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Taxacom: strict cladists war against paraphyletic taxa

Kenneth Kinman kinman at hotmail.com
Mon Dec 15 10:30:18 CST 2025 

Just a followup:
      Wikipedia has a great article on the traditional Two Empire/Two Superkingdom classification of life (https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fen.wikipedia.org%2Fwiki%2FTwo-empire_system&data%7C02%7Ctaxacom%40lists.ku.edu%7C9c3ce5fab33143b555d308de3bf73e54%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C639014130277247971%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C40000%7C%7C%7C&sdata=xxjbEsCA45Ib0KiOTLcabFAtKUXpk7acbUdV6ugXmf4%3D&reserved=0).
       Mayr 1998 called them Empire Prokaryota and Empire Eukaryota, which might be best if one wants to split them into Superkingdoms.  He strongly criticized Woese's Three Domain system.  Regarding the archaebacteria, Mayr said: "Instead Woese renamed them Archaea, retaining the inappropriate component?archae?and discarding the informative component?bacteria, which revealed their prokaryote nature." (https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpmc.ncbi.nlm.nih.gov%2Farticles%2FPMC33883%2F&data%7C02%7Ctaxacom%40lists.ku.edu%7C9c3ce5fab33143b555d308de3bf73e54%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C639014130277287678%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C40000%7C%7C%7C&sdata=RZKiLxPRF0WpsBFfCiroGZWeeUEci6xv9guMvSQmu6M%3D&reserved=0)
       The more recent classification of life (Ruggiero, et al, 2015 ( https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpmc.ncbi.nlm.nih.gov%2Farticles%2FPMC4418965%2F&data%7C02%7Ctaxacom%40lists.ku.edu%7C9c3ce5fab33143b555d308de3bf73e54%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C639014130277321633%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C40000%7C%7C%7C&sdata=rAdAkcnQp%2Blkry17Mq0eXPlYsKfeXTHuADP%2FVOxaQvA%3D&reserved=0 ) calls them Superkingdoms instead of Empires, but that is fine too.
                 -------------Ken
________________________________
From: Taxacom <taxacom-bounces at lists.ku.edu> on behalf of Kenneth Kinman via Taxacom <taxacom at lists.ku.edu>
Sent: Friday, December 12, 2025 11:05 AM
To: taxacom at lists.ku.edu <taxacom at lists.ku.edu>; Mikhail Daneliya <mdaneliya at gmail.com>
Subject: Re: Taxacom: strict cladists war against paraphyletic taxa

    Yes, thankfully most workers still recognize a paraphyletic Class Reptilia, a paraphyletic Class Amphibia, a paraphyletic Class Crustacea, etc.
      Unfortunately strict cladists have made a mess of the classification of life at the highest levels.  Particularly the Three Domain classification of prokaryotes.  The classification of Domain Archaea/Archaebacteria is now a mess of Kingdoms, and there is no clear evidence that Archaea are more archaic than Bacteria.  A single Kingdom Prokaryota giving rise to the eukaryotic Kingdoms still makes more sense.  Instead we have a mess and many still think "Archaea" is an appropriate taxon name.
          -----------------Ken

________________________________
From: Taxacom <taxacom-bounces at lists.ku.edu> on behalf of Mikhail Daneliya via Taxacom <taxacom at lists.ku.edu>
Sent: Friday, December 12, 2025 8:34 AM
To: taxacom at lists.ku.edu <taxacom at lists.ku.edu>
Subject: Re: Taxacom: strict cladists war against paraphyletic taxa

Thank you Marko!

At least you still have separate phorid genera.

The families indeed may be decided by someone to be synonymised with
Gammarids, but Baikalian genera cannot be made Gammarus by no means.

Paraphyly has been the way major evolutionary history went, as Paul noted.
Looking at a grand scale, Amphibians gave rise to Reptiles, and they still
exist. Reptiles - to birds and mammals, and they are still around. Insects
are nested within crustaceans. Would you prefer rather splitting
crustaceans? One can split or merge, but the history is there.

Mikhail



On Fri, 12 Dec 2025, 15:53 Marko Mutanen, <Marko.Mutanen at oulu.fi> wrote:

> Hei Mikhail,
>
> Some phorids, such as Nannohelea, are so distinctive that it would be
> difficult to recognize them as dipterans (or even as insects), let alone as
> phorids. They lack virtually all of the diagnostic morphological characters
> of Phoridae, yet they are still placed in the family simply because they
> are phorids.
>
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Facademic.oup.com%2Faesa%2Farticle%2F105%2F4%2F550%2F22206%3Flogin%3Dtrue&data%7C02%7Ctaxacom%40lists.ku.edu%7C9c3ce5fab33143b555d308de3bf73e54%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C639014130277347744%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C40000%7C%7C%7C&sdata=n0XF5eDNWyiDQduBMZmsbIcrsgXYE%2F%2BDyzHlgf4XuCE%3D&reserved=0
>
> There are many other similar examples.
>
> For this reason, I think fragmenting a morphologically uniform Gammarus
> solely because of unusual Baikal lineages would be more of a taxonomic
> disaster than the alternative. Treating the unusual Baikal forms as
> Gammarus seems the more reasonable and less disruptive solution. Comparable
> decisions have been made many times in other groups.
>
> Marko
>
>
> -----Original Message-----
> From: Taxacom <taxacom-bounces at lists.ku.edu> On Behalf Of Mikhail
> Daneliya via Taxacom
> Sent: perjantai 12. joulukuuta 2025 15.34
> To: taxacom at lists.ku.edu
> Subject: Re: Taxacom: strict cladists war against paraphyletic taxa
>
> Hei Marko,
>
> Your idea indeed came to minds of some researchers, but never materialised.
>
> Sometimes genera are really close to each other, and one may neglect that
> difference to merge. But if the difference is so large, merging would
> indeed be unnatural. For certain mindset it may seem like solving problems,
> but to a specialist it looks like no problems at all. On the contrary, if
> one ends up creating 1000 species of Gammarus looking more different than a
> sawfly and an ant, this will be a taxonomic disaster. I would not do that.
> I would rather accept things as they are, rather than putting facts into a
> frame of a dogma.
>
> Sincerely,
>
> Mikhail
>
> On Fri, 12 Dec 2025, 14:53 Marko Mutanen, <Marko.Mutanen at oulu.fi> wrote:
>
> > Hi Mikhail,
> >
> > This would not be an ideal solution. A much better approach would be
> > to merge all the Baikal taxa with Gammarus. In general, I believe this
> > would be the preferable outcome, although exceptions may certainly
> > occur. A comparable situation arose when several genera of Nematinae
> > (Tenthredinidae
> > sawflies) were merged into the large genus Euura. The change was not
> > universally welcomed, but the only real alternative - splitting them
> > into numerous small genera - would have been a far worse option,
> > especially since the species all look more or less the same.
> >
> > Best,
> >
> > Marko
> >
> > -----Original Message-----
> > From: Taxacom <taxacom-bounces at lists.ku.edu> On Behalf Of Mikhail
> > Daneliya via Taxacom
> > Sent: perjantai 12. joulukuuta 2025 14.04
> > To: taxacom at lists.ku.edu
> > Subject: Re: Taxacom: strict cladists war against paraphyletic taxa
> >
> > I have been working with amphipod crustaceans, and there is a
> > freshwater genus Gammarus. Everyone probably knows it. Its 200+
> > species look very similar. It is hard to doubt they belong to the same
> > genus. Suddenly DNA phylogenetics, and have done too, discovers that
> > the Lake Baikal radiation of amphipods - numerous endemic families,
> > genera and species of very bizarre looking creatures - clearly nests
> > within Gammarus. Would anyone dare to desintegrate Gammarus because of
> > its paraphaly? This looks like the way evolution goes.
> >
> > Sincerely,
> >
> > Mikhail Daneliya
> >
> > On Fri, 12 Dec 2025, 01:42 Kenneth Kinman via Taxacom, <
> > taxacom at lists.ku.edu>
> > wrote:
> >
> > > Hi All,
> > >      The war of strict cladists against paraphyletic taxa has been
> > > going on for over 50 years.  My question is how successful that war
> > > has been in regarding formal paraphyletic taxa as "unnatural" and to
> > > be
> > eliminated.
> > >  Or as noted below, does strict cladism actually promote "disastrous
> > > nomenclatural practices"?
> > >                         -------------Ken Kinman
> > > -------------------------------------------------------------
> > >
> > > Paraphyly again defended (and strict cladism promotes "disastrous
> > > nomenclatural practices) Kenneth Kinman kinman at
> > > hotmail.com<mailto:taxacom%40mailman.nhm.ku.edu
> > > ?Subject=Re%3A%20%5BTaxacom%5D%20Paraphyly%20again%20defended%20%28a
> > > nd
> > > %20strict%20cladism%20promotes%0A%20%22disastrous%20nomenclatural%20
> > > pr actices%29&In-Reply-To=%3CCY4PR11MB1480D1096C914E58FD056F53C1240%
> > > 40CY4PR11MB1480.namprd11.prod.outlook.com%3E>
> > > Mon Apr 15 20:20:45 CDT 2019
> > >
> > >   *   Previous message: [Taxacom] holotype designation<
> > > https://lists.ku.edu/pipermail/taxacom/2019-April/132964.html>
> > >   *   Next message: [Taxacom] Paraphyly again defended (and strict
> > cladism
> > > promotes "disastrous nomenclatural practices)<
> > > https://lists.ku.edu/pipermail/taxacom/2019-April/132971.html>
> > >   *   Messages sorted by: [ date ]<
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> > > [ thread ]<
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> > > >
> > > [ subject ]<
> > > https://lists.ku.edu/pipermail/taxacom/2019-April/subject.html#13297
> > > 0>
> > > [ author ]<
> > > https://lists.ku.edu/pipermail/taxacom/2019-April/author.html#132970
> > > >
> > >
> > > ________________________________
> > >
> > > Hi All,
> > >       I just ran across this 2016 paper.  Yet another publication
> > > defending the reality and need for paraphyletic taxa (for a variety
> > > of reasons), and it labels strict cladism as promoting "disastrous
> > > nomenclatural practices":
> > >
> > > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.microbiologyresearch.org%2Fdocserver%2Ffulltext%2Fijsem%2F66%2F12%2F&data%7C02%7Ctaxacom%40lists.ku.edu%7C9c3ce5fab33143b555d308de3bf73e54%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C639014130277376036%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C40000%7C%7C%7C&sdata=H4G9GrZjHmLukQ1FAcR62kIjcPD%2F3jEvcRLHegWmKX4%3D&reserved=0
> > > 49
> > > 24_ijsem001474.pdf?expires55377331&id=id&accname=guest&checksum=5
> > > 37
> > > 594F4A96BABC3F0564A74650291D5
> > >
> > > Abstract:
> > > "Yeast systematics has wholeheartedly embraced the phylogenetic
> approach.
> > > Central to this has been the unspoken convention that taxa at all
> > > ranks be strictly monophyletic. This can result in a proliferation
> > > of small genera and instances of nomenclatural instability, counter
> > > to the expected benefit of phylogenetic systematics. But the
> > > literature abounds with examples, at all taxonomic levels, where
> > > paraphyly is a reality that can no longer be ignored. The very
> > > concepts of Bacteria or Archaea, under the constraint of monophyly,
> > > are in peril. It is therefore desirable to effect a shift in
> > > practices that will recognize
> > the existence of paraphyletic taxa."
> > >
> > > Another Quote from the articles:
> > > "Taxonomy sits at an ill-defined confluence of science, craft,
> > > ontology and the law. Conscientious systematists aim at making sense
> > > of the living world by organizing species into categories that are
> > > meaningful not only to themselves, but also to other biologists and
> > > the rest of humanity. The last decades have seen undue emphasis
> > > placed on creating categories that reflect an erroneous model of
> > > cladogenesis, one that is strictly dichotomous and symmetrical. A
> > > large proportion of taxa arise not by fission of an ancestral
> > > progenitor, but by a budding process that leaves the progenitor
> > > enriched by the presence of its offspring. The retention of cohesive
> > > parent taxa under a single designation, at the same rank as progeny
> > taxa, has the potential to prevent disastrous nomenclatural practices."
> > >
> > >                 ------------------------Ken Kinman
> > >
> > > --------------------------------------------------------------------
> > > --
> > > ---------------------------------------------------------
> > >
> > > _______________________________________________
> > > Taxacom Mailing List
> > >
> > > Nurturing nuance while assailing ambiguity for 38 years, 1987-2025.
> > >
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> > >
> > >
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> >
> > Nurturing nuance while assailing ambiguity for 38 years, 1987-2025.
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> >
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