[Taxacom] Elimination of paraphyly: sensible or not?

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Thu Feb 8 18:53:58 CST 2018 

David said "The fundamental problem of the Phylocode is that the best way to convey phylogenetic information is through a phylogeny, and the most important
function of a system of biological nomenclature is to clearly convey what taxon we're talking about".

Just to clarify what I think David means, and to expand a little, "the most important function of a system of biological nomenclature" (i.e. to clearly convey what taxon we're talking about) is at odds with phylogeny because, I suggest, phylogeny is too fundamentally inconclusive and unstable. There is nothing worse than when an author changes the classification of a taxon (group) to fit their published phylogeny, and then the same things happens again for the next author with the next phylogeny, ad nauseam! Some say that this process brings us closer to some sort of truth (or at least future stability), but I personally doubt that it does. I suspect that it just sends us off in another random direction each time.

Stephen

--------------------------------------------
On Fri, 9/2/18, David Campbell <pleuronaia at gmail.com> wrote:

 Subject: Re: [Taxacom] Elimination of paraphyly: sensible or not?
 To: 
 Cc: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
 Received: Friday, 9 February, 2018, 12:53 PM
 
 A paper proposing an alternative
 approach, recognizing paraphyletic groups,
 is available at https://kuscholarworks.ku.edu/handle/1808/17551
 or
 http://www.bioone.org/doi/full/10.17161/PC.1808.17551
 
 The fundamental problem of the
 Phylocode is that the best way to convey
 phylogenetic information is through a
 phylogeny, and the most important
 function
 of a system of biological nomenclature is to clearly convey
 what
 taxon we're talking about.
 
 In some cases, eliminating
 paraphyly is practical and useful.  Eliminating
 polyphyly is usually desirable (although
 contexts exist where a
 polyphyletic group is
 useful, such as "algae" as an ecological
 category).
 But in other cases, eliminating
 paraphyly is not practical.  Replacing
 familiar names with new ones for every slight
 change in content is not
 helpful, though a
 strict reversion to original usage for every name would
 be disastrous as well - many Linnaean genera
 are at best families and at
 worst at least
 one would include most of Eukarya if it were expanded to
 the
 smallest monophyletic group including
 all originally included taxa.
 
 
 On Thu, Feb 8, 2018 at 5:42
 PM, Neal Evenhuis <neale at bishopmuseum.org>
 wrote:
 
 > I
 had a similar discussion with a pattern cladist once and his
 response
 > was “Hey, you’ve got a
 point …. but if you comb your hair differently, it
 > won’t show.”
 >
 >  -Neal
 >
 > On Stardate 2/8/18, 12:07 PM, Star-trooper
 "Taxacom on behalf of Stephen
 >
 Thorpe" <taxacom-bounces at mailman.nhm.ku.edu<mailto:taxacom-bounces@
 > mailman.nhm.ku.edu> on behalf of stephen_thorpe at yahoo.co.nz<mailto:
 > stephen_thorpe at yahoo.co.nz>>
 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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 -- 
 Dr. David
 Campbell
 Assistant Professor, Geology
 Department of Natural Sciences
 Box 7270
 Gardner-Webb
 University
 Boiling Springs NC 28017
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