[Taxacom] barcode of life

[Neil Snow]

The paper Dick J refers to is:

Davis, J. I., K. C. Nixon. 1992. Populations, genetic variation, and the delimitation of phylogenetic species.  Syst. Biol. 41(4): 432-435.



-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Dick Jensen
Sent: Wednesday, June 30, 2010 11:00 AM
To: Doug Yanega
Cc: TAXACOM at MAILMAN.NHM.KU.EDU
Subject: Re: [Taxacom] barcode of life



Good point, Doug.  



Davis and Nixon's phylogenetic species concept is based on diagnosability and, if I recall correctly, they included examples of genetically diagnosable entities.  The bottom line for this concept is that each group has one or more characters (states) not found in any other group.  


Cheers, 



Dick Jensen 





From: "Doug Yanega" <dyanega at ucr.edu> 
To: TAXACOM at MAILMAN.NHM.KU.EDU 
Sent: Wednesday, June 30, 2010 3:33:42 PM 
Subject: Re: [Taxacom] barcode of life 

David Schindel wrote: 

>As I feared, Taxacom is now arguing about their claims for what 
>others may have claimed for COI.  Can anyone site a single formal 
>description of a new species based only on COI differences and a 
>standard 2% threshold with no other delimiting features, or is this 
>an imaginary boogyman under the bed? 

By getting picky with the details, you avoid the general issue. By 
insisting on a FORMAL description, for example, you avoid the 
implications of published statements like this: 

"We DNA-barcoded 2,134 flies belonging to what appeared to be the 16 
most generalist of the reared tachinid morphospecies and encountered 
73 mitochondrial lineages separated by an average of 4% sequence 
divergence. These lineages are supported by collateral ecological 
information and, where tested, by independent nuclear markers (28S 
and ITS1), and we therefore view these lineages as provisional 
species." 

This is not the only paper in print discussing "provisional species" 
or "cryptic species" based on COI but not going so far as to try to 
*describe* them. It's a pretty darn subtle distinction between 
*recognizing* new species using COI and *describing* new species 
using COI. 

And by insisting that an example be based on COI only, you avoid 
cases like the Leache & Fujita paper discussed here on Taxacom just 
this month, where new gecko species *were* formally described based 
solely on genetics, but using combined mitochondrial and nuclear gene 
trees. The point remains that taxa such as these geckos would, in 
decades past, have been described as subspecies. Similarly, dodging 
the issue by saying "Well, when we go back and look, we can find 
subtle morphological characters that distinguish these taxa" is STILL 
no different from how past taxonomists have defined subspecies (I 
know of very few described subspecies that do not have diagnostic 
morphological characters), so the criticism still stands: the 
differences being seen and described in these studies is functionally 
no different from the differences that in the past were used to 
delimit subspecies, so people have simply redrawn the line as to 
where species start and stop, and that new line is genomic. This 
"redefinition" practice, where what constitutes a species can be 
delimited solely using genetics, is not imaginary. 

What I have yet to see, and would very much like TO see, is for a 
barcode proponent to explain the genetic criteria for delimiting 
subspecies. Or am I correct that they simply do not believe in 
subspecies, thereby - by default - leading to the conclusion that all 
genetically diagnosable taxa have to be recognized as species? 

Sincerely, 
-- 

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 

_______________________________________________ 

Taxacom Mailing List 
Taxacom at mailman.nhm.ku.edu 
http://mailman.nhm.ku.edu/mailman/listinfo/taxacom 

The Taxacom archive going back to 1992 may be searched with either of these methods: 

(1) http://taxacom.markmail.org 

Or (2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here 
_______________________________________________

Taxacom Mailing List
Taxacom at mailman.nhm.ku.edu
http://mailman.nhm.ku.edu/mailman/listinfo/taxacom

The Taxacom archive going back to 1992 may be searched with either of these methods:

(1) http://taxacom.markmail.org

Or (2) a Google search specified as:  site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here