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

Wed Oct 8 15:05:29 CDT 2025

I use molecular phylogenies because they are so much simpler
biogeographically. The problem with the morphological arrangements is not
so much the 'data' as the assumed homologies (which often date back to the
18th century).

On Thu, Oct 9, 2025 at 8:47 AM Marko Mutanen via Taxacom <
taxacom at lists.ku.edu> 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 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<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.
> _______________________________________________
> Taxacom Mailing List
>
> Nurturing nuance while assailing ambiguity for 38 years, 1987-2025.
>
> Send Taxacom mailing list submissions to: taxacom at lists.ku.edu
> For list information; to subscribe or unsubscribe, visit:
> https://lists.ku.edu/listinfo/taxacom
> You can reach the person managing the list at: taxacom-owner at lists.ku.edu
>
>
>

-- 
Dunedin, New Zealand.

My books:

*Biogeography and evolution in New Zealand. *Taylor and Francis/CRC, Boca
Raton FL. 2017.
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.routledge.com%2FBiogeography-and-Evolution-in-New-Zealand%2FHeads%2Fp%2Fbook%2F9781498751872&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cade761a3a02a40ceeb8e08de06a60edb%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955507437269368%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=O7zDB2ba4WYHb7%2FACgVOjNV4%2F9o4CnnETBm53tyPbts%3D&reserved=0

*Biogeography of Australasia:  A molecular analysis*. Cambridge University
Press, Cambridge. 2014. https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cambridge.org%2F9781107041028&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cade761a3a02a40ceeb8e08de06a60edb%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955507437296720%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=f%2BF%2FJnCD3SVPcyCXiAHW3wdLA8eDhVaUPPuHxaqUr7Q%3D&reserved=0

*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%7Cade761a3a02a40ceeb8e08de06a60edb%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955507437307406%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=45yxzuspdVvhl5RRUPK72xPcIi0cJVTl8%2FnPMMc26DQ%3D&reserved=0

*Panbiogeography: Tracking the history of life*. Oxford University Press,
New York. 1999. (With R. Craw and J. Grehan).
https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbooks.google.co.nz%2Fbooks%3Fid%3DBm0_QQ3Z6GUC&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cade761a3a02a40ceeb8e08de06a60edb%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955507437318064%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=WIyAtxTjWpKbqB4NfrC%2FYpg%2BDSsyOOCjMh57QCX680A%3D&reserved=0
<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbooks.google.co.nz%2Fbooks%3Fid%3DBm0_QQ3Z6GUC%26dq%3Dpanbiogeography%26source%3Dgbs_navlinks_s&data=05%7C02%7Ctaxacom%40lists.ku.edu%7Cade761a3a02a40ceeb8e08de06a60edb%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C638955507437328775%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=cKPhVejoSHL0dNQhLobol0QuXq6eVoWJCi2%2BqBBi2Dk%3D&reserved=0>