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

Sun Feb 21 12:13:07 CST 2021

With respect to Paul's comment on the situation in Fungi, I believe
comparable things are happening in Bacteria (I mean Prokaryotes) as well...
things looks pretty similar to everything else, but the DNA tells us it is
new. (Forgive me if I tread too lightly on this subject). At least they
have to deposit a type culture for the name to be valid (I think)...

Cheers - Tony

Tony Rees, New South Wales, Australia
https://about.me/TonyRees
www.irmng.org

On Sun, 21 Feb 2021 at 22:47, Paul Kirk via Taxacom <
taxacom at mailman.nhm.ku.edu> wrote:

> 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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