Taxacom: Minimalist revision of Mesochorus

Wed Aug 30 23:41:19 CDT 2023

Hi Scott,

> The ICZN code is for now still the code for fossil taxa, 

> as it is living. If we wish to maintain that we need to 

> ensure methodology can be used for both. DNA only 

> descriptions does not cut it and the paleos are being 

> left out. There is no DNA in a fossil.

I don’t think that anyone is advocating that the Code should be limited to descriptions using only DNA – I think everyone agrees that morphology-only descriptions should still be allowed.  The question is more about expanding the scope of what the Code allows in order to accommodate DNA-only (or DNA-supplemented) descriptions.  This certainly doesn’t stop the paleos from doing what the paleos have always done.

Aloha,

Rich

Richard L. Pyle, PhD

Senior Curator of Ichthyology | Director of XCoRE

Bernice Pauahi Bishop Museum

1525 Bernice Street, Honolulu, HI 96817-2704

Office: (808) 848-4115;  Fax: (808) 847-8252

eMail: deepreef at bishopmuseum.org

BishopMuseum.org

Our Mission: Bishop Museum inspires our community and visitors through the exploration and celebration of the extraordinary history, culture, and environment of Hawaiʻi and the Pacific.

From: Scott Thomson <scott.thomson321 at gmail.com> 
Sent: Wednesday, August 30, 2023 6:07 PM
To: Richard Pyle <deepreef at bishopmuseum.org>
Cc: Michael A. Ivie <mivie at montana.edu>; taxacom at lists.ku.edu
Subject: Re: Taxacom: Minimalist revision of Mesochorus

A great and important conversation.

I guess the thing that always gets me in any of these progressions in our methods of taxonomy is its utility across all taxa governed by the ICZN. I will not deny that I have a vested interest here. I probably am one of the few taxonomists who works with both living and fossil taxa. I even combine them into singular assessments for the more recent taxa and hence need characters or definitions that can be applied to both. Unlike many taxonomic groups turtles actually have a substantial fossil record. We have about 350 living species and 1200 fossil taxa in a group that spans 230 million years. Obviously barcodes or any DNA analysis when the only definition of a taxon cannot be applied to the fossil taxa. Further to this along I guess what Michael was pointing out, fossil taxa are usually unique and fossil holotypes do not get loaned, when you wish to examine a fossil holotype you must visit the museum in question, this means it is generally impossible to directly compare fossil and living taxa unless you can borrow the living taxa types, also not often possible, its also impossible to cart vertebrate caracases around the world from multiple countries anyway. For turtles mainly due to CITES among other legislations.

I have no issue with the use and development of molecular techniques, I have certainly used them in numerous papers. However, I will say I prefer a description of distinguishing characters to also be required.

I have watched taxonomy unfold for the last 35 years and I do not agree that the sole reason for loss of funding to taxonomy is the behavior of taxonomists. One of the major reasons is that the money for taxonomy has been funneled into universities where it is used primarily for molecular work which is faster, easier to teach and more repeatable among students at a pace in keeping with post graduate degrees. In other words there has been a major shift from museums to universities of the taxonomic dollar. Again to use the example of turtles, most taxonomists working on these species work on living species or on fossil species almost never on both. This divide is growing and the nomenclature used by these two groups is becoming more and more disparate over time. For many turtle paleos there is almost nothing published on living taxa that is of any use to their work, and vice versa. To my knowledge I am the only living person who has named both living and fossil turtles.

The ICZN code is for now still the code for fossil taxa, as it is living. If we wish to maintain that we need to ensure methodology can be used for both. DNA only descriptions does not cut it and the paleos are being left out. There is no DNA in a fossil.

Cheers Scott

On Wed, Aug 30, 2023 at 10:59 PM Richard Pyle via Taxacom <taxacom at lists.ku.edu <mailto:taxacom at lists.ku.edu> > wrote:

Thanks, Mike -- and I agree!

This is actually something I have thought about a lot, and alluded to indirectly on another post to the ICZN list.

Among the things the Code requires are these:
- designation of a name-bearing type
- description or definition that states in words characters that are purported to differentiate the taxon

Both serve similar functions, which is to "anchor" (good word -- it's the one I use as well) a name to a biological organism.  This is obviously a FUNDAMENTAL part of the nomenclatural game, without which we're swimming in a sea of nomina nuda.

However, pretty-much everyone I've discussed this with (including many Commissioners) agree that, in cases where these two aspects of a given species name do not agree, it's the type specimen(s) that "wins".  In other words, if the "description or definition that states in words characters that are purported to differentiate the taxon" is inconsistent with the actual attributes of the name-bearing type, the name is still objectively associated with the name-bearing type; not with the description or definition.  We accept that the accuracy of the "description or definition that states in words characters that are purported to differentiate the taxon" is not relevant to the availability of the name -- only that it must be included within the published work that proposes the name in an otherwise Code-compliant way.

In this context, the latter requirement (description or definition) has no real "function" (at least not one that is necessarily useful) in the business of nomenclature.  It certainly serves an extremely important function for *taxonomy*, and indeed a lot of the difference between "good" taxonomy and "bad" taxonomy boils down to how robust and accurate this description or definition is. But it serves almost no function for nomenclature sensu stricto.  The closest function it might serve for nomenclature is as a "backup" to the name-bearing type (when the latter is not accessible or is lost), and similarly as a guide for selecting a neotype or lectotype.  But even then, there are no rules in the Code that leverage the description or definition in this way.  The major role it plays in taxonomy (besides serving as potential metadata relevant to the name-bearing type) is to serve as a guide for taxonomists in deciding what scope of other (non-type) specimens/individual organisms fall within the taxonomic concept circumscription imagined (and I use that word very deliberately) by the person proposing the new name.

Coming back to your point, I see a DNA sequence derived directly from the name-bearing type as something of direct relevance to nomenclature, because it relates directly to the objective biological basis for which the name was proposed to represent.  But a DNA sequence taken from any other specimen that is not part of the name-bearing type or type series serves essentially the same function (under the current rules) as the description or definition.  That is, something that's incredibly useful to taxonomy, but of only marginal relevance to nomenclature.

I get that this discussion is much more about taxonomy than it is about nomenclature (several of us Commissioners chimed in on the nomenclatural angle mostly because of some of the remarks in the original post on this thread), so maybe this point is moot.  But what I, as a Commissioner, am very interested in, is whether the Code could or should play a more active role in bridging genetic information to nomenclature.  For example, in the event that a DNA sample cannot be extracted from a name-bearing type specimen (for whatever reason), should the Code provide a mechanism for attaching a DNA sequence from a non-name-bearing type specimen in some "official" and genuinely nomenclatural capacity?  I recall Godfray wrote an article along these lines in the 2000s (don't have the citation handy) proposing such a process.  While nothing like this exists in the current Code (although epitype is something that has been suggested), given what an (increasingly) important role DNA sequence data is and will play in taxonomy, perhaps we need a mechanism for building such a bridge (between DNA sequence and name) in a Code-enforceable way, in cases where it's not possible to extract a DNA sequence from the actual name-bearing type.

Another frustratingly long email from me, for which I apologize.  But as I said in my earlier post on this thread, I did have other comments I wanted to toss into the mix.

Aloha,
Rich

Richard L. Pyle, PhD
Senior Curator of Ichthyology | Director of XCoRE
Bernice Pauahi Bishop Museum
1525 Bernice Street, Honolulu, HI 96817-2704
Office: (808) 848-4115;  Fax: (808) 847-8252
eMail: deepreef at bishopmuseum.org <mailto:deepreef at bishopmuseum.org> 
BishopMuseum.org
Our Mission: Bishop Museum inspires our community and visitors through the exploration and celebration of the extraordinary history, culture, and environment of Hawaiʻi and the Pacific.

> -----Original Message-----
> From: Taxacom <taxacom-bounces at lists.ku.edu <mailto:taxacom-bounces at lists.ku.edu> > On Behalf Of Michael A.
> Ivie via Taxacom
> Sent: Wednesday, August 30, 2023 3:20 PM
> To: taxacom at lists.ku.edu <mailto:taxacom at lists.ku.edu> 
> Subject: Re: Taxacom: Minimalist revision of Mesochorus
> 
> Just a quick note:  There is a difference between "bad" solutions which give
> us undeciferable names (concepts really), and "good" solutions that may be
> suboptimal, but allow for easy discovery of synonyms in a relatively
> unambiguous manner.  In the old system, the type was that unambiguous
> anchor, but perhaps barcodes may be come a substitute/parallel system.  For
> instance, there is a huge beetle collection in Europe that now refuses to loan
> types and they hold a total stranglehold on a group that is taxonomically
> impossible from the literature (single terrible worker buggered it
> all  up).  Only a worker that can afford several months in one of the most
> expensive cities in the world can even start on the group.  If there were
> barcodes for each of those species, the unavailable types and bad
> descriptions would not have left the group un-worked and un-workable for
> 100 years.
> 
> Mike
> 
> On 8/30/2023 6:24 PM, Richard Pyle via Taxacom wrote:
> > **External Sender**
> >
> > Again, I think this is a really great and constructive discussion!  I limited
> myself in my previous post to "Commissioner-speak" with respect to the
> Codes, but the real crux of this discussion (as pointed out by others) is "good
> taxonomy" vs. "bad taxonomy".  The point I wanted to make is that this
> discussion -- like almost everything else in life -- boils down to a cost/benefit
> decision.  There are no "right" or "wrong" answers, but there can be "better"
> or "worse" answers depending on what the goal is.  In this case, we have two
> competing goals:
> >
> > 1) Increase the pace of documenting biodiversity, so we aren't so
> handicapped in the race against biodiversity loss as we are if we keep
> describing new species at historical rates.
> >
> > 2) Avoid making matters worse by cluttering the world with ambiguous and
> superfluous scientific names that cause more harm in terms of future
> taxonomists dealing with a mess of names.
> >
> > The good news is that these are not mutually exclusive goals, and I think
> Jose's excellent post did a fantastic job of making that point.  There are
> examples at both extremes (hyper-careful/robust taxonomy that yields 10
> new species after 20 years of work at one end; and mass minimalist cranking
> out of names at the other), but the real trick here is threading the needle in
> such a way that we get the most benefit (#1) at the lowest cost (#2).
> >
> > Discussions like this are extremely helpful (to me, at least) for figuring out
> how to thread that needle.  The ICZN Code is very limited in its role for
> promoting "good taxonomy", but that role is not zero. And it's one of the
> only actual "legal-ish" standards in biology, and thus has at least a small
> amount of influence over how taxonomists do their work.
> >
> > Aloha,
> > Rich
> >
> > Richard L. Pyle, PhD
> > Senior Curator of Ichthyology | Director of XCoRE Bernice Pauahi
> > Bishop Museum
> > 1525 Bernice Street, Honolulu, HI 96817-2704
> > Office: (808) 848-4115;  Fax: (808) 847-8252
> > eMail: deepreef at bishopmuseum.org <mailto:deepreef at bishopmuseum.org> 
> > BishopMuseum.org
> > Our Mission: Bishop Museum inspires our community and visitors through
> the exploration and celebration of the extraordinary history, culture, and
> environment of Hawaiʻi and the Pacific.
> >
> >> -----Original Message-----
> >> From: Taxacom <taxacom-bounces at lists.ku.edu <mailto:taxacom-bounces at lists.ku.edu> > On Behalf Of Neal
> >> Evenhuis via Taxacom
> >> Sent: Wednesday, August 30, 2023 10:44 AM
> >> To: taxacom at lists.ku.edu <mailto:taxacom at lists.ku.edu> 
> >> Subject: Re: Taxacom: Minimalist revision of Mesochorus
> >>
> >> Although I am an ICZN Commissioner, I am speaking here as a
> >> taxonomist who has described more than 700 new species of flies, all
> >> based on morphological characters (although I have used molecular
> >> ones to test hypothetical species groups to tell me I was either spot
> >> on or whacko in my hypotheses). To me, molecular characters are just
> >> another character set and not the end unto themselves. As has been
> >> pointed out, barcodes do not always = unique species and to use them
> >> without resort to morphological characters is, in my opinion, sloppy
> taxonomy.
> >>
> >> I was trained in taxonomy in an age where we were curious biologists
> >> and wanted to know not only the manifest of Spaceship Earth (yes, I’m
> >> from the Bucky Fuller era), but how things worked. We went into the
> >> field; hand- collected specimens, and watched our taxa live their
> >> lives and how they nourished, parasitized, predated, courted, mated,
> >> etc. When I describe species impaled on pins or floating in ETOH
> >> (thankfully I do not have to prepare them on slides – except
> >> genitalia), I am always asking myself how those species recognize each
> other in order to mate and have F1 generations.
> >> If Sharkey et al. are on the right path, then maybe they have sensory
> >> devices we have not found yet that can discern barcode sequences and
> >> those little wasps can confidently say with a wink after they have
> >> found one of their kind and the opposite sex -- “Whoowhee, baby! How
> YOU doin’ ACCGTCTAAGGT?”
> >> I doubt it. Insects have other sensory devices to discern their own
> >> species. I do not think males of Mesochorus in Guanacaste fly around
> >> humping everything that looks similar in hopes of a successful mating
> >> (maybe they do – do we know? That would be a step backward
> >> evolutionarily as wasteful energy epxediture). Instead I’d wager they
> >> discern their own species either visually or semiochemically. The
> >> former requires that each species is visually different somehow. The
> >> latter may require other techniques that include molecular - in hopes
> >> that what is used codes for those different semiochemicals. Barcodes
> >> do not. Nor do they always account for normal variation in a population of
> the same species.
> >>
> >> My hunch (having done taxonomy on tropical flies over the last 40+
> >> years  - in habitats similar to the dry-but-tropical Guanacaste) is
> >> they use visual characters. I am finding that some of the tropical
> >> flies I work with have unique Wing Interference Patterns (WIPs) that
> >> are used in species recognition. Males and females all have to rest
> >> and when they do and the sunlight hits their wings, they show a
> >> distinct pattern that is receptive to like- kind species. They
> >> sometimes vary geographically in the same species, but in restricted
> >> geographical populations where many occur sympatrically, they work
> >> well in differentiating otherwise cryptic species. There are other
> >> hard- to-see morphological characters to differentiate (some
> >> internally), but the WIPs cinch my hypotheses that the specimens are
> >> the same taxon and I hypothesize THAT is the way they find each
> >> other. Do Mesochorus use WIPs for species recognition? I don’t think
> >> Sharkey et al. ever tested that. And maybe WIPs won’t work and are
> >> indeed too variable. Apparently they are in other Hymenoptera like
> Figitidae. But rather than look for WIPs or other morphological sets of
> characters that may solve that problem, Sharkey et al.
> >> resorted to an expedient way of running sequences and putting names
> >> on BINs and letting future workers sort out the mess. I’m not a fan
> >> of that as a way to “solve” the taxonomic impediment – it just
> >> creates another impediment for future workers.
> >>
> >> We all want to solve the taxonomic impediment by finding expedient
> >> ways of naming all the undescribed species that are still out there
> >> (some of us are doing it, others are armchair pundits only but rally others
> toward that goal).
> >> But I would suggest not to fall back on the “easy way out” with the
> >> routine of “barcode first and ask questions later” -- but instead ask
> >> yourself -- if I were a [put taxon name here] how would I find a
> >> mate? and look for other morphological character sets -- and use
> >> barcodes as just another character set and not THE only one. I still
> >> am curious about biology and taxa and how things work in real life.
> Unfortunately, DNA sequences do not tell me that.
> >> Maybe we have lost the luxury of time to learn more about our taxa
> >> and have lost sight of that while keeping our eyes on the prize of
> >> describing as many things as fast as we can. I hope we taxonomists do
> >> not devolve into pipette jockeys and number crunchers and lose the
> >> curiosity of how things work in real life.
> >>
> >> Neal
> >>
> >> Neal L. Evenhuis
> >> Senior Curator of Entomology
> >> Bishop Museum
> >> Honolulu, Hawaii  96817-2704, USA
> >>
> >> On Stardate 8/30/23, 9:49 AM, "Taxacom"
> >> <taxacom-bounces at lists.ku.edu <mailto:taxacom-bounces at lists.ku.edu> >
> >> wrote:
> >>
> >> I think one thing that seems to be missed in the discussion is that,
> >> despite lacking a morphological diagnosis in words, the species
> >> presented in the Mesochorus paper do provide a substantial amount of
> >> biological information (identity of host parasitoid, caterpillar host
> >> of primary host parasitoid, host plant, plant community in which it
> >> is found) plus multiple photos showing the morphology, in addition to
> >> the barcodes and collection data. It could be argued that this
> >> combination of information is actually more extensive than the
> >> earlier descriptions in the group, and more useful to ecologists and
> >> other biologists. This is not to say it is the perfect solution, nor
> >> is it the way I typically work, but it is not quite so minimalist as it may be
> portrayed as being.
> >>
> >> Jim  Sent from my iPhone
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> >> Nurturing nuance while assailing ambiguity and admiring alliteration
> >> for about 36 years, 1987-2023.
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> >>
> >> Nurturing nuance while assailing ambiguity and admiring alliteration
> >> for about 36 years, 1987-2023.
> > _______________________________________________
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> >
> > Nurturing nuance while assailing ambiguity and admiring alliteration for
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> 
> --
> __________________________________________________
> 
> Michael A. Ivie, Ph.D., F.R.E.S.
> 
> NOTE: two addresses with different Zip Codes depending on carriers
> 
> US Post Office Address:
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> 
> UPS, FedEx, DHL Address:
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> 
> 
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Nurturing nuance while assailing ambiguity and admiring alliteration for about 36 years, 1987-2023.

-- 

Scott Thomson

Centro de Estudos dos Quelônios da Amazônia - CEQUA
Petrópolis, Manaus
State of Amazonas, 69055-010
Brasil

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