Shortcuts in systematics? A commentary on DNA-based taxonomy
Shortcuts in systematics? A commentary on DNA-based taxonomy
Shortcuts in systematics? A commentary on DNA-based taxonomy
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Update TRENDS <str<strong>on</strong>g>in</str<strong>on</strong>g> Ecology and Evoluti<strong>on</strong> Vol.18 No.2 February 2003 63<br />
such as fluorescence microscopy, can be used to count the<br />
number of prokaryotes <str<strong>on</strong>g>in</str<strong>on</strong>g> a sample, provid<str<strong>on</strong>g>in</str<strong>on</strong>g>g us with N tot .<br />
On the basis of these numbers, the authors make the<br />
follow<str<strong>on</strong>g>in</str<strong>on</strong>g>g diversity estimates: oceans, 160 ‘species’ ml 21 ;<br />
soil, 6400–38 000 g 21 ; sewage works, 70 ml 21 . This last<br />
number is a nice example of the paradox of enrichment, the<br />
phenomen<strong>on</strong> whereby fertilizati<strong>on</strong> (<str<strong>on</strong>g>in</str<strong>on</strong>g> the agricultural<br />
sense) reduces diversity. The low diversity estimated for<br />
the oceans and the high diversity for soils are c<strong>on</strong>sistent<br />
with results from studies us<str<strong>on</strong>g>in</str<strong>on</strong>g>g very different methodologies<br />
[8]. Understand<str<strong>on</strong>g>in</str<strong>on</strong>g>g this difference is as important<br />
as understand<str<strong>on</strong>g>in</str<strong>on</strong>g>g the latitud<str<strong>on</strong>g>in</str<strong>on</strong>g>al diversity gradients<br />
observed for macroscopic organisms. Also, the low diversity<br />
associated with high nutrient levels has also been<br />
observed <str<strong>on</strong>g>in</str<strong>on</strong>g> prokaryotic communities <str<strong>on</strong>g>in</str<strong>on</strong>g> sediments beneath<br />
fish farms [8].<br />
My previous remark about the statistics of N max /N tot <str<strong>on</strong>g>in</str<strong>on</strong>g><br />
small samples requires elaborati<strong>on</strong>. Suppose that, <str<strong>on</strong>g>in</str<strong>on</strong>g> the<br />
community, N max /N tot is actually quite small. Then it is<br />
possible that our sample will not actually c<strong>on</strong>ta<str<strong>on</strong>g>in</str<strong>on</strong>g> the most<br />
abundant species <str<strong>on</strong>g>in</str<strong>on</strong>g> the community. If we know the identity<br />
of this species, then we can restrict our analysis to samples<br />
that c<strong>on</strong>ta<str<strong>on</strong>g>in</str<strong>on</strong>g> it, although this would require a modificati<strong>on</strong> of<br />
the estimati<strong>on</strong> formula to accommodate this extra level of<br />
sampl<str<strong>on</strong>g>in</str<strong>on</strong>g>g. But if we have no means of restrict<str<strong>on</strong>g>in</str<strong>on</strong>g>g our analysis<br />
to such samples, then there appears to be no way to estimate<br />
diversity by this method, although this could simply be a<br />
failure of imag<str<strong>on</strong>g>in</str<strong>on</strong>g>ati<strong>on</strong> <strong>on</strong> my part.<br />
F<str<strong>on</strong>g>in</str<strong>on</strong>g>ally, this new paper raises very starkly an extremely<br />
<str<strong>on</strong>g>in</str<strong>on</strong>g>terest<str<strong>on</strong>g>in</str<strong>on</strong>g>g questi<strong>on</strong>: just what, precisely, is the community<br />
be<str<strong>on</strong>g>in</str<strong>on</strong>g>g sampled What does it mean to say that there<br />
are 70 species ml 21 <str<strong>on</strong>g>in</str<strong>on</strong>g> sewage works It could mean<br />
anyth<str<strong>on</strong>g>in</str<strong>on</strong>g>g from ‘there are 70 species <str<strong>on</strong>g>in</str<strong>on</strong>g> sewage works,<br />
period’ or ‘there are billi<strong>on</strong>s of species <str<strong>on</strong>g>in</str<strong>on</strong>g> sewage works’.<br />
Turn<str<strong>on</strong>g>in</str<strong>on</strong>g>g to macroscopic organisms, if we used this technique<br />
to estimate, say, tree diversity then we would need<br />
an understand<str<strong>on</strong>g>in</str<strong>on</strong>g>g of b diversity (how diversity changes<br />
through space) to go bey<strong>on</strong>d statements about numbers of<br />
trees ha 21 to numbers of trees <str<strong>on</strong>g>in</str<strong>on</strong>g> the world. In fact, it is<br />
entirely possible that the oceans of the world c<strong>on</strong>stitute a<br />
s<str<strong>on</strong>g>in</str<strong>on</strong>g>gle prokaryotic community, just as aquatic microbial<br />
eukaryotes appear to be ubiquitous as a c<strong>on</strong>sequence of the<br />
abundance and dispersal abilities of the organisms<br />
c<strong>on</strong>cerned [9]. But it is not obvious that there is no b<br />
diversity <str<strong>on</strong>g>in</str<strong>on</strong>g> soils [8], and this needs further <str<strong>on</strong>g>in</str<strong>on</strong>g>vestigati<strong>on</strong>.<br />
References<br />
1 Floyd, R. et al. (2002) Molecular barcodes for soil nematode identificati<strong>on</strong>.<br />
Mol. Ecol. Evol. 11, 839–850<br />
2 Lopez-Garcia, P. et al. (2001) Unexpected diversity of small eukaryotes<br />
<str<strong>on</strong>g>in</str<strong>on</strong>g> deep-sea Antarctic plankt<strong>on</strong>. Nature 409, 603–607<br />
3 Mo<strong>on</strong>-van der Staay, S.V. et al. (2001) Oceanic 18S r<strong>DNA</strong> sequences<br />
from picoplankt<strong>on</strong> reveal unsuspected eukaryotic diversity. Nature 409,<br />
607–610<br />
4 Zettler, L.A.A. et al. (2002) Eukaryotic diversity <str<strong>on</strong>g>in</str<strong>on</strong>g> Spa<str<strong>on</strong>g>in</str<strong>on</strong>g>’s River of Fire<br />
– this ancient and hostile ecosystem hosts a surpris<str<strong>on</strong>g>in</str<strong>on</strong>g>g variety of<br />
microbial organisms. Nature 417, 137–137<br />
5 Moreira, D. and Lopez-Garcia, P. (2002) The molecular ecology of<br />
microbial eukaryotes unveils a hidden world. Trends Microbiol. 10,<br />
31–38<br />
6 Kerr, R.A. (2001) Life – potential, slow, or l<strong>on</strong>g dead Science 294,<br />
1820–1821<br />
7 Curtis, T.P. et al. (2002) Estimat<str<strong>on</strong>g>in</str<strong>on</strong>g>g prokaryotic diversity and its limits.<br />
Proc. Natl Acad. Sci. U. S. A. 99, 10494–10499<br />
8 Torsvik, V. et al. (2002) Prokaryotic diversity – magnitude, dynamics<br />
and c<strong>on</strong>troll<str<strong>on</strong>g>in</str<strong>on</strong>g>g factors. Science 296, 1064–1066<br />
9 F<str<strong>on</strong>g>in</str<strong>on</strong>g>lay, B.J. (2002) Global dispersal of free-liv<str<strong>on</strong>g>in</str<strong>on</strong>g>g microbial eukaryote<br />
species. Science 296, 1061–1063<br />
0169-5347/02/$ - see fr<strong>on</strong>t matter q 2002 Elsevier Science Ltd. All rights reserved.<br />
PII: S0169-5347(02)00043-5<br />
| Letters<br />
<str<strong>on</strong>g>Shortcuts</str<strong>on</strong>g> <str<strong>on</strong>g>in</str<strong>on</strong>g> <str<strong>on</strong>g>systematics</str<strong>on</strong>g><br />
A <str<strong>on</strong>g>commentary</str<strong>on</strong>g> <strong>on</strong> <strong>DNA</strong>-<strong>based</strong> tax<strong>on</strong>omy<br />
Ole Seberg 1 , Chris J. Humphries 2 , Sandy Knapp 2 , Dennis Wm. Stevens<strong>on</strong> 3 ,<br />
Gitte Petersen 1 , Nikolaj Scharff 4 and Nils Møller Andersen 4<br />
1 Department of Evoluti<strong>on</strong>ary Botany, Botanical Institute, University of Copenhagen, Gothersgade 140,<br />
DK-1123 Copenhagen K, Denmark<br />
2 The Natural History Museum, Cromwell Road, L<strong>on</strong>d<strong>on</strong> SW7 5BD, UK<br />
3 The New York Botanical Garden, Br<strong>on</strong>x, New York, NY 10458, USA<br />
4 Entomology Department, Zoological Museum, University of Copenhagen, Universitetsparken 15,<br />
DK-2100 Copenhagen Ø, Denmark<br />
The primary aims of tax<strong>on</strong>omy are to name, circumscribe,<br />
describe and classify species. The first goal is c<strong>on</strong>venti<strong>on</strong><br />
but the rema<str<strong>on</strong>g>in</str<strong>on</strong>g>der are science. The Internati<strong>on</strong>al Codes<br />
of Nomenclature are legislative <str<strong>on</strong>g>in</str<strong>on</strong>g>struments and nomenclature<br />
is simply a mechanism to ensure that a species<br />
Corresp<strong>on</strong>d<str<strong>on</strong>g>in</str<strong>on</strong>g>g author: Ole Seberg (oles@bot.ku.dk).<br />
name is legitimately attached to a type specimen,<br />
regardless of scientific status. The type of a species does<br />
not serve, as Tautz et al. ([1,2], but see [3]) assert, as ‘the<br />
central reference for comparis<strong>on</strong>s’. The crucial l<str<strong>on</strong>g>in</str<strong>on</strong>g>k<br />
between names and scientific <str<strong>on</strong>g>in</str<strong>on</strong>g>vestigati<strong>on</strong> is species<br />
circumscripti<strong>on</strong> followed by descripti<strong>on</strong>. The Codes require<br />
L<str<strong>on</strong>g>in</str<strong>on</strong>g>naean b<str<strong>on</strong>g>in</str<strong>on</strong>g>omials: a genus name and a species epithet.<br />
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Update TRENDS <str<strong>on</strong>g>in</str<strong>on</strong>g> Ecology and Evoluti<strong>on</strong> Vol.18 No.2 February 2003<br />
The rules are totally silent about what c<strong>on</strong>stitutes a<br />
species; rather this is a key goal of biological <str<strong>on</strong>g>in</str<strong>on</strong>g>vestigati<strong>on</strong>.<br />
Circumscripti<strong>on</strong>s of genera and species evolve as science<br />
progresses.<br />
The L<str<strong>on</strong>g>in</str<strong>on</strong>g>naean b<str<strong>on</strong>g>in</str<strong>on</strong>g>omial system is not ‘<str<strong>on</strong>g>in</str<strong>on</strong>g>herently<br />
unstable’ but is used to <str<strong>on</strong>g>in</str<strong>on</strong>g>terpret the underly<str<strong>on</strong>g>in</str<strong>on</strong>g>g science.<br />
The problem that ‘a name that has been used for a l<strong>on</strong>g<br />
time thus can suddenly disappear’ (or reappear, for that<br />
matter) is a nuisance for every<strong>on</strong>e. However, if name<br />
changes are c<strong>on</strong>sidered a serious problem, then the<br />
c<strong>on</strong>servati<strong>on</strong> and rejecti<strong>on</strong> criteria available <str<strong>on</strong>g>in</str<strong>on</strong>g> the Codes<br />
can be <str<strong>on</strong>g>in</str<strong>on</strong>g>voked.<br />
Neither the Botanical nor the Zoological Code has a<br />
fixed authoritarian supervisory body; rather, they have<br />
committees chosen by a democratic process that oversee<br />
changes. The Codes work by c<strong>on</strong>sensus and are designed<br />
to be open and universally applicable [4]. Tautz et al. ([2],<br />
and see [3]) advocate universal, centralized, apparently<br />
obligatory registrati<strong>on</strong>, a c<strong>on</strong>cept emphatically rejected by<br />
the Internati<strong>on</strong>al Botanical C<strong>on</strong>gress <str<strong>on</strong>g>in</str<strong>on</strong>g> 1999. Tax<strong>on</strong>omists<br />
from develop<str<strong>on</strong>g>in</str<strong>on</strong>g>g nati<strong>on</strong>s led the move aga<str<strong>on</strong>g>in</str<strong>on</strong>g>st<br />
centralizati<strong>on</strong>, fearful that the wealthier nati<strong>on</strong>s were<br />
attempt<str<strong>on</strong>g>in</str<strong>on</strong>g>g to m<strong>on</strong>opolize <str<strong>on</strong>g>in</str<strong>on</strong>g>formati<strong>on</strong>. In our view, registrati<strong>on</strong><br />
would eventually strangle <str<strong>on</strong>g>systematics</str<strong>on</strong>g>, as debate<br />
will be discouraged.<br />
Most current tax<strong>on</strong>omy is pursued us<str<strong>on</strong>g>in</str<strong>on</strong>g>g low-cost<br />
technology. Mandatory <str<strong>on</strong>g>in</str<strong>on</strong>g>troducti<strong>on</strong> of <strong>DNA</strong> sequences<br />
<str<strong>on</strong>g>in</str<strong>on</strong>g>to tax<strong>on</strong>omy seems to us a retrograde step. In most<br />
<str<strong>on</strong>g>in</str<strong>on</strong>g>stances, a quick survey of morphology will serve the<br />
same purpose and, although morphology has its problems,<br />
<strong>DNA</strong> has as many pitfalls. A sufficiently different sequence<br />
might warrant the descripti<strong>on</strong> of a new species, as will a<br />
sufficiently different morphology. An expensive and centralized<br />
<strong>DNA</strong>-<strong>based</strong> tax<strong>on</strong>omy would <strong>on</strong>ly add to the<br />
North–South divide <str<strong>on</strong>g>in</str<strong>on</strong>g> tax<strong>on</strong>omy, and might exclude the<br />
many tax<strong>on</strong>omists who have limited access to sequenc<str<strong>on</strong>g>in</str<strong>on</strong>g>g<br />
technology.<br />
Acknowledg<str<strong>on</strong>g>in</str<strong>on</strong>g>g that there need not (or cannot) be<br />
universal agreement about which regi<strong>on</strong> of the genome to<br />
sequence, Tautz et al. suggest us<str<strong>on</strong>g>in</str<strong>on</strong>g>g house-keep<str<strong>on</strong>g>in</str<strong>on</strong>g>g genes,<br />
especially the ribosomal genes (at least <str<strong>on</strong>g>in</str<strong>on</strong>g> animals).<br />
Although abundant, ribosomal sequences might be an<br />
<str<strong>on</strong>g>in</str<strong>on</strong>g>appropriate choice <str<strong>on</strong>g>in</str<strong>on</strong>g> the l<strong>on</strong>g run, because they have<br />
profound alignment problems and are subject to different<br />
degrees of c<strong>on</strong>certed evoluti<strong>on</strong>.<br />
Match<str<strong>on</strong>g>in</str<strong>on</strong>g>g exist<str<strong>on</strong>g>in</str<strong>on</strong>g>g L<str<strong>on</strong>g>in</str<strong>on</strong>g>naean names with <strong>DNA</strong> sequences<br />
is fraught with hazards. Although it is tempt<str<strong>on</strong>g>in</str<strong>on</strong>g>g to create a<br />
new start<str<strong>on</strong>g>in</str<strong>on</strong>g>g date for priority for the Botanical and<br />
Zoological Codes [5], it seems futile to replace exist<str<strong>on</strong>g>in</str<strong>on</strong>g>g<br />
types (from which <strong>DNA</strong> <str<strong>on</strong>g>in</str<strong>on</strong>g> some cases cannot be extracted)<br />
with neotypes. As <str<strong>on</strong>g>in</str<strong>on</strong>g>dicated by the authors [1], expert<br />
tax<strong>on</strong>omists are <str<strong>on</strong>g>in</str<strong>on</strong>g> short supply and many important<br />
groups are neglected. It takes little imag<str<strong>on</strong>g>in</str<strong>on</strong>g>ati<strong>on</strong> to<br />
envisage the problems broad-scale designati<strong>on</strong> of neotypes<br />
would cause.<br />
Tautz et al. argue that exist<str<strong>on</strong>g>in</str<strong>on</strong>g>g <strong>DNA</strong> data bases<br />
represent bad tax<strong>on</strong>omy, as ‘there is no guarantee that<br />
the correct species names were assigned by the submitter<br />
of the sequence, because there are no established tax<strong>on</strong>omic<br />
standards under which such submissi<strong>on</strong>s have to<br />
be d<strong>on</strong>e’. The circumscripti<strong>on</strong> of a species is an op<str<strong>on</strong>g>in</str<strong>on</strong>g>i<strong>on</strong><br />
[6]. One might ask therefore who is go<str<strong>on</strong>g>in</str<strong>on</strong>g>g to decide <strong>on</strong><br />
‘tax<strong>on</strong>omic standards’. Circumscripti<strong>on</strong> changes with<br />
<str<strong>on</strong>g>in</str<strong>on</strong>g>creas<str<strong>on</strong>g>in</str<strong>on</strong>g>g knowledge; that’s the science. Many sequences<br />
are deposited <str<strong>on</strong>g>in</str<strong>on</strong>g> <strong>DNA</strong> data bases, but, if a specimen has<br />
been misidentified, <strong>on</strong>ly <str<strong>on</strong>g>in</str<strong>on</strong>g>specti<strong>on</strong> of the voucher can<br />
solve this problem. It is naïve to th<str<strong>on</strong>g>in</str<strong>on</strong>g>k that ‘phylogenetic<br />
analysis of query sequences, will readily place any<br />
sequences from new species’, as if the problems of homoplasy,<br />
alignment, and even phylogenetic methods would<br />
not add to the unreliability of <str<strong>on</strong>g>in</str<strong>on</strong>g>formati<strong>on</strong> <str<strong>on</strong>g>in</str<strong>on</strong>g> exist<str<strong>on</strong>g>in</str<strong>on</strong>g>g<br />
data bases.<br />
The role of collecti<strong>on</strong>s <str<strong>on</strong>g>in</str<strong>on</strong>g> <str<strong>on</strong>g>systematics</str<strong>on</strong>g> is vital. Collecti<strong>on</strong>s<br />
represent a comparative model of diversity, and therefore,<br />
as the authors [1] po<str<strong>on</strong>g>in</str<strong>on</strong>g>t out, specimens should be reta<str<strong>on</strong>g>in</str<strong>on</strong>g>ed<br />
as <str<strong>on</strong>g>in</str<strong>on</strong>g>tact as possible. Destructive sampl<str<strong>on</strong>g>in</str<strong>on</strong>g>g of type specimens<br />
for any characters has always been a severe problem<br />
and such procedures are accepted <strong>on</strong>ly as a last resort. To<br />
destroy a sample to extract its <strong>DNA</strong> might be <str<strong>on</strong>g>in</str<strong>on</strong>g>advisable<br />
<str<strong>on</strong>g>in</str<strong>on</strong>g> the light of future needs.<br />
With regard to tax<strong>on</strong>omic and phylogenetic studies,<br />
current practise attempts to create higher level<br />
classificati<strong>on</strong>s that do not c<strong>on</strong>flict directly with cladograms<br />
[7]. Today, phylogenetic methods applied to <strong>DNA</strong><br />
data are a str<strong>on</strong>g focus of <str<strong>on</strong>g>systematics</str<strong>on</strong>g> research, and it<br />
is difficult to believe that the pendulum might sw<str<strong>on</strong>g>in</str<strong>on</strong>g>g <str<strong>on</strong>g>in</str<strong>on</strong>g><br />
another directi<strong>on</strong>. However, methods do change and<br />
the fixed op<str<strong>on</strong>g>in</str<strong>on</strong>g>i<strong>on</strong>s of today might seem redundant <str<strong>on</strong>g>in</str<strong>on</strong>g><br />
the future.<br />
So what is the upshot Indeed, what has the<br />
molecular revoluti<strong>on</strong> really achieved for tax<strong>on</strong>omy<br />
The ma<str<strong>on</strong>g>in</str<strong>on</strong>g> advance is that it has provided access to<br />
copious data for cladistic analysis and, <str<strong>on</strong>g>in</str<strong>on</strong>g> our view, has<br />
provided new data sets and a new class of characters<br />
that can be extremely useful <str<strong>on</strong>g>in</str<strong>on</strong>g> broad-scale comparis<strong>on</strong>s<br />
of everyth<str<strong>on</strong>g>in</str<strong>on</strong>g>g from bacteria to mammals and plants.<br />
Often <strong>on</strong>e is forced to use <strong>on</strong>e, or a few, carefully selected<br />
specimens as representatives of a tax<strong>on</strong>, but experience<br />
has repeatedly shown that this can be a major mistake.<br />
Deliberately us<str<strong>on</strong>g>in</str<strong>on</strong>g>g a s<str<strong>on</strong>g>in</str<strong>on</strong>g>gle specimen as a representative<br />
of the tax<strong>on</strong> will <strong>on</strong>ly create havoc <str<strong>on</strong>g>in</str<strong>on</strong>g> tax<strong>on</strong>omy, a fact<br />
l<strong>on</strong>g realized by tax<strong>on</strong>omists work<str<strong>on</strong>g>in</str<strong>on</strong>g>g with other types of<br />
data. Individual bases and <strong>DNA</strong> sequences are simply<br />
characters, t<str<strong>on</strong>g>in</str<strong>on</strong>g>y fragments of the lifecycle. It seems<br />
perverse to us to advocate us<str<strong>on</strong>g>in</str<strong>on</strong>g>g a <strong>DNA</strong> sequence as a<br />
mandatory identificati<strong>on</strong> tag for a species, even as a first<br />
approximati<strong>on</strong>. Therefore, this plea for a <strong>DNA</strong>-<strong>based</strong><br />
tax<strong>on</strong>omy is little more than a cri de coeur for bio<str<strong>on</strong>g>in</str<strong>on</strong>g>formatics<br />
and <str<strong>on</strong>g>in</str<strong>on</strong>g>creased reliance <strong>on</strong> sequence data.<br />
We agree that there is a very str<strong>on</strong>g need for efficient,<br />
although perhaps not centralized, repositories for <strong>DNA</strong><br />
samples. How and where such samples should be<br />
curated, and how the curators should be funded, is an<br />
open questi<strong>on</strong>. We also agree that it would be a good<br />
idea to <str<strong>on</strong>g>in</str<strong>on</strong>g>clude <strong>DNA</strong> sequences <str<strong>on</strong>g>in</str<strong>on</strong>g> the diagnoses of<br />
taxa. However, we feel that a <strong>DNA</strong>-<strong>based</strong> tax<strong>on</strong>omy<br />
al<strong>on</strong>g the suggested l<str<strong>on</strong>g>in</str<strong>on</strong>g>es would catastrophically retard<br />
tax<strong>on</strong>omic activity, and it would certa<str<strong>on</strong>g>in</str<strong>on</strong>g>ly not relieve<br />
the need for many more tax<strong>on</strong>omists, especially <str<strong>on</strong>g>in</str<strong>on</strong>g> the<br />
tropics, for the good of tax<strong>on</strong>omy’s many dependent<br />
user groups.<br />
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References<br />
1 Tautz, D. et al. (2002) <strong>DNA</strong> po<str<strong>on</strong>g>in</str<strong>on</strong>g>ts the way ahead <str<strong>on</strong>g>in</str<strong>on</strong>g> tax<strong>on</strong>omy. Nature<br />
418, 479<br />
2 Tautz, D. et al. (2003) A plea for <strong>DNA</strong> tax<strong>on</strong>omy. Trends Ecol. Evol. 18<br />
DOI: 10.1016/S0169-5347(02)00041-1<br />
3 M<str<strong>on</strong>g>in</str<strong>on</strong>g>elli, A. (2003) The status of tax<strong>on</strong>omic literature. Trends Ecol. Evol.<br />
18 DOI: 10.1016/S0169-5347(02)00051-4<br />
4 Knapp, S. et al. (2002) Tax<strong>on</strong>omy needs evoluti<strong>on</strong>, not revoluti<strong>on</strong>.<br />
Nature 419, 559<br />
5 Godfray, H.C.J. (2002) Challenges for tax<strong>on</strong>omy. Nature 417, 17–19<br />
6 Mallet, J. (2003) Tax<strong>on</strong>omy: renaissance or Tower of Babel DOI:<br />
10.1016/S0169-5347(02)00061-7<br />
7 Lipscomb, D. et al. (2003) The <str<strong>on</strong>g>in</str<strong>on</strong>g>tellectual c<strong>on</strong>tent of tax<strong>on</strong>omy: a<br />
comment <strong>on</strong> <strong>DNA</strong> tax<strong>on</strong>omy. DOI: 10.1016/S0169-5347(02)00060-5<br />
0169-5347/02/$ - see fr<strong>on</strong>t matter q 2002 Elsevier Science Ltd. All rights reserved.<br />
PII: S0169-5347(02)00059-9<br />
The <str<strong>on</strong>g>in</str<strong>on</strong>g>tellectual c<strong>on</strong>tent of tax<strong>on</strong>omy:<br />
a comment <strong>on</strong> <strong>DNA</strong> tax<strong>on</strong>omy<br />
Diana Lipscomb 1 , N. Platnick 2 and Q. Wheeler 3<br />
1 Department of Biological Sciences, George Wash<str<strong>on</strong>g>in</str<strong>on</strong>g>gt<strong>on</strong> University, Wash<str<strong>on</strong>g>in</str<strong>on</strong>g>gt<strong>on</strong> DC 20052, USA<br />
2 Divisi<strong>on</strong> of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA<br />
3 Department of Entomology, Comstock Hall, Cornell University, Ithaca, NY 14853, USA<br />
Tautz et al. [1] propose to ‘solve’ the lack of adequate<br />
classificati<strong>on</strong>s and effective identificati<strong>on</strong> tools (the socalled<br />
‘tax<strong>on</strong>omic impediment’) by replac<str<strong>on</strong>g>in</str<strong>on</strong>g>g exist<str<strong>on</strong>g>in</str<strong>on</strong>g>g<br />
classificati<strong>on</strong>s with a system <str<strong>on</strong>g>in</str<strong>on</strong>g> which an <str<strong>on</strong>g>in</str<strong>on</strong>g>f<str<strong>on</strong>g>in</str<strong>on</strong>g>itesimally<br />
t<str<strong>on</strong>g>in</str<strong>on</strong>g>y fracti<strong>on</strong> of an organism’s genome is sequenced and<br />
used both to classify and identify the organism <str<strong>on</strong>g>in</str<strong>on</strong>g> questi<strong>on</strong>.<br />
The rati<strong>on</strong>ale for this suggested change, however, is<br />
specious and unlikely to produce a progressive research<br />
program. Such a system is already <str<strong>on</strong>g>in</str<strong>on</strong>g> use for unculturable<br />
prokaryotes, where the best we can do at present is collect<br />
sequence data from the envir<strong>on</strong>ment, compile data bases of<br />
the results, and c<strong>on</strong>struct ‘classificati<strong>on</strong>s’ that reflect <strong>on</strong>ly<br />
the degree of similarity displayed by those sequences. This<br />
produces what is at best a caricature of real tax<strong>on</strong>omy, <str<strong>on</strong>g>in</str<strong>on</strong>g><br />
which sequences that diverge by ,5% are c<strong>on</strong>sidered<br />
‘c<strong>on</strong>specific’ (never m<str<strong>on</strong>g>in</str<strong>on</strong>g>d that humans and chimpanzees<br />
might be far less divergent than that). Microbiologists<br />
would be the first to agree that, when the organisms can be<br />
cultured and their other attributes studied, we can do far<br />
better than this. Why, then, reduce the tax<strong>on</strong>omy of all<br />
other organisms to this impoverished state The supposed<br />
advantages of <strong>DNA</strong> tax<strong>on</strong>omy do not stand up to rigorous<br />
scrut<str<strong>on</strong>g>in</str<strong>on</strong>g>y. For example, the claim that a sequence ‘is not<br />
<str<strong>on</strong>g>in</str<strong>on</strong>g>fluenced by subjective assessments’ ignores the difficulty<br />
of align<str<strong>on</strong>g>in</str<strong>on</strong>g>g sequences of different length, dist<str<strong>on</strong>g>in</str<strong>on</strong>g>guish<str<strong>on</strong>g>in</str<strong>on</strong>g>g<br />
paralogs from orthologs, or even select<str<strong>on</strong>g>in</str<strong>on</strong>g>g appropriate<br />
genes for any particular tax<strong>on</strong>omic study. Similarly, the<br />
suppositi<strong>on</strong> that <strong>DNA</strong> identificati<strong>on</strong> will lessen the<br />
c<strong>on</strong>fusi<strong>on</strong> that sometimes results when tax<strong>on</strong>omic names<br />
change is unjustified. The <strong>on</strong>ly way that a <strong>DNA</strong> sequence<br />
identificati<strong>on</strong> tag could ameliorate c<strong>on</strong>fusi<strong>on</strong> would be if<br />
the gene sequence used were c<strong>on</strong>stant am<strong>on</strong>g all members<br />
of the species but different <str<strong>on</strong>g>in</str<strong>on</strong>g> all other species. There is no<br />
evidence that most genes meet these criteria, and any<br />
Corresp<strong>on</strong>d<str<strong>on</strong>g>in</str<strong>on</strong>g>g author: Diana Lipscomb (biodl@gwu.edu).<br />
diagnostic character that meets these criteria would work<br />
– it need not be molecular.<br />
The ‘tax<strong>on</strong>omic impediment’ is more effectively<br />
addressed by other means. Tautz et al. [1] are, <str<strong>on</strong>g>in</str<strong>on</strong>g> essence,<br />
suggest<str<strong>on</strong>g>in</str<strong>on</strong>g>g that if we all become as ignorant of our<br />
organisms as are, perforce, those microbiologists work<str<strong>on</strong>g>in</str<strong>on</strong>g>g<br />
<strong>on</strong> currently unculturable taxa, the world would no l<strong>on</strong>ger<br />
suffer when knowledgeable specialists <str<strong>on</strong>g>in</str<strong>on</strong>g> a group die<br />
without hav<str<strong>on</strong>g>in</str<strong>on</strong>g>g communicated all their knowledge to<br />
others. Programs such as the US–NSF’s PEET [Partnerships<br />
for Enhanc<str<strong>on</strong>g>in</str<strong>on</strong>g>g Expertise <str<strong>on</strong>g>in</str<strong>on</strong>g> Tax<strong>on</strong>omy (2003): http://<br />
www.nsf.gov/pubsys/ods/getpub.cfmnsf00140], which provides<br />
fund<str<strong>on</strong>g>in</str<strong>on</strong>g>g to tra<str<strong>on</strong>g>in</str<strong>on</strong>g> a new generati<strong>on</strong> of systematists,<br />
represent soluti<strong>on</strong>s far more effective than simply<br />
discard<str<strong>on</strong>g>in</str<strong>on</strong>g>g everyth<str<strong>on</strong>g>in</str<strong>on</strong>g>g we have learned to date about<br />
organismic diversity. Tax<strong>on</strong>omy might <str<strong>on</strong>g>in</str<strong>on</strong>g>deed be<br />
threatened, but the greatest threats might be from<br />
those who would usurp the resources that it needs to<br />
grow and thrive.<br />
Tautz et al. [1] emphasis <strong>on</strong> the task of identificati<strong>on</strong><br />
<str<strong>on</strong>g>in</str<strong>on</strong>g>dicates a fundamental misunderstand<str<strong>on</strong>g>in</str<strong>on</strong>g>g of the <str<strong>on</strong>g>in</str<strong>on</strong>g>tellectual<br />
c<strong>on</strong>tent and rigorous hypothesis test<str<strong>on</strong>g>in</str<strong>on</strong>g>g that characterize<br />
c<strong>on</strong>temporary tax<strong>on</strong>omy. Reduc<str<strong>on</strong>g>in</str<strong>on</strong>g>g tax<strong>on</strong>omy to<br />
identificati<strong>on</strong> al<strong>on</strong>e makes it a technical task rather than a<br />
hypothesis-driven science. There is no credible reas<strong>on</strong> to<br />
give <strong>DNA</strong> characters greater stature than any other<br />
character type. When species descripti<strong>on</strong>s are <strong>based</strong> <strong>on</strong> a<br />
broad range of data, they become <str<strong>on</strong>g>in</str<strong>on</strong>g>terest<str<strong>on</strong>g>in</str<strong>on</strong>g>g scientific<br />
hypotheses mak<str<strong>on</strong>g>in</str<strong>on</strong>g>g explicit predicti<strong>on</strong>s about the distributi<strong>on</strong><br />
of attributes am<strong>on</strong>g organisms. We rec<strong>on</strong>struct<br />
phylogenies to expla<str<strong>on</strong>g>in</str<strong>on</strong>g> patterns of organismic diversity.<br />
Molecular data certa<str<strong>on</strong>g>in</str<strong>on</strong>g>ly c<strong>on</strong>tribute, but when noth<str<strong>on</strong>g>in</str<strong>on</strong>g>g is<br />
known about organisms except their <strong>DNA</strong>, there are no<br />
evoluti<strong>on</strong>arily <str<strong>on</strong>g>in</str<strong>on</strong>g>terest<str<strong>on</strong>g>in</str<strong>on</strong>g>g patterns to expla<str<strong>on</strong>g>in</str<strong>on</strong>g> – just a<br />
tedious pattern of sequence similarity. The advocates of<br />
<strong>DNA</strong> tax<strong>on</strong>omy seem not to understand the peerless<br />
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