Barcoding (animal) life

John Noyes jsn at NHM.AC.UK
Tue Feb 4 18:13:26 CST 2003


Andrew,

As you seem to be the person contributing to this discussion who is the
most in favour of DNA bar-coding can you please explain to us (in simple
terms) how sampling the biota using DNA 'bar-coding' methods could be done?
If you were to be given three separate pots containing samples of insects
collected in one month by Malaise trap in say South Africa, Kenya and
Nigeria could you tell us using DNA barcoding only, and without the help of
any taxonomic specialists, how many species were in which and what species
were common between the two samples? Let's say that each sample may contain
upwards of 5000 insects and 500 species. How would you separate them into
species and how would you compare the samples? I would not expect the
species to be identified (most would probably be undescribed anyway). If
this can be done then I and others might be converted. Can you do it now
realistically? If so will you do it, or someone else out there. It should
not be very expensive and it could make a very nice grant application. A
major problem would be that it may not be possible for taxonomists to check
the results because more than half the specimens will have been completely
destroyed in  the course of DNA extraction (most individuals would be so
small that the whole animal would have to be used). My point is that if you
cannot do this then why bother with 'bar-coding' in the first place. All
you are doing is sampling the genetic diversity without any idea of taxon
diversity, faunistic similarities, overlaps, endangered species, etc. etc.

Believe it or not I am pretty open minded on this.

John

At 05:18 PM 2/4/2003 +0200, Andrew Mitchell wrote:
>Richard Zander wrote:
>>Great statement by A. Mitchell . . . we needed a clear political
>exposition
>>on the subject.
>Well you know what they say about sarcasm as a form of wit!
>
>>Note the figure mentioned of 1 billion dollars.
>Do you think the cost is excessive? The human genome project is
>estimated to have cost $3 billion over 15 years. Why not $1 billion over
>20 years as suggested. This is money that might otherwise be spent on
>tax cuts for the rich or something like that (I assume that few
>taxacomers fall into that category).
>
>>This is not for sequencing
>>all the genes of all taxa, but for sampling.
>Sequencing all the genes of all the taxa? THAT would indeed be a waste
>of time and money. Why determine a few billion nucleotides from each
>species when a few thousand will do the job? 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.
>
>>Samples don't include all the
>>genetic info we need and don't include important associated
>phenological,
>>ecological, biogeographical info.
>As I stated, how long should we wait for people to gather all that
>other info while biodiversity is disappering at an unprecedented rate?
>And why shouldn't we proceed with DNA sampling in the mean time?
>Molecular and morphological/phenological/ecological etc. work can
>proceed simultaneously.
>
>>What (selected) small samples do (and this is indeed marvelous!) is
>>approximately match our general intuitive ideas of evolutionary
>>relationships. But that's all.
>On the contrary, I find that "(selected) small samples" more often than
>not yield a few surprises, leading to the collection of further data
>which either corroborate the initial novel finding or simply underscore
>the importance of taxon sampling density (which is why at least $1
>billion would be needed).
>
>>Demonstrable reliability is lacking for DNA
>>results in most cases for resolving actual problems, such as (1)
>certain
>>questions of relationship not soluble with morphology and (2)
>selection of
>>one solution when relationships implied by morphology and DNA, or by
>>different genes, conflict.
>>
>>This is in addition to the usual horrors of sample error (wrong
>sequences),
>>dubious alignment, model choice when there are reasonable
>alternatives, and
>>differential gene histories, all of which can reduce the chance of
>being
>>correct.
>
>Your points about taxon sampling density, horizontal transfer, etc. are
>well taken and have to be considered in the planning stages of a
>"barcoding" project, but they do not in themselves constitute reasons
>for not starting such a venture. Nobody pretends that DNA data is
>perfect. I hope you wouldn't pretend that morphological data is perfect.
>However, your dismissal of DNA data is cavalier. Sure there are some
>poor molecular studies in the published literature (as indeed there are
>bad morphological studies) but many are preliminary studies that have
>gone on to produce very robust phylogenies once more data has been
>gathered. Those "progress report" papers are necessary to assess
>progress, generate continued funding if appropriate, and they provide
>useful heuristics for further research of both molecular and
>morphological persuasions.
>
>>Our main problem is that molecular analysis remains a crap shoot. Take
>any
>> <deleted>
>
>Yaaaaawn... as I said previously, I won't be drawn into an outdated
>line of argument that polarizes molecules and morphology (4 legs good, 2
>legs bad!).
>
>Andrew
>
>------------------------------------------------------------------------
>Andrew Mitchell
>Senior Lecturer, Molecular Phylogenetics
>School of Molecular and Cellular Biosciences
>University of Natal
>Private Bag X01
>Scottsville, 3209
>SOUTH AFRICA
>
>Tel:  +27 (0)33 260 5815
>Fax: +27 (0)33 260 5462
>
>http://www.nu.ac.za/biogen/mitchell.htm
>
>

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