[Taxacom] Elimination of paraphyly: sensible or not?

Thu Feb 8 19:02:22 CST 2018

Mike said: "... in the face of ever advancing understanding of the evolution of life on earth"

It is a moot point whether cladistics/phylogenetics does in fact advance understanding of the evolution of life on earth! It seems to me to be little more than a paint by numbers approach which can in theory be replicated by anyone else who uses the same character weightings, etc., but replicability alone does not imply that we are actually advancing understanding of the evolution of life on earth"!

You also misunderstood my comments about retaining birds and mammals as named taxa. They ARE monophyletic, and I didn't say to necessarily retain them as taxa of equal rank to reptiles (so subtaxa of reptiles are indeed fine to me also), I just meant that we don't want to simply dump them into reptiles such that Reptilia simply contains various subtaxa from each in a way that doesn't group bird (or mammal) subtaxa together under a name.

I'm surprised that anyone finds "interesting" the inconclusive and ephemeral results of phylogenetic studies!

Stephen

--------------------------------------------
On Fri, 9/2/18, Michael A. Ivie <mivie at montana.edu> wrote:

 Subject: Re: [Taxacom] Elimination of paraphyly: sensible or not?
 To: taxacom at mailman.nhm.ku.edu
 Received: Friday, 9 February, 2018, 12:56 PM

 Hi Stephan,

 It seems to me that you have this premise
 backwards.  Rather than there 
 being a
 cabal of rabid cladists obsessed with eliminating paraphyly,
 I 
 think there is a cabal of rabid
 revanchists obsessed with hanging on to 
 familiar paraphyletic taxa in the face of ever
 advancing understanding 
 of the evolution of
 life on earth.  In actual practice, most advocates 
 of a monophyly standard continue to use and
 propose taxa that cannot be 
 shown to be
 monophyletic, but if we have evidence, why not use it?

 You say "We wish to
 retain birds and also mammals as useful monophyletic 
 taxa, for obvious reasons."  How, if you
 mean as 
 nomenclaturally-recognized taxa at
 a level equal to reptiles, is this 
 obvious,
 or to be wished for?  We have the words "birds"
 and "mammals" 
 for the folk
 taxonomy, but why not recognize them for what they really

 are? Subtaxa of Reptiles works fine for
 me.

 As for why look for
 monophyletic lineages?  Because scientifically, 
 doing phylogenetics is INTERESTING.  I myself
 do mostly alpha taxonomy, 
 because I
 don't have the skill set to be a leading
 phylogeneticist, but 
 I find their results
 to be very thought provoking, interesting and even 
 exciting.  It is not that they get too much
 funding, it is that 
 faunistics and taxonomy
 get to little.

 Mike

 On
 2/8/2018 3:07 PM, Stephen Thorpe wrote:
 >
 Hi all,
 > I have been giving some thought
 to the cladistic obsession of eliminating paraphyly in
 taxonomic classification. For many taxa (above species), the
 subtaxa consist of one or more clearly monophyletic groups,
 plus a possibly paraphyletic residue (i.e. no apomorphies to
 bind the residue together into a monophylum). So, if we must
 eliminate paraphyly (or possible paraphyly), the only
 options are to either: (1) subsume the monophyletic subtaxa
 into the paraphyletic residue; or (2) break up the
 paraphyletic residue into monophyletic subtaxa. Effectively
 the two options may actually be equivalent. An example might
 help to illustrate my point. Let's take a simplistic
 view of reptiles as scaly tetrapods, birds as feathery
 winged bipeds derived from reptiles, and mammals as hairy
 tetrapods derived from reptiles. So, amniotes (reptiles,
 birds and mammals) are a monophyletic group, as are birds
 and also mammals, but not reptiles (reptiles being the
 "paraphyletic residue"). We wish to retain birds
 and also mammals as useful monophyletic taxa, for obvious
 reasons. So, what to do? Luckily, within reptiles there are
 some monophyletic subgroups of sufficient diversity to be
 useful, but this might not have been the case if all
 reptiles were just basically "skinks", with only
 species or perhaps also generic differences between them.
 Had this been so, amniotes would have to be taxonomically
 split between numerous (maybe hundreds) virtually identical
 taxa of "skinks", plus birds and also mammals as
 just two taxa at the same level (not necessarily a ranked
 level, but direct child taxa of amniotes). Would this be a
 useful classification of amniotes? I suggest that it would
 be far more useful to recognise a single paraphyletic taxon
 of reptiles (all the "skinks" in the hypothetical
 example), plus birds and also mammals (i.e. just 3 direct
 child taxa of amniotes). I wonder for plants, fungi and also
 invertebrates, if there might be many taxa analogous to the
 above hypothetical example, with a paraphyletic residue
 consisting of hundreds of "skinks", but also with
 just one or two very distinct and diverse monophyletic
 subtaxa? If so, would it be sensible to eliminate paraphyly
 or best just to live with a known paraphyletic residue as a
 unified subtaxon? Given the amount of limited resources
 which are being allocated to projects to eliminate
 paraphyly, to the detriment of alpha taxonomy, it would be
 nice to think that there was a clearly good reason for the
 elimination of paraphyly, but I'm not so sure that there
 is! The usual argument seems to be that you cannot make
 meaningful predictions from paraphyletic taxa, but how much
 biology does rely on the making of predictions based on
 taxon membership, and what proportion of those predictions
 end up being true anyway? For example, you might predict
 that a newly discovered braconid is a parasitoid, but a few
 braconids are phytophagous anyway. So, I guess that the main
 question that I am posing is whether we think that the
 benefits of monophyly justify the spending of so much
 limited resources on the elimination of paraphyly? Perhaps
 the elimination of paraphyly is being driven instead by
 economic factors, doing phylogenies being a more cost
 efficient way for institutional scientists to spend their
 time on than alpha taxonomy?
 >
 Stephen
 >
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 -- 
 __________________________________________________

 Michael A. Ivie, Ph.D.,
 F.R.E.S.

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 Assaulting Ambiguity for 31 Some Years, 1987-2018.