[Taxacom] describing species based on DNA sequences alone

Scott Thomson scott.thomson321 at gmail.com
Mon Jan 16 07:33:41 CST 2017


Personally I am against the naming of species without a morphological
analysis including a differential diagnosis, preferably one that actually
works.

Sorry, I have to repeat myself – naming species without a morphological
analysis IS NOT THE SAME as actually performing such an analysis and NOT
FINDING any useful features that can be included in an actually working
differential diagnosis.

No it is not, but my argument is that at this point you need to keep
looking.


I will concede that the fact I work with fossils as well as living taxa
probably biases me somewhat as a morphological analysis is the only thing
that permits me to include the fossils in the phylogeny, and I do not
consider phylogenies particularly useful, or accurate, without the fossils.

Unfortunately some animals just do not have decent fossil record

No they do not and this is particularly true of soft bodied species. Hence
I acknowledged my bias here as I work with vertebrates.


I do not think it should be done and although I know of plenty of cases
where cryptic species were initially identified using molecular evidence
including some I later described, once the morphology was done including
detailed internal morphology that these so called cryptics were actually
not so cryptic.

Exactly what I said before – if it takes a dedicated study that can be
performed only by specialist working on the group to reveal very obscure
morphological differences, such differences cannot provide a differential
diagnosis that actually works. In this case, why not use a working
molecular differential diagnosis?

Morphological characters used in a phylogenetic analysis and can also be
used in the differential diagnosis can be obscure and be as specialised as
running gels. This is not the same as keying species out for the purposes
of a field key. I write keys to species groups also, I do not necessarily
use the same characters in those that were used to describe the species.
The biggest problem I see in cryptic species is that people are trying to
use established characters to diagnose the taxa, when you have a new
species you may need to find new characters. The highly specialised
diagnosis using skeletal characters, for example, cannot be seen on a
living specimen yet can form a diagnosis. Detailed internal anatomy is no
more specialised than a molecular analysis. Both are tools for the purpose
of describing taxa, both should be used where possible.

I see plenty of recent descriptions where it is obvious that the
description is based on a molecular only study. They have a morphological
differential diagnosis because with many vertebrates its unlikely a name
will be accepted without one, however, this morphological diagnosis is
based only on poor quality characters they get from literature review that
the authors clearly do not understand. The diagnosis also clearly does not
work, of course in nomenclature it does not have to work, just has to be
there. ie "purports to diagnose the taxon". But if you actually look at
those taxa the diagnostic characters, that do work, are there.

Cheers, Scott

On Mon, Jan 16, 2017 at 7:44 AM, Redhead, Scott <Scott.Redhead at agr.gc.ca>
wrote:

> Actually, the type of Rhizopogon kretserae is a collection of dried
> mycorrhizal root tips , in this one case, not the culture.
>
> Scott
>
>
> Scott A. Redhead, Ph.D.
> Curator - National Mycological Herbarium / DAOM
> Ottawa Research and Development Centre
> Science and Technology Branch, Agriculture and Agri-Food Canada
> 960 Carling Ave., William Saunders Building (Bldg. 49)
> Ottawa, Ontario  K1A 0C6  CANADA
>
> scott.redhead at agr.gc.ca
> Telephone 1+613+759-1384
> Facsimile 1+613+759-1599
>
> http://www.agr.gc.ca/eng/science-and-innovation/research-centres/ontario/
> ottawa-research-and-development-centre/canadian-national-mycological-
> herbarium-daom/?id=1436530824740
>
>
> Government of Canada | Gouvernement du Canada
>
>
>
>
>
>
> -----Original Message-----
> From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of
> Urmas Kõljalg
> Sent: January-16-17 2:38 AM
> To: Adolf Ceska
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] describing species based on DNA sequences alone
>
> Rhizopogon kretserae has actually holotype which is fixed specimen of
> living culture. Living culture itself is deposited in DAOM. Code allows to
> describe fungi based on living cultures.
>
> Urmas Kõljalg
>
> _______________
> Prof. Urmas Kõljalg
> 40 Lai Str.
> Institute of Ecology and Earth Sciences
> University of Tartu
> EE-51005 Tartu
> Estonia
>
> UNITE - A molecular database for the identification of fungi
> http://unite.ut.ee
>
>
>
> On 16.01.2017, at 6:00, Adolf Ceska <aceska at telus.net> wrote:
>
> > Here is one example I came across: this mycorrhizal fungus was described
> from the root tips DNA. No sporocarps seen.
> >
> > Grubisha, Lisa C., Nicholas J. Dowie, Steven L. Miller, Christina
> Hazard, Steven M. Trowbridge, Thomas R. Horton, and Matthew R. Klooster.
> "Rhizopogon kretzerae sp. nov.: the rare fungal symbiont in the tripartite
> system with Pterospora andromedea and Pinus strobus." Botany 92, no. 7
> (2014): 527-534.
> >
> > Adolf Ceska, Victoria, BC, Canada
> >
> >
> > ---
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> > https://www.avast.com/antivirus
> >
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-- 
Scott Thomson
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