[Taxacom] Species Definition?

John Grehan calabar.john at gmail.com
Tue May 23 11:21:25 CDT 2017

I concur with much of what Scott says about the practical realities,
particularly how DNA differences may be subordinating morphology. This is
already well established in phylogeny construction where for many groups
the molecular tree is considered a falsifier of any conflicting
morphological tree (the human-great ape phylogeny being classic). And it is
in this light that the use of fossils is relied on to calibrate molecular
clock ages (which are then misrepresented, often quite deliberately, as
actual rather than minimal dates). And of course if morphology is
unreliable, how can one have any confidence that a fossil has any
particular relationship with a molecularly defined group? Of course it does
not help much if such calibrators do not search the literature for fossil
records rather than relying on a particular compilation (I presume the 100
million year old chelid examples are published and accessible to any
reasonable literature search).

Morphology (or more accurately, morphological systematics) has been under
the molecular downgrade for decades now and shows no sign of abatement.
Molecular resources will always be greater since molecular work can be tied
to the income (and student) stream of molecular biology in general
(especially the genetic disease industry). Of course conflation of results
is not restricted to molecular activity, witness the mess that often ensues
with morphological studies of primate fossils due to low grade application
of systematics principles (even to the extent of including mismatched
fragments within a single type). In biogeography the situation has been
summed up by Heads as one where technical advances have been confused with
conceptual advances. We may sometimes have very sophisticated technologies
but still live in medieval world of thinking.

John Grehan

On Tue, May 23, 2017 at 11:58 AM, Scott Thomson <scott.thomson321 at gmail.com>

> For myself I agree with the notion that as a taxonomist I am trying to
> identify populations that do not interbreed (rather than saying
> significantly I would say in a way that is deleterious to the species
> boundary, most of the time anyway). I admit I approach this from the point
> of view of a vertebrate taxonomist which is a bias in my view.
> First up with respect to comments on conservation. I do not think that we
> can mix conservation priorities into the equation. I have had this issue
> put directly in my face. When I described Elseya albagula I had activist
> conservation groups literally corner me at a conference yelling at me to
> restrict the species to a single drainage (it occurs in 4 drainages) they
> wanted to stop a dam being built and wanted to make Elseya albagula a
> showcase endangered species to do this. If I were to describe it from a
> single drainage this would shoot it up the IUCN rankings permitting
> significant conservation value, which in turn could be used to stop the
> dam. Supposedly. First up this is a circular argument, ie describe a
> species make it restricted in distribution in order to get conservation
> value, then use that value to stop a project. That is a circular argument
> and will be shredded by any half decent lawyer. Second it was not supported
> by the data. They were so admanet about this that several hundred thousand
> dollars was spent after I named it to fund a PhD using molecular techniques
> to split Elseya albagula, again so they could increase its supposed rarity,
> The result of which was demonstrating that I was correct. Waste of money.
> All to stop a dam. Please do not misunderstand, I was sympathetic and did
> not want the dam either, but the science is the science and I published
> what it showed. This is why I do not like mixing taxonomy and conservation
> management.
> Ok DNA techniques. Using next gen sequencing we are getting 100's thousands
> of BP, whole mtDNA genomes etc. I think there are three things this is
> doing to taxonomy that is negative. First up it is one of the causes of the
> defunding of morphological taxonomy and museums. Second I think many of the
> DNA researchers are probably confusing pedagrees with phylogenies at this
> point. I am saying that harshly and overstating it to make the point. But
> they are way below the species level, probably at times below the
> subspecies level. However like all workers dealing with phylogenies naming
> taxa in papers is a measure of their work. So they are applying binomials
> to populations that show little to no real difference, cannot be
> distinguished morphologically, are known to be capable of interbreeding.
> The entire radiation of the Galapagos Tortoises, currently all considered
> species have less genetic diversity than our species does. So should they
> be species? subspecies? forms? I have heard their excuse for this,
> apparently humans are an exception and these molecular techniques do not
> apply to us. Yes that has been said. Lastly it is causing a chasm between
> paleontology and taxonomy, that should not exist. These workers are using
> paleontological works without reference, understanding, phylogenetic backup
> to date their molecular trees. They look them up on fossilworks, shove them
> into their analysis and run BEAST.  The results are like WOW. You have to
> be kidding. Three papers in a 2 year period dated the family Chelidae at
> 57M, 35M and 22M for the entire radiation. Yet I have three fossil chelids
> from modern genera that are over 100M so how does that make sense.
> I think molecular tools are significant and important tools in
> phylogenetics, but it must stay in touch with morphology and through this
> the fossil record. It needs to look at its models and figure out what they
> are distinguishing.
> Cheers, Scott
> On Tue, May 23, 2017 at 6:35 AM, Richard Pyle <deepreef at bishopmuseum.org>
> wrote:
> > ....hence my qualification of "most" taxonomic communities.
> >
> >
> > > -----Original Message-----
> > > From: Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz]
> > > Sent: Monday, May 22, 2017 10:58 PM
> > > To: taxacom at mailman.nhm.ku.edu; deepreef at bishopmuseum.org
> > > Subject: RE: [Taxacom] Species Definition?
> > >
> > > Asexual lineages pose a problem to this simple concept, however!
> > >
> > > --------------------------------------------
> > > On Tue, 23/5/17, Richard Pyle <deepreef at bishopmuseum.org> wrote:
> > >
> > >  Subject: RE: [Taxacom] Species Definition?
> > >  To: "'Stephen Thorpe'" <stephen_thorpe at yahoo.co.nz>,
> > > taxacom at mailman.nhm.ku.edu
> > >  Received: Tuesday, 23 May, 2017, 6:31 PM
> > >
> > >  > I still go along with
> > >  species are populations which
> > >  > do not
> > >  freely interbreed (to a significant extent) under natural  conditions.
> > >
> > >  Yup.  I
> > >  reckon that most taxonomic communities use something along  these
> lines
> > as
> > > the center-of-mass for what they,  collectively, use to say what a
> > species is.
> > >
> > >  Aloha,
> > >  Rich
> > >
> > >
> >
> >
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> >
> > Nurturing Nuance while Assaulting Ambiguity for 30 Years, 1987-2017.
> >
> --
> Scott Thomson
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