[Taxacom] Paraphyletic groups as natural units of biological classification
Kenneth Kinman
kinman at hotmail.com
Tue Sep 30 18:44:52 CDT 2014
Hi Stephen,
I agree with you that angiosperm classification is not a typical case (having been so intensely studied and most of the higher taxa being extant). Most cases involve a basal paraphyletic remainder (I don't like calling them a residue) that is either too hard to crack or won't be cracked for a long time. But even in the case of angiosperms, I believe it is more memorable (and intuitive) and extremely useful to divide angiosperms into just three formal classes (Liliopsida, Rosopsida, and Magnolipsida%) for monocots, eudicots, and the paraphyletic basal remainder. As I recall, Stuessy (2010) recognized the same three classes, but with non-typified names (calling the basal remainder Archaeangiospermae). I suppose one could put the paraphyletic group in quotes, but I still prefer to mark it with the % symbol (and Cavalier-Smith just uses an asterisk). I've long thought that it would become obvious that the pendulum swing to purely holophyletic classifications ("cladifications", as Mayr called them) had too many drawbacks that it would become glaringly apparent that it was causing as much harm as good. Unfortumately the followers of Hennig have been swayed by the successes and blissfully ignore the failures. The biggest failure is the supposed holophyly of three Domains of life, which still has widespread support even though it has been thoroughly discredited by some of the greatest minds in biology. Such a simple explanation of the tree of life is just... simplistic (and the result of using Archaebacteria to root the Eubacteria), but the more likely alternative trees are unfortunately more complex and will take much more data and time to sway the majority. Only then will that majority finally return to dividing cellular life into its two fundamental organizational types (Prokaryota and Eukaryota), and finally declare that a Three Domain Tree based mainly on too few molecular sequences is (and always has been) a horrible mistake. Another failure is the much older debate over the classification and phylogeny of Metazoan phyla. The clade Ecdysozoa could well be truly holophyletic, but Platyzoa was recently shown to be paraphyletic, and I have been harping on the paraphyly of the supposed "clade" Lophotrochosa even since it was proposed almost 20 years ago. Of course, the damage has been even greater at lower taxonomic ranks, since there are a lot more taxa at such ranks. Vertebrates classes are now a taxonomic mess (even though heavily studied).
------------------------Ken
----------------------------------------------------------------------------------------------------------------
> Date: Sat, 27 Sep 2014 20:29:39 -0700
> From: stephen_thorpe at yahoo.co.nz
> To: lists at curtisclark.org; taxacom at mailman.nhm.ku.edu; weakley at bio.unc.edu
> Subject: Re: [Taxacom] Paraphyletic groups as natural units of biological classification
>
> But this example doesn't illustrate the terms of the debate, as I see it. As you describe the example, we have a rare case of an uncontroversial and fully determined monophyletic classification of flowering plants which leaves (no pun intended!) no paraphyletic residue. Examples of this kind are rare, I suggest, and the typical case involved only moderately supported phylogenies and a basal paraphyletic residue that is too hard to crack.
>
> Stephen
>
> --------------------------------------------
> On Sun, 28/9/14, Weakley, Alan <weakley at bio.unc.edu> wrote:
>
> Subject: Re: [Taxacom] Paraphyletic groups as natural units of biological classification
> To: "Curtis Clark" <lists at curtisclark.org>, "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
> Received: Sunday, 28 September, 2014, 3:09 PM
>
> Here seems to be
> "the thing".
>
> The "basal angiosperms" or
> "primitive dicots" or "ANITA and the
> Magnoliids" or... are clearly a basal grade to other
> angiosperms, based on all recent analyses. Amborellales
> sister to all other angiosperms. Then Nymphaeales sister
> to all the rest, then... ETC. Whether you have access to
> all the papers, a good summary of the current consensus can
> be had online at the Angiosperm Phylogeny Website, at MoBot,
> compiled by Peter Stevens. This clearly shows a grade of
> various orders (all small, currently) and then also the
> magnoliids (mostly small, currently, except especially, the
> Lauraceae and somewhat less so the Piperaceae).
>
> So, the "basal
> angiosperms" are not monophyletic. And yet, it is
> "useful" and "convenient" to refer to
> them as a group -- to classify them as a unit. In
> teaching, and in floras (Flora of Virginia 2012, Flora of
> the Southern and Mid-Atlantic States 2014)), it is
> "handy" ("useful") to divide the
> vascular flora into: Lycophytes, Ferns, Basal Angiosperms,
> Monocots, and Eudicots. It seems
> "disproportionate" to treat 4 or more units
> (small, currently, a genus or two, a hundred species or
> less, each) at equivalent rank to Monocots or Eudicots,
> which have many more orders, families, genera, and
> species. Especially, as their morphological differences
> seem relatively obscure, abstruse, and non-obvious. If the
> morphological distinctions were completely obvious, maybe we
> would be more accepting -- no-one seems to have a hard time
> with Ginkgo or Welwitschia as (modern) monotypes:
> uncontroversial monotypic orders.
>
> So, Judd et al., for instance, in their
> textbook, Plant Taxonomy: a Phylogenetic Approach, use
> quotes to indicate units that are not monophyletic but yet
> are "useful". There is an interesting tension
> here between "strict monophyly" and
> "intuitive (useful) classification
> units". Units with quotes seem to flag
> something like "this is not monophyletic but sure is
> handy so we will keep using it informally".
>
> I'm not taking sides here
> (I am conflicted). But... it may be instructive to
> contemplate that other "intuitive (useful)
> classification units" ("plants",
> "animals", "algae", "fungi",
> "birds", "bacteria",
> "slime-molds", ) have fared increasingly poorly
> over time as real classification units. I was taught as a
> college botany student in the 1970s that there were 2 main
> types of algae (a kind of plant): prokaryotic
> ("blue-green algae") and eukaryotic (green, red,
> brown, etc., algae) -- several decades on, this looks
> laughable (and in no way "useful" or
> "convenient" in any respect). On the other hand,
> the "Basal Angiosperms" seem a "useful"
> unit for teaching and organization and classification, even
> if monophyly is uncertain or even disproved...
>
> -----Original Message-----
> From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
> On Behalf Of Curtis Clark
> Sent: Saturday,
> September 27, 2014 9:29 PM
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Paraphyletic groups as
> natural units of biological classification
>
> On 2014-09-27 6:59 AM, John
> Grehan wrote:
> > Since you have some
> expertise and strong opinions on paraphyly I
> > presume you have read the citation of
> Stuessy (2010) on basal
> > angiosperms
> being a paraphyletic group. As I do not have immediate
> > access to that paper perhaps you could
> describe in what way that group was paraphyletic.
>
> Some of its members
> (Austrobaileyaceae?) are more closely related to the rest of
> the angiosperms than others are. (Same definition as
> usual.)
>
> --
> Curtis Clark http://www.csupomona.edu/~jcclark
> Biological Sciences
> +1 909 869 4140
> Cal Poly
> Pomona, Pomona CA 91768
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