cking, Robert <R.Luecking at bo.berlin>; John Grehan <
> calabar.john at gmail.com>; Kuoi Zhang <zhang.guo-yi at outlook.com>
> *Cc:* taxacom at lists.ku.edu <taxacom at lists.ku.edu>
> *Subject:* Re: Taxacom: On describing new taxa without using
> phylogenetics: some suggestions
>
> Dear Robert, all,
>
> I agree with you. Morphological evolution is indeed fascinating, but it
> should be studied in the context of DNA-based phylogenies rather than by
> continuing to infer evolutionary relationships solely from morphology,
> which is highly prone to homoplasy. Of course, when dealing with fossils,
> we must still rely on morphological data, but this inevitably introduces
> substantial uncertainty into the taxonomy of extinct taxa - likely
> persisting indefinitely.
>
> Sincerely,
>
> Marko M.
>
> -----Original Message-----
> From: Taxacom <taxacom-bounces at lists.ku.edu> On Behalf Of L?cking, Robert
> via Taxacom
> Sent: keskiviikko 8. lokakuuta 2025 18.51
> To: John Grehan <calabar.john at gmail.com>; Kuoi Zhang <
> zhang.guo-yi at outlook.com>
> Cc: taxacom at lists.ku.edu
> Subject: Re: Taxacom: On describing new taxa without using phylogenetics:
> some suggestions
>
> Dear John,
>
> homoplasy in phenotype is much more frequent than homoplasy in DNA
> sequence data. Also, the number of characters in sequence data is larger by
> up to several orders in magnitude. So yes, I would say that there are
> substantial differences between these types of data and molecular data
> cannot be considered equal to phenotype data. That said, DNA sequence data
> are not the answer to everything and often provide conflicting results
> between different markers or for example multimarker vs. phylogenomic data.
> One always has to remain critical but unless DNA sequence data can be
> proved erroneous, I would go with the hypothesis that in case of conflict
> between molecular and morphological data, the molecular data are
> objectively more likely to show the correct relationships. E.g. crocodiles
> with birds and humans with chimps. If you get such constellations
> repeatedly with different kinds of molecular data using different
> analytical tools, it becomes really difficult to doubt or reject them.
>
> Regards
> Robert
>
>
>
> Von: John Grehan <calabar.john at gmail.com>
> Gesendet: Mittwoch, 8. Oktober 2025 17:38
> An: Kuoi Zhang <zhang.guo-yi at outlook.com>
> Cc: L?cking, Robert <R.Luecking at bo.berlin>; taxacom at lists.ku.edu
> Betreff: Re: Taxacom: On describing new taxa without using phylogenetics:
> some suggestions
>
> " rue, that's the point. But many of the new taxa are not proposed by
> monophyly and characters."
>
> Interested in an example, but even so, such entities may be falsifiable in
> the sense that subsequent analysis could show them to not be monophyletic,
> or that some such characters are insufficient to meet those standards.
>
> "I think molecule-based or morphology-based is not fundamentally
> different; they are all characters."
>
> In that sense one might say that cladistics and phenetics (overall
> similarity) are not all that different either. Might as well say that
> cladistically crocodile/alligator sister group with birds is not all that
> different from phenetically being sister group of lizards or some other
> extant reptile group.
>
> "P.S. Note, in my comments above I have avoided any reference to
> "molecular" vs. "morphological" characters as the basis for taxonomic
> analysis.  My comments above are all independent of this (somewhat dubious)
> distinction."
>
> Interested to know the context of the distinction being 'dubious' Agree
> that in general sense DNA molecules and developmental genetics (morphology)
> are both 'morphology, but they can generate very different conflicting
> results - e.g. the human-chimp clade (supported by molecules) vs the
> human-orangutan clade (supported by morphology). At present there is no
> objective way to chose between them.
>
> Cheers, John
>
> On Tue, Oct 7, 2025 at 10:24?PM Kuoi Zhang <zhang.guo-yi at outlook.com
> <mailto:zhang.guo-yi at outlook.com>> wrote:
> "disagree with the statement....all new taxa that are proposed are
> hypotheses that can be refuted and falsified" If a taxon is proposed based
> on evidence of monophyly then it would seem that the monophyly claim is
> potentially open to refutation and falsification.
>
> True, that's the point. But many of the new taxa are not proposed by
> monophyly and characters.
>
> "cladistics? is now often understood as referring specifically to
> parsimony-based approaches" I believe this is a misunderstanding.
> Cladistics, in its original form, was about grouping taxa according to
> uniquely shared features. Parisony was just one of many potential
> algorithms for making a judgement about how to balance out conflicting
> relationships indicated by different uniquely shared features. I know of
> some cladists who are not enamoured with standard parsimony methods (e.g.
> PAUP). I am not sure that molecular methods are 'cladistic' in the original
> sense, especially if uniquely shared molecular characters are only defined
> after the tree is selected.
>
> I remember there was a discussion on a blog, but anyway, it's a language
> philosophy. I followed the common usage, especially after the "parsimony
> gate", which is a choice by the "previous" Cladistics journal, Willi Hennig
> Society, and Ernst Mayr's comments to people who supported the opinion of
> Willi Hennig. I think molecule-based or morphology-based is not
> fundamentally different; they are all characters.
>
> "as fossil taxa can indeed be placed within a phylogenetic framework using
> morphological characters." Problem occurs when clades are supported by
> molecular features that are not known for fossils. For example, molecular
> folk argue for a human-chimp sister group, in which case there is no
> evidence for fossils such as Australopiths being placed within a
> human-chimp clade. Ironically there is evidence to place them in a
> human-orangutan clade. In another irony, there was a prominent
> paleoanthropologist, Pilbeam, who dismissed morphology in favor of
> molecules because he made a mistake with one of his fossil assignments, but
> then later went on to present himself as an authority on what fossils were
> hominids (i.e. within the human lineage). He had his cake and ate it too.
>
> Thanks for sharing these dramas. Paleoanthropology always has quite a lot
> of dramas. You may miss the point. The point is that someone thinks fossils
> can't be placed in phylogenetics because most of them have no molecules
> available. It's not about conflicts between morphology and molecule.
>
> As for having a phylogeny, whether morphological or molecular, not always
> possible.  For example, in my group of study (Hepialidae), there are two
> genera in S Africa, Eudalaca and Gorgopis, for which neither have any
> identifiable autapomorphy. Probably they are a mix, and maybe in the future
> prove to be a single taxon, or two or more taxa under a different
> arrangement. It is possible to find new species and see that they fall
> within one or other genus as currently circumscribed by currently named
> species, and in one of them, to compare with the type species as a
> reference point. Under this circumstance I will make the best argument
> possible for assigning a new species to one or other genus and leave it to
> future research to conform or falsify my current choice. To me this is
> better than not describing and naming these entities at all just because
> there is no resolved phylogeny.
>
>  I may disagree with you on describing species. We wrote the last
> paragraph on describing new taxa and open nomenclature, including the
> morphological code widely used in Australia.
>
> 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%7C02%7Ctaxacom%40lists.ku.edu%7Cdcfc68356c6b43ade9e108de07504321%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956239406962766%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C80000%7C%7C%7C&sdata=zOG%2FBm90RI3ErxAPiluL0DfJHZxFJkiuuhd2p%2BjelVY%3D&reserved=0
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> School of Biological, Earth and Environmental Sciences University of New
> South Wales Australian Museum Research Institute Australian Museum
>
> ________________________________
> From: John Grehan <calabar.john at gmail.com<mailto:calabar.john at gmail.com>>
> Sent: Wednesday, 8 October 2025 12:49
> To: L?cking, Robert <R.Luecking at bo.berlin>
> Cc: Kuoi Zhang <zhang.guo-yi at outlook.com<mailto:zhang.guo-yi at outlook.com>>;
> taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu> <taxacom at lists.ku.edu
> <mailto:taxacom at lists.ku.edu>>
> Subject: Re: Taxacom: On describing new taxa without using phylogenetics:
> some suggestions
>
> Hi Guyoi,
>
> Just a couple of off the cuff remarks as I have not read the paper in the
> link and am not deep into the metaphysics of taxonomy or systematics (I
> leave that to those who are).
>
> "disagree with the statement....all new taxa that are proposed are
> hypotheses that can be refuted and falsified" If a taxon is proposed based
> on evidence of monophyly then it would seem that the monophyly claim is
> potentially open to refutation and falsification.
>
> "cladistics? is now often understood as referring specifically to
> parsimony-based approaches" I believe this is a misunderstanding.
> Cladistics, in its original form, was about grouping taxa according to
> uniquely shared features. Parisony was just one of many potential
> algorithms for making a judgement about how to balance out conflicting
> relationships indicated by different uniquely shared features. I know of
> some cladists who are not enamoured with standard parsimony methods (e.g.
> PAUP). I am not sure that molecular methods are 'cladistic' in the original
> sense, especially if uniquely shared molecular characters are only defined
> after the tree is selected.
>
> "as fossil taxa can indeed be placed within a phylogenetic framework using
> morphological characters." Problem occurs when clades are supported by
> molecular features that are not known for fossils. For example, molecular
> folk argue for a human-chimp sister group, in which case there is no
> evidence for fossils such as Australopiths being placed within a
> human-chimp clade. Ironically there is evidence to place them in a
> human-orangutan clade. In another irony, there was a prominent
> paleoanthropologist, Pilbeam, who dismissed morphology in favor of
> molecules because he made a mistake with one of his fossil assignments, but
> then later went on to present himself as an authority on what fossils were
> hominids (i.e. within the human lineage). He had his cake and ate it too.
>
> As for having a phylogeny, whether morphological or molecular, not always
> possible.  For example, in my group of study (Hepialidae), there are two
> genera in S Africa, Eudalaca and Gorgopis, for which neither have any
> identifiable autapomorphy. Probably they are a mix, and maybe in the future
> prove to be a single taxon, or two or more taxa under a different
> arrangement. It is possible to find new species and see that they fall
> within one or other genus as currently circumscribed by currently named
> species, and in one of them, to compare with the type species as a
> reference point. Under this circumstance I will make the best argument
> possible for assigning a new species to one or other genus and leave it to
> future research to conform or falsify my current choice. To me this is
> better than not describing and naming these entities at all just because
> there is no resolved phylogeny.
>
> Just my two cents worth, and mostly out of ignorance no doubt.
>
> Cheers, John
>
> On Tue, Oct 7, 2025 at 1:53?AM L?cking, Robert via Taxacom <
> taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu>> wrote:
> Dear Guoyi,
>
> your point is well founded. The confusion may be in the term
> "phylogenetics". This term relates to the establishment of genealogies,
> regardless of the methods used. What you refer to is the use of
> quantitative methods, even when only morphological data are available. I
> believe the term is then "cladistics", which came long after the use of
> "phylogenetics". There are also other quantitative methods, including an
> array of multivariate analyses and phenotype-based phylogenetic binning
> (which was precisely designed for fossils but can be used for any kind of
> phenotype data).
>
> Regards
> Robert
>
>
> -----Urspr?ngliche Nachricht-----
> Von: Taxacom <taxacom-bounces at lists.ku.edu<mailto:
> taxacom-bounces at lists.ku.edu>> Im Auftrag von Kuoi Zhang via Taxacom
> Gesendet: Dienstag, 7. Oktober 2025 03:52
> An: Taxacom (taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu>) <
> taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu>>
> Betreff: 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%7C02%7Ctaxacom%40lists.ku.edu%7Cdcfc68356c6b43ade9e108de07504321%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956239407037567%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C80000%7C%7C%7C&sdata=OxXskoO1IVrC1%2B2%2BOCoTx6%2FjmDFpHpEIrdMV33KYD3k%3D&reserved=0
> <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1080%2F00222933.2025.2564347&data%7C02%7Ctaxacom%40lists.ku.edu%7Cdcfc68356c6b43ade9e108de07504321%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956239407051353%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C80000%7C%7C%7C&sdata=DJbapLRJQqzPV1ZV%2FML1KwJI0woJk8ZHCj%2BjkZLKrt8%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%7C02%7Ctaxacom%40lists.ku.edu%7Cdcfc68356c6b43ade9e108de07504321%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956239407065325%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C80000%7C%7C%7C&sdataÏ9S9oV7NdbjXWPs89Hg8iCkLGnHZ6tnODDpOZ2fx%2Fw%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%7C02%7Ctaxacom%40lists.ku.edu%7Cdcfc68356c6b43ade9e108de07504321%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956239407079899%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C80000%7C%7C%7C&sdata=PPp3qmhVCPb7wLFB9vRiLKHjiiYBBPY1WseIe9pXSHQ%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%7C02%7Ctaxacom%40lists.ku.edu%7Cdcfc68356c6b43ade9e108de07504321%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638956239407094674%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C80000%7C%7C%7C&sdata=sL%2FPGP4OPGT5vdOd1PimGrNlYv1KdmHGKCfyPqksRxU%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<
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