[Taxacom] FW: [iczn-list] GENERAL CALL TO BATTLE

Paul Kirk P.Kirk at kew.org
Sun Feb 21 05:47:32 CST 2021 

I initially resisted the temptation to contribute to this 'discussion' but hey, it's the weekend and the temperature here in SE England is heading for 15C (quite a contrast with that in Texas) - but I digress.

In the Fungi (not plants ... honorary animals for those who use the phrase 'animals and plants' for life on the third rock from the sun), almost 100% of new species are recognized based on analysis of DNA data; mainly ITS but regularly three or more gene segments. The cladogram provides the 'diagnosis' but almost always comprehensive but not diagnostic traditional descriptions are laboriously constructed as are visually appealing full colour illustrations. The illustrations take the form of ... here is a spherical spore of new species 1, and here is a spherical spore of new species 2, and here is a spherical to slightly ellipsoid to spore of new species 3 (I think you get the picture).

The Fungi (and those organisms traditionally treated as Fungi - members of the Amoebozoa and achlorophyllous seaweeds ... and organism treated as animals which some mycologists think belong to the fungi [microsporidia, rozellids, aphelids]) are likely 80% un-named (i.e. we only know 10-20% of the species), this in the context of for each taxonomic mycologist there are likely 100 taxonomic botanists. All this in the context of 1,000 acres of lost Amazonian rainforest (and the associated unique un-named biota) in the time it has taken me to type this email.

Nice weekend to all 😊

Paul M. Kirk (without my tricorder)
(Index Fungorum curator)

-----Original Message-----
From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> On Behalf Of Jared Bernard via Taxacom
Sent: 21 February 2021 01:41
To: Taxacom <taxacom at mailman.nhm.ku.edu>
Subject: Re: [Taxacom] [iczn-list] GENERAL CALL TO BATTLE

 If we don't write descriptions, how would we produce diagnostic keys?
While I trust Sharkey et al. know what they're doing with braconids, I can't help but think they should still provide a diagnostic key to others, both in and outside the field, such as conservation workers in Costa Rica who might need to sort through wasp collections.

Obviously a primary aim of taxonomy is to use some evidence to say a specimen represents a distinct species, but we should also provide diagnostic tools to non-taxonomists so they can identify their samples. The most accessible tool would be user-friendly keys, because aside from the pitfalls of barcodes, we can't assume people have access or funds for genetics -- even if costs of sequencing are low, they probably need to be done in batches.

I definitely think accessioning genetic information along with new species descriptions is ideal -- the more genetic markers the better, seeing as they often have different rates of evolution. But, I'm skeptical of using genetics, especially barcodes, as the primary basis for determining new species. Aside from the above complaint about the responsibility of making keys, here are a few other concerns:

   - There are various sources of error, including during sequencing and
   assembly.
   - Determining whether a barcode matches a taxon in GenBank can be
   misleading, as I suspect there are loads of misidentified things on GenBank
   (e.g., Pentinsaari et al. 2020, doi: 10.1371/journal.pone.0231814).
   - Different clades have different rates of evolution or amounts of
   conspecific variation, so judging how much sequence divergence should
   separate species would be difficult. On this last point, some of you have
   noted that a species' name is attached to a holotype, not a species. When
   discussing this thread with my colleague, he told me that using a COI
   barcode isn't worse than using a holotype. This is a fair point. However,
   even if a standardized percentage of divergence could delimit species, 3%
   divergence of a barcode is likely not the same as 3% divergence of a
   morphological trait, which is usually the product of a network of
   interacting genes (probably under selective pressure), including epistasis
   and pleiotropy. (As a point of interest, Russell Lande suggested in 1980
   that sister species should be separated by at least 4–5 "phenotypic
   standard deviations" [http://www.jstor.org/stable/2460440], although this
   doesn't account for cryptic species.) Nevertheless, I've wondered lately
   whether assigning a series of syntypes would be better to account for
   variation (Art. 72.1.2).

Jared

On Mon, Feb 15, 2021 at 5:23 PM JF Mate via Taxacom < taxacom at mailman.nhm.ku.edu> wrote:

> I like this diagnosing scale! I can’t decide where I lie on it 
> exactly, but I guess I am on number 3 because I suspect that there are 
> limitations with BCs, like with any other source of data, but I think 
> that once everybody has access to the technology (or at least in the 
> same ballpark as access to a microscope) the extent of the mismatch will become clearer.
>
> As for the authors, they appear at face value to be solidly on number 
> five, but as Stephen has mentioned, they use morphology when BCs stop 
> working and they extensively use other phenotypic data as well so they 
> are probably closer to four in spite of the title.
>
> Stephen, I don’t think that pointing out the parallels between 
> genotype descriptions/data and phenotypic ones means being on one side or the other.
> If anything, it shows that BC-only descriptions are likely to suffer 
> the same methodological biases inherent in humans.
>
>
> Best
>
>
> Jason
>
> On Tue, 16 Feb 2021 at 12:40, Stephen Thorpe via Taxacom < 
> taxacom at mailman.nhm.ku.edu> wrote:
>
> >  Rich,You are clearly advocating for DNA-only descriptions (with 
> > some reservations yes, but ultimately in favour). Good for you, but 
> > I think it is a bad idea. DNA sequences and morphology are NOT 
> > equivalent for the purposes of taxonomy. Theoretically, they may be, 
> > if we were to start de novo, but it would obviously be preposterous 
> > to throw out more than 2 centuries of accumulated taxonomic 
> > knowledge. Because morphology has been of primary importance up to 
> > now, it simply must remain that way, with sequencing playing a 
> > supporting role only. As I said, molecular
> taxonomists
> > are inevitably going to have to ignore many existing species names 
> > which lack associated sequences.Cheers, Stephen
> >     On Tuesday, 16 February 2021, 02:22:07 pm NZDT, Richard Pyle via 
> > Taxacom <taxacom at mailman.nhm.ku.edu> wrote:
> >
> >  Hi Ross,
> >
> >
> >
> > > - Entire Genomic Sequencing versus genome sample sequencing
> >
> > > - Mitochondrial DNA considerations v Genomic DNA
> >
> > > - Homogenized DNA from several individuals, as mentioned elsewhere
> >
> > > here, or a Type series ie distinct unique individual sequences not
> > amalgamated (which is nonsensical IMO)
> >
> > > - The need for any DNA based description and nomen to be
> >
> > > linked to a secure Type specimen and not some amorphous and
> >
> > > merely asserted (untestable) Base Sequence code repository.
> >
> >
> >
> > Would you agree that all four of these have exactly the same 
> > equivalents for morphologically-based descriptions?  To wit:
> >
> >
> >
> > - Describing every single morphological character versus a subset of 
> > morphological characters
> >
> > - Osteological considerations vs. coloration vs. morphometrics vs.
> > meristics (etc.)
> >
> > - Summaries of morphological characters from several individuals to 
> > form
> a
> > consensus diagnosis
> >
> > - The need for any morphology-based description and nomen to be 
> > linked to a secure Type specimen and not some amorphous and merely 
> > asserted
> > (untestable) set of morphological characters
> >
> >
> >
> > If you assert that such parallels do not exist or are false
> equivalencies,
> > I’d like to understand why you think so.
> >
> >
> >
> > 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
> >
> >  <http://hbs.bishopmuseum.org/staff/pylerichard.html>
> > 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: Ross Wellington <rwrossco at gmail.com>
> > Sent: Monday, February 15, 2021 1:50 PM
> > To: Richard Pyle <deepreef at bishopmuseum.org>
> > Cc: Taxacom <taxacom at mailman.nhm.ku.edu>; iczn-list at afriherp.org
> > Subject: Re: [iczn-list] [Taxacom] GENERAL CALL TO BATTLE
> >
> >
> >
> > There are a huge number of issues and expansions on the discussion 
> > points raised here.
> >
> >
> >
> >
> >
> > Type Specimen based species nomenclature is and should remain 
> > fundamental to the basis on which a species is defined and named 
> > IMO, DNA characterization or not.
> >
> >
> >
> > But even this has its problems as already there have been examples 
> > of shenanigans with institutional Types being fiddled with and/or 
> > replaced
> > (Neotype) on sometimes spurious grounds or are arguably invalidly
> assigned
> > (inconsistent with original description or inappropriate location). 
> > So photographic repositories of Types (existing and new) on which 
> > nomen are based should be mandatory or at least a priority.
> >
> >
> >
> > But that last issue aside the DNA issue immediately at hand must 
> > also
> deal
> > with:
> >
> >
> >
> > - Entire Genomic Sequencing versus genome sample sequencing
> >
> > - Mitochondrial DNA considerations v Genomic DNA
> >
> > - Homogenized DNA from several individuals, as mentioned elsewhere 
> > here, or a Type series ie distinct unique individual sequences not 
> > amalgamated (which is nonsensical IMO)
> >
> > - The need for any DNA based description and nomen to be linked to a 
> > secure Type specimen and not some amorphous and merely asserted
> > (untestable) Base Sequence code repository.
> >
> >
> >
> > The list goes on and on
> >
> >
> >
> > Regards
> >
> >
> >
> > Ross Wellington
> >
> > _______________________________________________
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> 1987-2021.
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> >
> > Nurturing nuance while assaulting ambiguity for about 34 years,
> 1987-2021.
> >
> _______________________________________________
> Taxacom Mailing List
>
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> For list information; to subscribe or unsubscribe, visit:
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>
> Nurturing nuance while assaulting ambiguity for about 34 years, 1987-2021.
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