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

Richard Zander Richard.Zander at mobot.org
Mon Sep 19 07:46:57 CDT 2011


It seems that some barcoding operations have phenomenal balance between classical taxonomy and molecular analyses. This is wonderful. Most of my objurgations on Taxacom have addressed the fundamental change in paradigm that evolution be redefined as base changes over time in mostly non-coding DNA sites. As an editor, I received a manuscript from an author with no key to genera. When queried, the author said oh everything is molecular now. I insisted on a key, and got one that kind of looked okay, but see my past plaints about multiple tests in systematics (chance alone will guarantee a set of morphologicla traits for most DNA clusterings).
 
You are correct, James, in apprehension that classical taxonomy is often not clearly based on analytic or synthetic methods. Chesterton famously said: "A philistine is someone who knows he is right but does not know why." And how is this different from an expert in classical taxonomy, where the traditional knowledge is "a species is whatever an expert in the group says it is"? I'm working up a paper that formalizes at least a few of the heuristics used by classical taxonomists which is why I brought up the concept of large-scale sampling distributions. We classical taxonomists, for example, need to explain why we focus on conservative traits, what are they, how we identify them. How these help organize groups, how they figure in evolution. Why they must be explained in an overarching theory when classical and molecular systematics disagree.
 
I've found (on the average from several morphological treatments) that the (a-)b-c(-d) paradigm of measurements is affected by the geometric mean, commonly used in analyses of proportions. Because zero is often close to "b" and "b-c" is a large portion of "a-c", the quantity "a-b" is usually much smaller than "b-c" and somewhat smaller than "c-d". The geometric mean of "a-d" is about that of "b-c". The arithmetic means don't match as well.  Usually the geomean is better than the arithmetic mean, but not always. Should it be? If there is a difference, does that mean the taxonomist is biased? or the variation in the taxon is genetically set to be biased? Interesting, and this comes from attempted formalization of our "expert" heuristics.
 
Taxonom is where we can complain about the faults of others, but also discover our own occasionally salient, egregious and outstanding misapprehensions and lacunae. Being wrong, it seems, is a necessary part of doing science. 
 
 
_______________________
Richard H. Zander
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166 U.S.A.
richard.zander at mobot.org
 

________________________________

From: James Whitfield [mailto:jwhitfie at life.illinois.edu]
Sent: Sun 9/18/2011 7:13 PM
To: Richard Zander
Cc: mivie at montana.edu; James Whitfield; taxacom at mailman.nhm.ku.edu
Subject: RE: [Taxacom] very nice opinion article in today's Zootaxa



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
>>
>>
>> _______________________________________________
>>
>> 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) by visiting http://taxacom.markmail.org <http://taxacom.markmail.org/> 
>> <http://taxacom.markmail.org/>
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>> (2) a Google search specified as:
>> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
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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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