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

Peter Stevens peter.stevens at mobot.org
Mon Sep 19 12:04:19 CDT 2011


Just got to my mail.  I could not agree with paragraph 2 more - also  
speaking as a descriptive taxonomist who is trying to finish off some  
monographs.  I might add that at least in some cases the result is  
very broadly distributed and variable species....

P.
On Sep 18, 2011, at 7:13 PM, James Whitfield wrote:

> Many of the papers have in the HUNDREDS of samples per species.   
> Where are
> you looking??? For the roughly 500 reared species of ACG microgastrine
> braconid wasps, for instance, we have a total of thousands of reared
> samples (most of them with many individuals per sample), each with
> ecological data and a taxonomist's ID.
> The controversial Astraptes study was based on about 2,500 field  
> samples,
> 466 of which were subsampled to make the barcode tree for 10 species.
>
> One recurring problem in these discussions is that (some) museum
> taxonomists often insist that they treat large samples within species,
> while molecular systematists have not.  While it is true that they  
> likely
> have sorted out large numbers of specimens and thus have a general  
> "feel"
> for the variation they are encompassing within a species  
> delineation, it
> is extremely rare for them to have analyzed this variation in any
> statistical way. And even rarer for them to have incorporated  
> ecological
> data for a large sample. As that kind of descriptive taxonomist  
> myself, I
> lament this absence of data but it's just where we often are with  
> sampling
> things (and also with the shortage of time we all have). We do the  
> best
> with what we have. Let's just not pretend we have knowledge that we  
> don't!
>
> Some of the Janzen studies have amazingly extensive ecological  
> data, some
> (albeit maybe minimalist) morphological data, some genetic data, and
> perhaps the best publicly available documentation and vouchering we  
> have
> virtually anywhere. I feel very grateful to have that kind of base for
> some of my taxonomic work.
>
> Jim
>
>> I've looked over the barcode papers I've got as pdfs, and most  
>> have maybe
>> 4 to 10 samples of each species. An adequate sample is 30, which  
>> ensures
>> as a rule of thumb that you have a normal distribution of sampling  
>> so you
>> can gauge the skewness of the distribution. "Lots" would mean more  
>> than
>> 30.
>>
>> To gauge the kind of multi-modal distribution one might have from  
>> a number
>> of cryptic species, you would need, let me guess since I'm not a
>> statistician, 30 for each cryptic species you think you may have.  
>> "Lots"
>> would be more than x times 30.
>>
>> By samples, I mean not samples of just the mitichondrial or  
>> chloroplast
>> barcoding sequence, but all the other traits used to consolidate the
>> cryptic species, e.g. as in barred skipper the feeding habits of the
>> larvae and everything else in the multi-dimensional data space we
>> taxonomists evaluate.
>>
>> We taxonomists use heuristics, usually involving conservative  
>> (appear in
>> many environments) traits, to deal with the multi-dimensional tensor.
>>
>> Too little, too late.
>>
>> _______________________
>> Richard H. Zander
>> Missouri Botanical Garden
>> PO Box 299
>> St. Louis, MO 63166 U.S.A.
>> richard.zander at mobot.org
>>
>>
>> ________________________________
>>
>> From: Michael A. Ivie [mailto:mivie at montana.edu]
>> Sent: Fri 9/16/2011 6:39 PM
>> To: James Whitfield
>> Cc: Richard Zander; taxacom at mailman.nhm.ku.edu
>> Subject: Re: [Taxacom] very nice opinion article in today's Zootaxa
>>
>>
>>
>> Could we have the rule that  people who have not read the papers  
>> under
>> discussion should not have opinions about those papers?  Geez!  It  
>> seems
>> to me that only Jim and John have any basis for what they are saying.
>>
>> Mike Ivie
>>
>>
>>> Not to argue for using only one sample to stand for a species, or  
>>> only
>>> one
>>> DNA barcode, as I agree with you that it is a bad idea.
>>>
>>> But if people would bother to look carefully at the original papers,
>>> they
>>> are based on LOTS of molecular samples from each species.  It is the
>>> CONSISTENCY of the molecular or morphological differences that is
>>> critical, not how major the differences are. In this case the  
>>> molecular
>>> and morphological differences are consistent across many samples  
>>> within
>>> putative species and do indeed support one another.
>>>
>>> Most species descriptions based on morphology (probably 95% + of all
>>> species descriptions?) do not have any convincing analysis  
>>> associated
>>> with
>>> them. We are in the habit of trusting the experts in this case  
>>> rather
>>> than
>>> requiring strong evidence.  Most of the time this works really  
>>> well, I'd
>>> say.
>>>
>>> Jim
>>>
>>>
>>>
>>>
>>>> Exactly. The question is whether a one specimen sample will  
>>>> suffice for
>>>> a
>>>> species description. YES, that the specimen is connected to a
>>>> systematic
>>>> morphological study of many specimens is importanat, but it is not
>>>> support
>>>> or refutation of the morphological conclusions. Only if the  
>>>> molecular
>>>> analysis can stand on its own can it either support or refute  
>>>> another
>>>> concept.
>>>>
>>>> _______________________
>>>> Richard H. Zander
>>>> Missouri Botanical Garden
>>>> PO Box 299
>>>> St. Louis, MO 63166 U.S.A.
>>>> richard.zander at mobot.org
>>>>
>>>>
>>>> ________________________________
>>>>
>>>> From: taxacom-bounces at mailman.nhm.ku.edu on behalf of Doug Yanega
>>>> Sent: Thu 9/15/2011 5:05 PM
>>>> To: TAXACOM at MAILMAN.NHM.KU.EDU
>>>> Subject: Re: [Taxacom] very nice opinion article in today's Zootaxa
>>>>
>>>>
>>>>
>>>> Among the references that John Shuey listed, I noted the following
>>>> one, which I had not seen before:
>>>>
>>>>> 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)? And, given that subspecies are typically
>>>> morphologically distinct, then, by extension, barcodes could never
>>>> help distinguish species from subspecies - only ecology (i.e.,
>>>> breeding experiments, etc.) would be definitive - in which case
>>>> barcoding is of rather more limited utility than its proponents
>>>> generally claim; it would seem to come into play only if one has  
>>>> two
>>>> otherwise very similar sets of organisms whose barcodes are
>>>> *dramatically different*. That's certainly potentially useful in  
>>>> some
>>>> contexts, but far from a solution to the "taxonomic impediment" as
>>>> was initially claimed by Hebert, and only serves to enhance my
>>>> already skeptical view of the barcoding enterprise.
>>>>
>>>> Or am I missing something here?
>>>> --
>>>>
>>>> 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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>>>
>>>
>>> --
>>> James B. Whitfield
>>> Department of Entomology
>>> 320 Morrill Hall
>>> 505 S. Goodwin Avenue
>>> University of Illinois
>>> Urbana, IL 61801
>>> http://www.life.illinois.edu/whitfield
>>>
>>>
>>> _______________________________________________
>>>
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>>>
>>
>>
>> --
>> Michael A. Ivie, Ph.D., F.R.E.S.
>> Montana Entomology Collection
>> Marsh Labs, Room 50
>> 1901 S. 19th Ave
>> Montana State University
>> Bozeman, MT 59717-3020
>> USA
>>
>> (406) 994-4610 (voice)
>> (406) 994-6029 (FAX)
>> mivie at montana.edu
>>
>>
>>
>>
>>
>
>
> -- 
> James B. Whitfield
> Department of Entomology
> 320 Morrill Hall
> 505 S. Goodwin Avenue
> University of Illinois
> Urbana, IL 61801
> http://www.life.illinois.edu/whitfield
>
>
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