david.orlovich at BOTANY.OTAGO.AC.NZ
Sat Feb 1 10:57:28 CST 2003
On Saturday, February 1, 2003, at 10:20 AM, Erast Parmasto wrote:
> There are cases when DNA profile of fungal species have been
> using wrongly identified specimens, or pure cultures produced from
> specimens later lost or not easily available. Trash is accumulating in
> GenDatabanks. That is that.
yes, but it is actually measurable by phylogenetic analyses of GenBank
accessions at different taxonomic levels - I think Paul Bridge and
co-workers from the UK tried this and found something like 10 - 20% of
Genbank sequences were wrong (for various reasons). I would tend to
see this as a known evil - better the devil you know. OTOH, what we
DON'T know is an even greater volume of information about diversity
than the number of incorrect (or non-vouchered) sequences on Genbank.
So, being pragmatic, what's the harm in taking a molecular approach to
biodiversity assessment to establish a framework for more "traditional"
(bad term, I think) systematics.
In some cases molecular classification has raced ahead in front of
traditional taxonomy. Take the ectomycorrhizal fungus Pisolithus
tinctorius. It was thought to be ubiquitous, including being found in
Australia - but with molecular work, the Australian taxon has been
shown to belong to more than one clade, neither of which I think are
the same clade of northern hemisphere collections of the fungus.
Taxonomy of the Australian species has lagged behind the molecular
work, and it's much easier now to refer a specimen to a clade with an
ITS sequence than by traditional method.
I think what we have with the conflict between molecular and
traditional systematics are a whole lot of "works-in-progress" that
will eventually (hopefully) result in circumscriptions of each taxon by
morphological and molecular means (and whatever future tools might be
available). Some people are comfortable with traditional methods, some
with molecular methods, some with both - we're all working towards the
same goal (and admittedly competing for the same pool of funds).
That brings me to my main thought. Someone expressed concern that the
provocative comments of Paul Herbert would cause harm to taxonomy and
systematics because administrative bean-counters might find the idea
attractive, and channel money away from traditional systematics
research. Let's use the other half of the brain for a moment ... apart
from salary (which I'll assume for this argument is paid for by your
institution), what is the most expensive aspect of non-molecular
systematics research? I'd say field work. So, if you're going to
write a grant application to carry out traditional systematics
research, how will you get the most amount of money? Molecular
projects need fieldwork too, so you'll get fieldwork with a molecular
project, molecular projects need herbarium consumables (for vouchers
etc, so you can ask for all of those), molecular projects use a lot of
chemical consumables, so you can order all your histological stains,
mounting media etc there. The big bonus is that once you've run out of
traditional items to put into your budget, you can add molecular things
- dedicated sets of automatic pipetters, molecular biology consumables,
sequencing costs etc - and what's more, if you use them, you'll get all
this extra data that you didn't have before. You'll be able to start
asking evolutionary questions not possible with traditional
systematics. You'll be able to test your hypotheses of relationships,
you'll be able to compare genetic variation with morphological
variation ... lots of things.
So, if some people don't like the provocative comments from a "DNA is
the only things that exists"-type of scientist, then I reckon the idea
is to add value to the DNA with whatever means you have, be it
traditional or otherwise, and look for holistic approaches to
systematics, and not get into an "us and them" argument about it. If
the bean counters (and media) like the DNA aspect, then don't bite that
hand - it could feed you in the next grant round if you apply a bit of
Cheers, David Orlovich.
> Erast Parmasto
> On Fri, 31 Jan 2003, Richard Jensen wrote:
>> Correct me if I'm wrong, but don't most systematists who establish
>> DNA profiles
>> for taxa base their information on data derived from specimens that
>> they either
>> know, or assume, belong to the taxa in question?
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