Barcoding: sample size
SDMANNING at ASUB.EDU
Fri Feb 7 13:16:10 CST 2003
At 04:24 PM 2/6/03 +0000, jason mate wrote:
>Richard Zander wrote:
>>>that what taxonomists do? Identify organisms?
>>>I think taxonomists do a lot more. As to money, we taxonomists have 250
>>>years of the Linnaean endeavor behind us and have generated or mediated
>>>great economic gains for the human race.
>Technically yes, that is all that the word taxonomy means. As for the value
>of this work, currently it is in the eye of the beholder.
>>>_Everybody_ ducks my concerns about the statistical basis behind
>>>of phylogenetic estimation.
>The aforementoined problems with phylogenetics also affect morphological
>and/or any other source of data currently in use. Morphology is by no means
>superior or inferior to DNA: each has their place.
>Steve Manning wrote:
>>Maybe the codes need to be modified to require a sample
>>of ten or more specimens, as randomly selected and hopefully as
>>ecologically and geographically diverse as possible, to qualify as the
>>"type" of a taxon for future species descriptions, unless fewer than ten
>>specimens are available. I acknowledge that it probably won't be easy to
>>require broadening the type specimen concept to the point of assuring its
>>statistical validity, but nothing ventured nothing gained.
>I can think of many reasons why this is a bad idea, but maybe the easiest is
>"cryptic species". There is a reason why taxonomy/systematics has moved
>away from the type series to the holotype. Granted, variation is not
>embodied in the type, but hopefully the researcher had the good sense of
>looking at more
>than one specimen when publishing the description.
>>If we ever do get to the point of using Bar Codes or other means of
>>categorizing DNA diversity, I hope it can be made essentially mandatory
>>that a sample of a statistically valid number of specimens (10?) (100?) and
>>gene sequences per specimen (10?) (100?) be included in the DNA analysis in
>>order for the analysis to be recognized as valid.
>Again, multiple specimens of a species, but how do you know that they are
>the same species?
I would not know they were the same species, but probably would have relied
on prior identifications by others. I would hope, however, that if my
sample size were large enough, any major differences between specimens
would be detected (one of the main reasons for large sample sizes), which
in turn might or might not suggest adjustment of the species'
circumscription. Maybe this would even point the way to some of those
> And if you do, why do several of them?
Because of the normal genetic variation within species which is an
important part of DNA diversity (as well as the reason in the preceding
paragraph). If it turned out that a certain gene sequence was identical in
100 specimens of a species, reporting this would be more convincing than a
report that one specimen had a particular sequence with no reference to
other members of the species.
>>If the above were implemented, it ought to be able to generate more
>>funding for both morphological and molecular taxonomists!
>Yes, due to the overwhelming redundancy.
You could call this redundant info. but it seems to me that that would be
known only after the data collection, not before. Obviously it would like
anything else be a matter of prioritization as to how to spend research
time, money and equipment, but I would be much more comfortable with being
overthorough than the reverse until a large amount of data had been
gathered about the particular group I was working with. This of course
applies to morphological as well as DNA work.
>Jason F. Mate
>4th Fl Entomology
>The Natural History Museum
>Cromwell Road SW75BD
>>>Richard H. Zander
>>>Missouri Botanical Garden
>>>PO Box 299
>>>St. Louis, MO 63166-0299
>>>richard.zander at mobot.org <mailto:richard.zander at mobot.org>
>>>From: Andrew Mitchell [mailto:MitchellA at NU.AC.ZA]
>>>Sent: Tuesday, February 04, 2003 9:18 AM
>>>To: TAXACOM at USOBI.ORG
>>>Subject: Re: [TAXACOM] Barcoding (animal) life
>>>We *sample* taxa not only
>>>because of limits of time and money but because of the law of
>>>diminishing returns. We want to be able to reliably identify organisms
>>>and as an added bonus work out their evolutionary history, not count all
>>>stomata on all specimens in the herbarium just for the fun of it.
>>>Molecular and morphological/phenological/ecological etc. work can
>>Stephen D. Manning, Ph.D.
>>Professor of Biology
>>Mathematics and Science Division
>>Arkansas State University - Beebe
>>P. O. Box 1000
>>Beebe, Arkansas 72012-1000
>Chat online in real time with MSN Messenger http://messenger.msn.co.uk
Stephen D. Manning, Ph.D.
Professor of Biology
Mathematics and Science Division
Arkansas State University - Beebe
P. O. Box 1000
Beebe, Arkansas 72012-1000
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