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

[Kirk Fitzhugh]

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%7Cce77adaa5e9641b1e68208de06a6091a%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955507343080846%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=hDz0UvwFjhMlNRwCtzG8JBTxAO9Lco4AfsAbmo5l%2Bco%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%7Cce77adaa5e9641b1e68208de06a6091a%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955507343103771%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Ygg72DW8V6vfRljOg9lLbmoS8QupL%2FVajx0Cwbd42k0%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%7Cce77adaa5e9641b1e68208de06a6091a%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955507343119534%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=9%2F%2FlBg3cyz09BaXKWygVklZAH2EH6lS3JwlD2lkt9YY%3D&reserved=0).

Kirk

On Wed, Oct 8, 2025 at 12:47 PM Marko Mutanen <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>
> *Sent:* keskiviikko 8. lokakuuta 2025 22.18
> *To:* 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
> *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> 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
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