[Taxacom] very nice opinion article in today's Zootaxa

John Shuey jshuey at TNC.ORG
Mon Sep 19 10:23:33 CDT 2011


>>Burns, J. M., D. H. Janzen, M. Hajibabaei, W. Hallwachs and P. D. N. 
>>Hebert 2007. DNA barcodes of closely related (but morphologically 
>>and ecologically distinct) species of skipper butterflies 
>>(Hesperiidae) can differ by only one to three nucleotides. Journal 
>>of the Lepidopterists' Society, 61:138-153.

>If that title is taken at face value, would this not invalidate the 
>premise that patterns of sequence divergences on a tree can be used 
>to recognize species boundaries? The implication of the parenthetical 
>phrase above is that morphology and ecology MUST be given primary 
>credence, which runs contrary to what many seem to be preaching 
>and/or practicing; that is, if it is admitted that barcodes alone are 
>insufficient for the task of species delimitation, then what is the 
>justification for studying and promoting barcodes alone? If good 
>species can differ by one base pair, then (a) how could one *ever* 
>know whether a single base pair difference is or is not indicative of 
>a species-level difference without morphology to back it up, and (b) 
>can we not therefore assume that there must be many cases where 
>species have ZERO base pair differences (i.e., that barcodes are not 
>unique, as claimed)? ....


>Or am I missing something here?
______________________________________________________

 Yes - perhaps reading beyond the title would help....   Here's the link
to the pdf.

http://peabody.research.yale.edu/jls/pdfs/2000s/2007/2007(3)137-Burns.pd
f

And if you can't be bothered to do that - here are the last two
paragraphs of the paper..., 

"Close examination of the barcode nucleotides showed that the two
species of Polyctor consistently differ at three nucleotide positions
(610, 616, and 625), and the two species of Neoxeniades, at one (115).
Similarly, the two species of Cobalus differ in one nucleotide (at
position 181), except for two females of C. virbius (04- SRNP-21798 and
06-SRNP-22664) whose "diagnostic" nucleotide is the same as that of the
C. fidicula specimens. The two females of C. virbius whose barcodes
match those of C. fidicula are not the two females of C. virbius (noted
above, under "Morphologic differences" [with voucher codes 92-SRNP-340
and 06-
SRNP-13344]) whose hindwing facies approaches that of C. fidicula
females. Because, in each pair of skipper species, the interspecific
nucleotide differences are very few (compared with many species of
skippers previously examined), full-length, high-quality barcode
sequences (~650 bp) are critical for distinguishing the species in each
pair. Of course, characters of this kind-like many others-may vary
geographically."
"The levels at which these species are distinguished is so low that, in
many other circumstances, their differences could easily qualify as
nothing more than individual variation. It follows that the designation
of some percentage or degree of divergence as a point below which
individuals should be considered conspecific is unrealistic (even though
many taxonomists have done so, in various contexts, for a great many
years). Speciation is not tidy. "


The entire point of the paper addresses the primary criticism people
throw at Herbert, Janzen and Burns - that they are somehow facilitating
the mindless descriptions of new species based on barcodes (again -
ironically that would be Brower doing that).  Indeed it seems that the
crux of criticism in the Brower paper is effectively eviscerated by the
thoughtful analysis and discussion in the paper. But of course, if you
are setting up a straw man, it's easier to knock it down if you hide its
legs from the viewing audience - no?

To quote Brower - "My role here is simply that of a responsible citizen
who, confronted by a sort of taxonomic oil slick, has taken it upon
himself to clean it up."  I have to laugh...  how can he even tell the
oil slick from the oozy sheen that must constantly surround him...?



Please consider the environment before printing this email 

John A Shuey, Ph.D.
Director of Conservation Science

jshuey at tnc.org
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-- 

Doug Yanega        Dept. of Entomology         Entomology Research
Museum
Univ. of California, Riverside, CA 92521-0314        skype: dyanega
phone: (951) 827-4315 (standard disclaimer: opinions are mine, not
UCR's)
              http://cache.ucr.edu/~heraty/yanega.html
   "There are some enterprises in which a careful disorderliness
         is the true method" - Herman Melville, Moby Dick, Chap. 82

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