[Taxacom] Fungal barcodes required for species descriptions

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Fri Oct 9 16:08:12 CDT 2015


Given that sequencing isn't necessary if the correct spore bearing structures are present, it seems to be an unjustified burden on the describer to have to do unnecessary sequencing. What we want is a way to dispose of, or at least deal with, names based on inadequate descriptions. There are various possible solutions. One is just to not get so obsessed with the idea that every valid name has to link to an identifiable species. In zoology, one just has to treat such a name as a nomen dubium, and it can be quietly forgotten about (relegated to an appendix listing such nomina dubia).

Stephen

--------------------------------------------
On Sat, 10/10/15, Bevan Weir <WeirB at landcareresearch.co.nz> wrote:

 Subject: [Taxacom]  Fungal barcodes required for species descriptions
 To: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
 Received: Saturday, 10 October, 2015, 9:51 AM
 
 Starting a new thread, since this is
 getting pretty off topic.
 
 This is not (yet) a formal proposal, but mandatory barcodes
 if possible is something I would support for fungi. The
 reason is that many are impossible to distinguish without
 DNA sequences, especially plant pathogens, and for others
 they can be difficult to correctly identify without the
 correct spore bearing structures (that may not be
 fruiting).
 In essence this makes them useless to the end user. Before
 we had mandatory name registration it was even worse as if
 it was published in an obscure journal it would be difficult
 to know if the taxon even existed.
 
 For a better explanation see this talk by Pedro Crous:
 https://www.youtube.com/watch?v=kkzth6h-_Wk
 The most relevant bit is from 9:08 in if you don’t want to
 watch the lot. He considers fungi without sequences
 “incomplete species hypotheses”.
 
 The problem is that not everyone can afford to sequence. We
 don’t want to stop those people from describing new taxa.
 Pedro in his talk says that he will sequence any culture
 submitted to his collection for free and give the sequence
 back to the author.
 Here in NZ I am happy to do the same for any
 culture/specimen from New Zealand if someone can’t afford
 it.
 
 Cheers,
 Bevan
 
 BEVAN WEIR | SCIENTIST / ICMP CURATOR
 MYCOLOGY & BACTERIOLOGY SYSTEMATICS
 LANDCARE RESEARCH MANAAKI WHENUA
 DDI: +64 9 574 4115 | W: www.landcareresearch.co.nz
 PUBLICATIONS: www.rhizobia.co.nz/papers
 
 
 
 Bevan,
 
 Fungi are somewhat of a special case, given that if it ain't
 fruiting, then there's nothing much to describe without
 looking at DNA. So, there might be an advantage in making
 use of DNA for fungi. But why make it mandatory? That seems
 a tad heavy handed of whoever is pushing for this. Is there
 a pressing need to describe new fungi without waiting for
 fruiting material?
 
 Cheers, Stephen
 
 
 
 From: John Grehan [mailto:calabar.john at gmail.com]
 Sent: Friday, 9 October 2015 4:22 p.m.
 To: Bevan Weir
 Cc: Stephen Thorpe; Taxacom
 Subject: Re: [Taxacom] manuscript name question
 
 OK, you've got me already. Since you bring this up, what is
 your opinion and on what basis?
 
 John Grehan
 
 On Thu, Oct 8, 2015 at 11:06 PM, Bevan Weir <WeirB at landcareresearch.co.nz>
 wrote:
 I can't wait for Taxacom to explode when we get the
 requirement for DNA barcodes to be part of a valid species
 description for fungi.
 Perhaps half of currently described fungal species have no
 DNA data.
 
 Bevan
 
 
 -----Original Message-----
 From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
 On Behalf Of John Grehan
 Sent: Friday, 9 October 2015 3:57 p.m.
 To: Stephen Thorpe
 Cc: Taxacom
 Subject: Re: [Taxacom] manuscript name question
 
 Stephen,
 
 I don't think anyone is guilty of 'knee jerk' reactions. I
 think everyone, including yourself, is genuinely trying to
 articulate their various points of view as best or as
 precisely as they can. I have found all points of view, and
 responses, of interest.
 
 John Grehan
 
 On Thu, Oct 8, 2015 at 10:43 PM, Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
 wrote:
 
 > I really hate the way that distinct issues are being
 conflated on this
 > matter! The essence of the matter has nothing to do
 with photographs,
 > but with preservation of primary types. Can you
 describe a new species
 > without preservation of the (designated) primary type?
 Whether you
 > include a photo, or a drawing, or just provide written
 description is
 > not the issue. But there are two distinct scenarios:
 (1) your
 > description is based on examination of the primary
 type, which is then
 > discarded; or (2) you only know the primary type by way
 of a photo. In
 > this case (the fly), we have scenario (2). Sure, just
 having a photo
 > is nowhere near as good as having a whole specimen, but
 then having a
 > fossil is nowhere near as good as having a freshly
 killed specimen.
 > So, given a choice, one would prefer to have a freshly
 killed specimen, and one would prefer to preserve it
 indefinitely.
 > But, if you only have a fossil, or only have a photo,
 and you have at
 > most only a slim  chance of ever getting hold of a
 freshly killed
 > specimen, then it makes sense to make the most of what
 one does have.
 > Hence, species are described based on fossil
 impressions in rock,
 > cloudy amber inclusions, etc. So why not a photograph
 of a living
 > specimen? Whether Marshall & Evenhuis should have
 waited to see if new
 > material could be obtained is a moot point. There may
 not have been
 > any real need to describe this fly now, except to feed
 the fires of
 > Pensoft's desire for publicity. But these are all
 distinct issues to
 > be weighed up and thought about. Knee jerk reactions
 against
 > describing new species from photos really isn't
 helpful.
 >
 > Stephen
 >
 > --------------------------------------------
 > On Fri, 9/10/15, JF Mate <aphodiinaemate at gmail.com>
 wrote:
 >
 >  Subject: Re: [Taxacom] manuscript name question
 >  To: "Taxacom" <taxacom at mailman.nhm.ku.edu>
 >  Received: Friday, 9 October, 2015, 3:00 PM
 >
 >  Dean:
 >
 >  “There seems to be a negative reaction to the
 term "dead  bodies" for
 > animals  that are preserved in museum collection.
 I find that
 > curious.”
 >
 >  I have never seen this term used in journals,
 which makes me  suspect
 > it was used as click-bait. It is not a direct way to
 explain  things
 > to  “non-native” speakers, it is a catchy
 title plonked  there in the
 > hopes  that BBC or CNN will report the paper (as
 they sometimes  do).
 > But  publicity in a matter like this could have
 unintended
 > consequences. It  is already hard enough
 collecting “dead bodies”,
 > imagine  if you give  them (PETA, WWF, any
 bureaucratic body,...) ammo
 > through  scientific  legitimacy.
 >
 >  “As to whether it's worth putting a name to
 a  distinctively new
 > species,  isn't that rather the whole point of
 nomenclature?”
 >
 >  You misunderstand me Dean. The point I am trying
 to make is  that, if
 > a  particular species is doomed, keeping a couple
 of pictures  is
 > pretty  much useless other than serving to name
 something.
 >  Nomenclature is
 >  important because it is the bedrock of something
 (biology,  ecology,
 > etc). Otherwise it is just a rock, a list of names (and
 you  wouldn´t
 > even be certain that the list is correct nor have the
 means  to
 > check).
 >  And physcial specimena or, lacking that, tissue
 samples,  contain the
 > information that gives “value” to the name.
 >
 >  With a physical specimen I can not only verify
 the original
 > hypothesis  in the future, but also access a large
 amount of
 > information  pertaining to the species itself
 (biology, phylogenetics,
 > feeding,  etc). With a photograph I only have
 pixels, and they will be
 > the same  pixels forever.Its value as a store of
 information
 > diminishes with the  passage of time whereas
 physical specimens become
 > more  valuable (DNA,
 >  X- ray microtomography are just two recent
 examples I can  think of).
 >  Photographs should be, IMO, a last resort when
 faced with no  other
 > choice, and to me this fly isn´t such a case. Fast
 and  loose is a
 > slippery slope to aliens and Nessie.
 >
 >  Best
 >
 >  Jason
 >  _______________________________________________
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 at:
 > http://taxacom.markmail.org
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 >
 > Celebrating 28 years of Taxacom in 2015.
 >
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