[Taxacom] Fungal barcodes required for species descriptions

Bevan Weir WeirB at landcareresearch.co.nz
Fri Oct 9 15:51:31 CDT 2015


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
>  _______________________________________________
>  Taxacom Mailing List
>  Taxacom at mailman.nhm.ku.edu
>  http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
>  The Taxacom Archive back to 1992 may be searched at:
> http://taxacom.markmail.org
>
>  Celebrating 28 years of Taxacom in 2015.
>
> _______________________________________________
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> The Taxacom Archive back to 1992 may be searched at:
> http://taxacom.markmail.org
>
> Celebrating 28 years of Taxacom in 2015.
>
_______________________________________________
Taxacom Mailing List
Taxacom at mailman.nhm.ku.edu
http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
The Taxacom Archive back to 1992 may be searched at: http://taxacom.markmail.org

Celebrating 28 years of Taxacom in 2015.

________________________________
Please consider the environment before printing this email
Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails.
The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz


________________________________

Please consider the environment before printing this email
Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails.
The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz


More information about the Taxacom mailing list