[Taxacom] Fungal barcodes required for species descriptions

Fri Oct 9 16:17:22 CDT 2015

PS: Bevan, if your concern is to try to prevent people from publishing inadequate descriptions, because they are a waste of time to read, then that is a different problem. There are, and have always been, inadequate descriptions being published of all sorts of taxa. The "Hoser Problem" is one such example. But, I'm afraid that unless you are "King of the World" or "Supreme Master of the Universe", you cannot control what everyone else does or doesn't do. Besides, if you do make sequencing mandatory, I can foresee some taxonomists either faking it or providing a low grade, error ridden useless and/or contaminated sequence, either because they cannot afford good equipment, or because they just don't care.

Stephen

--------------------------------------------
On Sat, 10/10/15, Stephen Thorpe <stephen_thorpe at yahoo.co.nz> wrote:

 Subject: Re: [Taxacom]  Fungal barcodes required for species descriptions
 To: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>, "Bevan Weir" <WeirB at landcareresearch.co.nz>
 Received: Saturday, 10 October, 2015, 10:08 AM

 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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