[Taxacom] Anolis classification (was: taxonomic impediment redux)

Scott Thomson scott.thomson321 at gmail.com
Mon Nov 5 08:51:11 CST 2018


Hi Kenneth,

I am neutral on the idea of whether or not the Anolis should be split, its
not a group I know well enough. In a recent discussion I also stated that
if it had been me I would have gone the subgenus route based on what I
could see. My point was more the reasons for not accepting the published
works of taxonomists and what seemed to be required these days to reject
it. Looking at other groups it seems also that depending on the popularity
of the group your dealing with the harder it is to propose taxonomic
changes.

Phylocode is another issue, and one that has yet to have a solution.

Cheers Scott



On Mon, Nov 5, 2018 at 12:29 AM Kenneth Kinman <kinman at hotmail.com> wrote:

> Hi Scott,
>       When it comes to the Anolis debate, I have to side with those who do
> not want to split Anolis into separate genera.  I think the compromise of
> recognizing the 8 subgroups as subgenera is optimal in that it recognizes
> the most recent molecular/cladistic splitting without too much disruption.
> I think the subgeneric splitting is a win/win solution.
>        As for recognizing the cladistic splitting of species groups within
> those subgenera, I would suggest that some sort of alpha-numeric coding
> would be just fine, especially since some of those lower-level
> relationships would be more likely to need adjustments in the future.  Or
> just a simple cladogram in the left margin would also work.  Trying to
> stretch the Linnaean system far beyond the normal categories is just an
> excuse of strict cladists for abandoning Linnaean categories altogether
> (and always has been).    There are solutions that would satisfy the needs
> of cladistics without abandoning Linnaean categories if we acted more like
> scientists and less like politicians.  Otherwise, the Phylocoders will lead
> us into total chaos.  They done enough damage already.
>
> ------------------------------
> *From:* Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of Scott
> Thomson <scott.thomson321 at gmail.com>
> *Sent:* Saturday, November 3, 2018 12:39 PM
> *To:* Richard.Zander at mobot.org
> *Cc:* taxacom
> *Subject:* Re: [Taxacom] taxonomic impediment redux (was Re: Earth
> BioGenome Project)
>
> Interesting discussion.
>
> A view I have held for a while and was in my mind with some of the things
> we said in the PLoS paper was that Universities have effectively wrenched
> the study of taxonomy in a direction that is good for funding agencies,
> good for Universities but bad for taxonomy. In other words the almost total
> reliance on molecular phylogenetics at most Universities and no funding to
> going to the broader science of taxonomy. I am not the first, wont be the
> last and am not unique in that view. At a conference I recently provided
> example after example of the downside of this, poor taxonomic and
> nomenclatural decision making with no reference to types, no way of pinning
> the decisions being made to existing nomenclature. Incorrect nomenclatural
> acts frequently made and being accepted. All my examples were vertebrates.
>
> So to me the standoff is that almost all funding for genuine taxonomic
> research has been funneled into quick and easy molecular analysis. To me
> this is one of the biggest issues facing taxonomy. As another example of
> this it was recently proposed, for about the third time, by taxonomists to
> split the genus Anolis (500 species) into about 8 genera. This has been
> rejected by the Anole community on the grounds that they do not like it and
> they do not see why their community should be beholden to a small group of
> taxonomists. I do not know how much merit of splitting the genus has, but
> some of those who worked on the group really wanted this, others who were
> more conservation, medical and other research oriented did not. So clearly
> proposals by taxonomists do not carry much weight these days.
>
> I think that some form of international taxonomic body as Doug described
> would be a good idea, however I also think it is unlikely to happen. I also
> agree we are basically out of time. I really do not see how this can be
> repaired easily. Perhaps the only real way is to clearly and publicly
> reject the mistakes being made by this type of research. In particular not
> examining types, using websites such as fossilworks to justify the position
> of fossils in molecular trees for dating exercises which borders on a joke.
> It is not impossible to bring types into molecular data, I have a paper
> submitted now that sequences 22 types (23 attempted so one failed). The
> funding agencies are complicit in the madness of this, and yes so are
> government agencies. Only way to change this is to show them how idiotic it
> is.
>
> Cheers Scott
>
> On Sat, Nov 3, 2018 at 11:24 AM Richard Zander <Richard.Zander at mobot.org>
> wrote:
>
> > In reply to Doug Yanega, who wrote in part:
> > "In an ideal world, there would be a Global Taxonomic Institute that
> would
> > have centers of research on every continent, staffed by thousands of
> > taxonomists worldwide, whose jobs would be to describe and identify
> > organisms (including confirmation of others' IDs), whose salaries would
> be
> > permanently supported, and without whose "seal of approval" nothing would
> > get into print that relied upon identification. That is certainly never
> > going to happen. A few of you may even recall the "All-Species
> Initiative",
> > which proposed to do something along those lines, and it died on the
> vine."
> >
> > This not so unreachable. Consider the following:
> > With climate change, say 3 or 4 degrees C, ecosystems and communities are
> > going to move or die (a metaevolution). Because of differential migration
> > rates, the species will smear out. Lots of competition and selection will
> > ensue. A paper I recently read predicted that the changes to ecosystems
> > after the most recent glaciation may well happen in the next 100 to 150
> > years, a catastrophic compression.
> >
> > This means that our keys to species will not work for a given geographic
> > area, nor will out floristic and faunistic checklists. One might say
> > taxonomy will be obsolescent. Is this true?
> >
> > I believe that it is time for the systematics community to repurpose its
> > collections and retool its expertise. Surely, our present collections can
> > be used as benchmarks for biodiversity change from preindustrial times to
> > say 1960 (beginning of exponential rise in population), then  to present,
> > to help infer possible composition of mostly novel ecosystems of the
> > future. Maximizing biodiversity of such future ecosystems should be an
> > activity fundable by government, with considerable oversight regarding
> > nonsensical, unhelpful, or bad science.
> >
> > I suggest a focus on maximizing evolutionary and ecological redundancy.
> > Some suggestions on how to do that are in the last two chapters of my
> book:
> >
> >
> https://www.researchgate.net/publication/324363615_Macroevolutionary_Systematics_of_Streptotrichaceae_of_the_Bryophyta_and_Application_to_Ecosystem_Thermodynamic_Stability_Edition_2
> > , which as an aside now has 1100 "views" on ResearchGate which might mean
> > downloads and perhaps interest on the part of some.
> >
> > The systematics community has the facilities, data, and expertise to
> > directly address coming massive change in fauna and flora (including
> crops
> > and livestock). A " Global Taxonomic Institute" is not a pipe dream. One
> > might rename such a thing an "Ecosystematics Institute" following Duke's
> > 1978 coining of word ecosystematics, as a combination of taxonomy,
> ecology
> > and evolution.
> >
> > Richard Zander
> >
> >
> > -------
> > Richard H. Zander
> > Missouri Botanical Garden – 4344 Shaw Blvd. – St. Louis – Missouri –
> 63110
> > – USA
> > richard.zander at mobot.org Ofc: +1 314 577-0276
> > Web sites: http://www.mobot.org/plantscience/bfna/bfnamenu.htm and
> > http://www.mobot.org/plantscience/resbot/
> >
> > -----Original Message-----
> > From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu
> <taxacom-bounces at mailman.nhm.ku.edu>] On Behalf Of
> > Doug Yanega
> > Sent: Friday, November 02, 2018 1:10 PM
> > To: taxacom at mailman.nhm.ku.edu
> > Subject: [Taxacom] taxonomic impediment redux (was Re: Earth BioGenome
> > Project)
> >
> > On 11/1/18 3:32 PM, KD Dijkstra wrote:
> >
> > Hi all,
> >
> > I was just pondering the announcement when Tony's message came in. The
> > Earth BioGenome Project states that "we desperately need to catalogue
> life
> > on our planet now". Their solution is to spend 5 billion dollars on
> reading
> > the genomes of 1.5 million (described?) species.
> >
> > I've lately developed the feeling that a new problem is arising on top of
> > the 'old' taxonomic impediment (i.e. the phenomenon that taxonomists
> can't
> > keep up with biodiversity's extent). We might call the new issue the
> > "taxonomic standoff": we can now generate so much data (specimen records
> on
> > GBIF, DNA-barcodes on BOLD, and now apparently millions of billions
> genomic
> > data) that there's a risk that remaining experts won't keep up with the
> > verification and eventually give up, making most of the effort redundant.
> > This occurs if investment in innovations that could (and indeed were
> > intended to) strengthen biodiversity expertise is so disproportionate
> that
> > it tips the balance between quantity and quality. The entire effort to
> > catalogue biodiversity would then effectively collapse under its own
> weight.
> >
> > So my questions to the taxonomic community are (1) whether such a
> > "taxonomic standoff" is indeed unfolding and (2) if taking a collective
> > stance relative to this latest initiative (which will make huge demands
> of
> > the community, but might benefit it too) would be a way to strengthen our
> > position.
> >
> >
> >
> > A colleague just this week showed me a paper he had been sent for review
> > by an established, peer-reviewed journal, that is instructive in this
> > regard.
> >
> > In it, a number of plant-feeding insects and their presumed parasites
> were
> > listed, all identified to species, but not a single one of which had been
> > identified by a taxonomist. They had all been IDed by simply looking for
> > the nearest match in GenBank. They were all in genera that contained
> dozens
> > to over a hundred species for which no GenBank sequences were available
> > (and, on top of that, a quick check revealed that a few of the taxa
> showing
> > on GenBank clearly have sequences from multiple species represented, and
> no
> > way to know which ones actually were the taxon named). Several of the
> > resulting IDs were therefore of species that didn't even occur in that
> > Hemisphere, and all but one or two of the rest were almost certainly
> wrong.
> > The authors saw nothing wrong with this, the editor that sent the
> > manuscript out for review saw nothing wrong with this, and the odds are
> > good that my colleague may be the only one of the reviewers who DID see
> > anything wrong with this. That is, it may indeed get published, despite
> > being absolute rubbish.
> >
> > This is the old taxonomic impediment, but now it's just being ignored, by
> > removing taxonomy from the equation entirely.
> >
> > There is no way to prevent this from happening, that I can see, given
> > certain unavoidable realities. IN PRINCIPLE, every editor of every
> journal
> > would know that this is unacceptable, and reject every such submission.
> If
> > attempting to publish such a paper was 100% guaranteed to fail, then
> > researchers would be forced to incorporate support for taxonomy into
> their
> > research, or they would risk losing funding, and losing their jobs. But
> the
> > reality is that for every journal that rejects an unacceptable paper,
> there
> > are dozens of journals that will happily accept it and print it (and that
> > number keeps growing). So long as authors know that they can get things
> > published without involving taxonomists, they will have incentive to do
> > exactly that.
> >
> > So long as papers lacking taxonomic involvement are being published,
> > funding agencies won't cut off funding to the researchers publishing
> them -
> > they're just looking for "deliverables". They're effectively funding
> > homeopathic taxonomy; something that might look and smell like taxonomy
> but
> > is so hopelessly diluted as to be meaningless. We live in a world where
> > Wikipedia has higher standards of verifiability and accountability than
> > half the journals in print*, so expecting funding agencies to look for
> > verifiability and accountability seems like it's going to get harder and
> > harder, rather than the converse.
> >
> > If the funding agencies don't see or understand how their funding
> > priorities thereby undermine legitimate science, then who will explain
> this
> > to them, and convince them to stop supporting bad science? Unless I'm
> > missing something, the people at the top of the proverbial pyramid are
> NOT
> > listening to taxonomists, since we're the bearers of bad news, and I
> don't
> > see what options we have to get them to listen to us. We have no lobby,
> no
> > union, no advocacy group that can compel anyone to do anything on our
> > behalf (what leverage do we have?), and - perhaps just as bad - even if
> we
> > had their attention, we really don't have anything especially positive to
> > say to those funding agencies. There are an estimated 10 to 50 million
> > undescribed species out there (mostly arthropods), and what's the average
> > number of species that a fully-funded taxonomist can describe in a year?
> > What are the odds that any random organism will even have a living
> > taxonomist who can recognize it? It's hard to portray alpha taxonomy as a
> > cost-effective investment, when it moves at a relative snail's pace, and
> > it's a very hard sales pitch trying to tell someone that something that
> > isn't cost-effective is nonetheless an absolute necessity. If every
> dollar
> > spent on genome sequencing was matched by 100 dollars on taxonomy, could
> we
> > even hope to keep pace? In the face of this, what "collective stance" can
> > we possibly take that would be persuasive?
> >
> > In an ideal world, there would be a Global Taxonomic Institute that would
> > have centers of research on every continent, staffed by thousands of
> > taxonomists worldwide, whose jobs would be to describe and identify
> > organisms (including confirmation of others' IDs), whose salaries would
> be
> > permanently supported, and without whose "seal of approval" nothing would
> > get into print that relied upon identification. That is certainly never
> > going to happen. A few of you may even recall the "All-Species
> Initiative",
> > which proposed to do something along those lines, and it died on the
> vine.
> >
> > Again, this still comes back to the taxonomic impediment, but the gap
> > between the increasing pressure for "deliverables" and the capacity for
> > conventional taxonomy to deliver is getting worse. If anyone here sees a
> > practical solution, I think we'd all love to hear it.
> >
> > Sincerely,
> > --
> > * I was recently told, by an editor at Wikipedia, that Wikipedia policy
> > prohibits people from correcting misspellings in Wikipedia of scientific
> > names that appear in print, even if correcting those errors is mandated
> by
> > the ICZN, and even if the person making the corrections is an ICZN
> > Commissioner, because Wikipedia requires independent third-party
> > verification for any proposed edits (i.e., proof, in print, that there
> > really is an error at all).
> >
> > --
> > Doug Yanega      Dept. of Entomology       Entomology Research Museum
> > Univ. of California, Riverside, CA 92521-0314     skype: dyanega
> > phone: (951) 827-4315 (disclaimer: opinions are mine, not UCR's)
> >              http://cache.ucr.edu/~heraty/yanega.html
> >   "There are some enterprises in which a careful disorderliness
> >         is the true method" - Herman Melville, Moby Dick, Chap. 82
> > _______________________________________________
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>
>
> --
> Scott Thomson
> Museu de Zoologia da Universidade de São Paulo
> Avenida Nazaré, 481, Ipiranga
> 04263-000, São Paulo, SP, Brasil
>
> Chelonian Research Institute
> 402 South Central Avenue,
> Oviedo, 32765, Florida, USA
>
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-- 
Scott Thomson
Museu de Zoologia da Universidade de São Paulo
Avenida Nazaré, 481, Ipiranga
04263-000, São Paulo, SP, Brasil

Chelonian Research Institute
402 South Central Avenue,
Oviedo, 32765, Florida, USA

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