[Taxacom] Paraphyletic groups as natural units of biological classification

Sat Sep 27 23:25:06 CDT 2014

The problem here is that your second list isn't a fully fledged Linnean classification, as the items in the list have different levels (some are families, some are orders, etc.) The difficulty arises in trying to construct a Linnean classification, whereby, for any taxon, *all taxa at the next lowest level are monophyletic*

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: "Weakley, Alan" <weakley at bio.unc.edu>, "Curtis Clark" <lists at curtisclark.org>, "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
 Received: Sunday, 28 September, 2014, 4:08 PM

 Put another way.

 And see:  http://www.mobot.org/MOBOT/research/APweb/

 If, in vascular plants, one wanted to create a broad set of
 groups useful for classification, teaching, recognition,
 etc., one might want to recognize:

 1.  Lycophytes
 2.  Ferns
 3.  "Basal angiosperms"
 4.  Monocots
 5.  "Basal Eudicots"
 6.  Rosids s.l.
 7.  Asterids s.l.

 Each of these is diagnosable morphologically, and each has a
 clear evolutionary position relative to the others. 
 But 3 and 5 are not monophyletic, they are grades (as based
 on current phylogenetic reconstructions):  3 a grade
 relative to clade 4+5+6+7, and 5 a grade relative to clade
 6+7.  Making the entities in grade 3 separate
 monophyletic units makes an additional 3 or more
 units.  Making the entities in grade 5  separate
 monophyletic entities makes 5-6 (or more) additional
 units.  1 is monophyletic, but includes very ancient
 (Devonian) (and morphologically easily distinguishable)
 entities.

 So, with good basis and with (only a little) less angiosperm
 bias, one could easily substitute for 1-7 above, and with
 strict monophyly:

 1.  Huperziaceae
 2.  Lycopodiceae
 3.  Equisetaceae
 4.  Psilotaceae
 5.  Ophioglossaceae
 6.  Horsetails
 7.  Ferns
 8.  Amborella trichopoda (1 species)
 9.  Nymphaeaceae
 10.  Austrobaileyales
 11.  Magnoliales 
 12.  Monocots
 13.  Ceratophyllum (6 species)
 14.  Ranunculales
 15.  Proteales
 16.  Trochodendrales
 17.  Buxales
 18.  Gunnerales
 19.  Dilleniaceae
 20.  "Rosids"
 21.  Santalales
 22.  Berberidopsidales
 23.  Caryophyllales
 24.  Cornales
 25.  Ericales
 26.  "Asterids"

 Note that while each of 1-7 are monophyletic, each contains
 divisions (not shown) that are older and "more fundamental"
 than any of those in 9-26.  

 -----Original Message-----
 From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
 On Behalf Of Weakley, Alan
 Sent: Saturday, September 27, 2014 11:09 PM
 To: Curtis Clark; taxacom at mailman.nhm.ku.edu
 Subject: Re: [Taxacom] Paraphyletic groups as natural units
 of biological classification

 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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