Molecular taxonomy: on way out?

B.J.Tindall bti at DSMZ.DE
Mon Jul 18 08:16:22 CDT 2005

As you will all be aware bacteriological taxonomy doesn't have the same
"morphological benefits" as plants and animals. The result is that the
science has become largely molecular. However, this is also due to a lack
of understanding of the transition from a gene to the end product.
Prokaryotes have much smaller genomes, which means that we are going to be
collecting and evaluating the data fairly rapidly, but this doesn't mean
that we will arrive at answers any quicker. There are a number of problems
(in addition to what Richard lists below):
1) the problem of homology at the different levels - far too many people
mistake similarity with homology at the molecular level - if you go back to
the 1960's one finds clear and unambiguous reference to the fact that
similarity alone is not homology
2) most molecular data is treated in a linear fashion ("in silico").
However, genes generally code for either proteins or RNA, both of which
have three dimensional structures. The debate between one dimensional vs.
three dimensional analysis also goes back to the 1960's. I belong to the
3-D camp.
3) the best examples of 3-D molecular analysis include cytochrome c (and
haemoglobin) analysis (which goes back to the 1960's) and more recent work
on the structure of the ribosome.
4) complexity is, indeed an aspect which plays an important role, and is
often forgotten in the light of analysing single genes. In many cases
complex interactions are the order of the day (even in bacteria ;-) ).
5) genes being turned on and off, and (perhaps) accumulating mutations in a
more "random" fashion is part of the "flickering genes" hypothesis.
Bacteriochorophyll expression in certain groups of bacteria (which may or
may not be photosynthetic) may be a good example of this hypothesis.
There is certainly something to be said for looking at the value of
different data sets - such as the morphology of an organism and the genes
and regulatory pathways responsible for that morphology. The type of
problems which Richard mentions - splitting of groups based on molecular
grounds also surfaces in bacteriology, but is generally ignored simply
because much faith (word chosen with care ;-)) was put in a single gene.
That such effects can surface is now documented by comparing genes (a
principle outlined by Peter Sneath in 1974). If you accept that one gene
may not be accurate, then you may also spot other "errors", and not only at
the gene level, but also at the phenoytpic level.
It will all come out in the wash ....

At 15:26 16.7.2005 -0500, Richard.Zander at MOBOT.ORG wrote:
>Molecular taxonomy will be old hat sooner than you think. And the leading
>expositor on Taxacom for a new and better way to evaluate evolutionary
>patterns as they may be used in taxonomy in the future is . . . (wait for
>it). . . John Grehan.
>In my opinion, John got to the right conclusion with metaphysical premises.
>We, rightly, disagreed with Grehan's "molecular drive" and other
>generalizations as an alternative to modern molecular systematics. I've been
>looking, however, in the evo-devo literature recently, and in fact there is
>some (not much, but some) evidence that evolution commonly involves large
>gene complexes regulated (e.g. turned off and on) by non-coding regulatory
>genes. This makes for a sloppy evolutionary tree because the silenced gene
>complexes can travel the lineage byways for up to 10 million years before
>being degraded.
>The problem is that some major morphological complexes are greatly split by
>molecular systematics. Although statistically the molecular split is well
>supported, that split statistically contravenes Dollo's Law that it is not
>to be expected by chance alone that two taxa sharing many complex
>morphological characters should separately exactly re-evolve (by gradual
>accumulation of traits).
>Molecular systematics, in my opinion, tracks reproductive splits assuming a
>Biological Species Concept (iffy for plants), which mainly also reflects
>evolutionary changes (to the extent it matches expectations from
>morphological analysis), but instances of apparent massive homoplasy can be
>mediated by identical or little changed shared gene complexes turned on by
>selection on regulatory genes. It is the only explanation of such homoplasy,
>it is not mystical, and it builds on Darwinian thinking.
>The human-chimp relationship is statistically supported by molecular studies
>as a sister group, but we share too many critical morphological traits with
>the patristically more distant orangutan not to suspect some kind or degree
>of direct shared genetic past, a deep homology.
>If demonstrably shared evolution is more important to systematics and
>classification than tree-like segregation of gradually accumulated changes
>in introns and junk DNA, and if evolution may not be recovered in at least
>some salient cases by molecular systematics, then careful examination of
>morphology is a major clue to evolutionary relationships. So, dust off your
>1970's phenetic analysis software! Morphology will rule again!
>Richard H. Zander
>Bryology Group, Missouri Botanical Garden
>PO Box 299, St. Louis, MO 63166-0299 USA
>richard.zander at <mailto:richard.zander at>
>Voice: 314-577-5180;  Fax: 314-577-9595
>Bryophyte Volumes of Flora of North America:
>Res Botanica:
>Shipping address for UPS, etc.:
>Missouri Botanical Garden
>4344 Shaw Blvd.
>St. Louis, MO 63110 USA
>-----Original Message-----
>From: Robin Leech [mailto:releech at TELUSPLANET.NET]
>Sent: Friday, July 15, 2005 1:37 PM
>Subject: Re: [TAXACOM] Insect patronym auction (>$10,000)
>If the SYSTEM found it hard to keep, finance and/or justify alpha
>and beta taxonomists, how long can it keep on financing and justifying
>molecular taxonomists who, for the most part, are not solving problems
>at the higher taxa levels, but most often at the genus and species level?
>It takes a great deal of money to keep a molecular biologist in equipment,
>and upgrades of equipment, in first-class space to keep all this equipment,
>and a fair degree of high maintenance of all the equipment.
>I guess my main question is this: how much longer will this molecular fad
>continue until the common sense of alpha and beta taxonomists returns to
>the funding agencies?
>Recently, as an associate editor of The Canadian Entomologist, I had the
>surprise of finding that taxonomists whom I have known for years could
>not deal with a manuscript sent to us.  We sent the MS to two people,
>neither of whom i a beetle taxonomist, but both of whom are molecular
>taxonomists.  Apparently it is the analytical process that has to stand up.
>In my mind, I could not help but compare the molecular biology approach
>to that of numerical taxonomy (Sokal and Sneath) of the early 60s.  Will
>molecular taxonomy go the same route as numerical taxonomy?
>Robin Leech

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