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

Thu Oct 9 03:05:14 CDT 2025

'We know even without molecular data that the similar shapes evolved
through convergence' - or they are the result of ancestral polymorphism.
(The characters already existed in the ancestral population before the
origin of the modern clades).

On Thu, Oct 9, 2025 at 7:53 PM Lücking, Robert via Taxacom <
taxacom at lists.ku.edu> wrote:

> Dear Kirk,
>
> and on the idea that "Characters by themselves aren't biased."
>
> A matrix of phenotype characters that includes "shape" as a character,
> with different states, one being streamlined. The taxa in the matrix
> include sharks, dolphins, penguins, and mosasaurs, among others. All will
> code identically for shape. We know even without molecular data that the
> similar shapes evolved through convergence, so are homoplastic. Yet, in a
> matrix a priori they are coded as homologies. Only when we include the
> entire set of anatomical etc. characters the homoplasy is revealed. So yes:
> any character that needs to be coded by humans is, by default, potentially
> biased. Other example: flower colors. Two flowers may have exactly the same
> color, but for different reasons (e.g. different pigment chemistry).
> Biased, since it gives a false impression of identity.
>
> DNA uses an already existing code. You do not have to define nucleotides
> and their states a priori. The only issue with DNA is the reconstruction of
> character homology using alignments, such as ambiguously aligned regions or
> paralogs. Things can go wrong there, but there are objective means for
> testing and sorting these out.
>
> Regards
> Robert
>
>
>
> Von: Kirk Fitzhugh <kfitzhugh at nhm.org>
> Gesendet: Mittwoch, 8. Oktober 2025 22:05
> An: Marko Mutanen <Marko.Mutanen at oulu.fi>
> Cc: Lücking, Robert <R.Luecking at bo.berlin>; John Grehan <
> calabar.john at gmail.com>; Kuoi Zhang <zhang.guo-yi at outlook.com>;
> taxacom at lists.ku.edu
> Betreff: Re: Taxacom: On describing new taxa without using phylogenetics:
> some suggestions
>
> Marko,
>
> What I said applies both philosophically and practically. To say,
> "morphology, or certain other types of data, are so noisy [sic] that they
> mislead more than they inform," implies that one can readily discern when
> homologous characters are indeed not homologous, in which case you'd need
> to rename those as different characters (see Fitzhugh 2022:
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1007%2Fs10441-021-09412-4&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C50cbda6c045745bb39e808de070a9b9b%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955939311024031%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=9c28ITRHFqzkteGGKDIm8LUwygXdGt87w15b7anAIn4%3D&reserved=0) before proceeding with
> inferring explanatory hypotheses. In the absence of such knowledge,
> eliminating explanations of homologous characters without any empirical
> evidence that they are not homologous makes no sense.
>
> The view that "morphological and DNA data often produce highly
> contradictory phylogenies" is a popular point of view but one that is
> epistemically specious (see Fitzhugh 2014:
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.24199%2Fj.mmv.2014.71.07&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C50cbda6c045745bb39e808de070a9b9b%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955939311047860%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=hyZT0Pq9BxR8VmFpDEAg9rewBDT92sfb4PqJ09P4cBM%3D&reserved=0). Comparing tree topologies has
> no meaning since the trees imply sets of hypotheses inferred from entirely
> different sets of premises. Once again, a violation of the requirement of
> total evidence. Saying "DNA provides far more information and tends to be
> less biased" carries no weight. Amount of information is irrelevant to what
> we are attempting to achieve, which is causal understanding. Characters by
> themselves aren't biased.
>
> "It should also be remembered that all taxonomically relevant
> morphological information is ultimately encoded in DNA, so combining both
> raises additional philosophical challenges." That is true, which raises the
> spectre of downward causation. Something that has yet to be given serious
> consideration by those claiming sequence data have some priority over
> morphology (see Fitzhugh 2016: https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1007%2Fs10441-016-9277-0&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C50cbda6c045745bb39e808de070a9b9b%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955939311064280%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=H3DWq4FdWOYkvKFdEdWsk6fUR4gp4t%2Fw1pIvl2oZEA0%3D&reserved=0).
>
> Kirk
>
> On Wed, Oct 8, 2025 at 12:47 PM Marko Mutanen <Marko.Mutanen at oulu.fi
> <mailto:Marko.Mutanen at oulu.fi>> wrote:
> Dear Kirk, Thanks for your comment. I agree that this is true at a
> philosophical level, but it does not necessarily hold true at a practical
> level. It is quite possible that morphology, or certain other types of
> data, are so noisy that they
> Dear Kirk,
>
> Thanks for your comment.
>
> I agree that this is true at a philosophical level, but it does not
> necessarily hold true at a practical level. It is quite possible that
> morphology, or certain other types of data, are so noisy that they mislead
> more than they inform. In my experience, morphological and DNA data often
> produce highly contradictory phylogenies. A consensus between the two is
> not necessarily more reliable than one based solely on large amounts of DNA
> data.
>
> I recognize the philosophical weaknesses of this reasoning, but as Robert
> noted, DNA provides far more information and tends to be less biased. It
> should also be remembered that all taxonomically relevant morphological
> information is ultimately encoded in DNA, so combining both raises
> additional philosophical challenges. Homoplasy in morphology often results
> from natural selection, but this convergence rarely translates into DNA.
> Although DNA also contains homoplasy, it tends to be random, whereas
> morphological homoplasy is often systematic and directional.
>
> Sincerely,
>
> Marko M.
>
> From: Kirk Fitzhugh <kfitzhugh at nhm.org<mailto:kfitzhugh at nhm.org>>
> Sent: keskiviikko 8. lokakuuta 2025 22.18
> To: Marko Mutanen <Marko.Mutanen at oulu.fi<mailto:Marko.Mutanen at oulu.fi>>
> Cc: Lücking, Robert <R.Luecking at bo.berlin>; John Grehan <
> calabar.john at gmail.com<mailto:calabar.john at gmail.com>>; 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>
> Subject: Re: Taxacom: On describing new taxa without using phylogenetics:
> some suggestions
>
> Marko Mutanen,
>
> Given that our intent with phylogenetic inferences is to causally account
> for observed homologous characters, and this occurs via the non-deductive
> form of reasoning known as abduction, there are no logical arguments
> supporting the view that sequence data has some priority over other classes
> of characters. Homoplasy is an ad hoc hypothesis that is the product of
> inferring hypotheses, so it can't be used as an excuse to exclude
> morphological characters (indeed, one can just as easily argue that
> sequence data are just as prone to lead to hypotheses of homoplasy). The
> only rational approach to abductively inferring phylogenetic hypotheses is
> to abide by the requirement of total evidence (sensu Carnap 1950) and
> consider all relevant observed characters.
>
> Kirk Fitzhugh
>
> On Wed, Oct 8, 2025 at 12:02 PM Marko Mutanen via Taxacom <
> taxacom at lists.ku.edu<mailto:taxacom at lists.ku.edu>> wrote:
> 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
>
> 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.
>
>
> --
>
> --
>
> “Wrong does not cease to be wrong because the majority share in it.”
>
> ― Leo Tolstoy
>
> -------------------------------------------------
>
> J. Kirk Fitzhugh, Ph.D.
>
> Curator of Polychaetes
>
> Research & Collections Branch
>
> Natural History Museum of Los Angeles County
>
> 900 Exposition Blvd
>
> Los Angeles CA 90007
>
> Phone: 213-763-3233
>
> e-mail: kfitzhugh at nhm.org<mailto:kfitzhugh at nhm.org>
>
> -------------------------------------------------
>
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*Biogeography and evolution in New Zealand. *Taylor and Francis/CRC, Boca
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*Biogeography of Australasia:  A molecular analysis*. Cambridge University
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*Molecular panbiogeography of the tropics. *University of California Press,
Berkeley. 2012. https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ucpress.edu%2Fbook.php%3Fisbn%3D9780520271968&data=05%7C02%7Ctaxacom%40lists.ku.edu%7C50cbda6c045745bb39e808de070a9b9b%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955939311111175%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Nl2X55Iu9NXwOk89I%2Fk8Iem3Agaa8pyYSt0lfwAnP6s%3D&reserved=0

*Panbiogeography: Tracking the history of life*. Oxford University Press,
New York. 1999. (With R. Craw and J. Grehan).
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