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

Wed Oct 8 16:51:03 CDT 2025

Lots of interesting comments. When I first delved into this over a decade
ago, I found that for primate molecular studies, matching bases involved
genes of unequal length, so a best fit program was developed to 'balance'
gaps and substitutions. Result was that base homologies across taxa were
not empirically observed, but created by an algorithm - and a best fit
algorithm seems like an overall measure of similarity.

Regarding the number of characters in sequence data being larger by up to
several orders in magnitude. I think this is called the 'law of large
numbers' If you have more, then you will be more accurate. Basically
argument by morphological pheneticists.

Fossils are the spanner in the works. Most can only be done through
morphology. If molecular trees have morphological correlates, then no
problem. Otherwise there is trouble. Even if a match, there is still the
problem of using morphological evidence that is a priori considered
unreliable in molecular focused studies. I am mostly intrigued by the
situation where there is a conflict involving morphology with hardly any
homoplasy (e.g. orangutan-huma clade supported by 28 apomorphies, vs 2 for
human-chimp.). That study included a review (taking several years) of many
other features supposed to support human-chimp were found not to be viable
(either incorrectly identified or present in outgroups).

But as Michael Heads notes, molecular phylogenies can give
biogeographically coherent results.  Any misgivings I have aside, I will
use molecular data in biogeographic studies, but I won't preclude using
morphological results. In both cases I take results at face value since I
have no expertise in the respective studies. But when there is substantial
conflict I remain intrigued by what that might really mean. I am in an
interesting circumstance to assess molecular findings in the hopefully near
future for a group that is currently lacking phylogenetic resolution for
various clades, or there are some clades or affinities that appear to be
strong in morphology. So I have some 'preconceived' notions and it will be
interesting to see how these compare to the molecular findings when they
are available.

Cheers, John

On Wed, Oct 8, 2025 at 4:05 PM Kirk Fitzhugh <kfitzhugh at nhm.org> wrote:

> 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%7Cef3ded383d3145566f7c08de06b4de37%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955571048609802%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=tzRkFSMa6SWrg6bue61IENhaKBYWs%2FOkshAO%2FspaIzw%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%7Cef3ded383d3145566f7c08de06b4de37%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955571048635472%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=Xc6pDh8DNGDUs%2ByASoEF7gEH4ui4hPFC1PWXD7I841s%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%7Cef3ded383d3145566f7c08de06b4de37%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955571048646574%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=97Anh34Goe09Asb9Ymvbbt%2FDBnsdO0iPPg%2B5rwKT5qs%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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