From: crogers at ecoanalysts.com (Christopher Rogers) on 2008.07.21 at 23:38:28(18209)
This is a really important issue. The same thing is happening in the
zoological realm as well. There is a big misconception that genes are all
you need. Taxonomy and systematics is being forced into purely molecular
based research, ignoring the ecological and morphological aspects. Genes are
but one tool (and a very good tool) in the tool box for identifying
organisms. The problems are as follows:
1. Less than one tenth of one percent of the species of the world have
had their genes sequenced. So, this makes it difficult to define taxa.
2. Morphological identifications are used to identify the organisms
before they are sequenced, so despite what some genetic only proponents say,
you still need morphology to have a starting point.
3. It is a very rare thing that any more than one or two individuals
from a population are sequenced. This often results in two or more
populations called out as separate species, when no one really knows what
the inherit genetic variability of the species is in the first place. This
is painfully obvious in groups like the naked mole rats of Africa and the
Middle east which are morphologically indistinguishable, yet molecularly can
be separated into two or three species up to 50% genetically different,
verses the Hawaiian fruit flies which morphologically, behaviorally, and
ecologically can be separated into several well reproductively isolated
species (they literally cannot eat the same food, cannot live in the same
humidity, are sexually active at different times of the year, and live at
different altitudes), yet genetically they are less than 1% different.
4. I am an associate editor for an international zoological journal,
and I am always receiving and rejecting genetic papers where the
researcher(s) did not deposit any specimens. One of the tenants of the
scientific method is reproducibility. Anyone should be able to reproduce the
results of someone else?s experiment. It amazes me how often some genetics
type will revise a genus, family, or species group, but does not deposit any
specimens in a museum. If I cannot go to the museum, find their material and
recreate their work, it is not science.
5. Genetic barcoding and Phylocode are also problematic.
The vast majority of my professional work and the work of my colleagues is
bioassessment, in which we use invertebrate community structure as a meter
stick of habitat health functionality. This type of habitat assessment is
far more accurate and precise at measuring habitat functionality then
chemical testing, because you are gauging the suitability and health of the
habitat using the organisms that are actually using the habitat: organisms
that are adapted to a given habitat or niche. I conduct this work in aquatic
and terrestrial habitats. What does this have to do with the classification
debate? The traditional Linnaean classifications provide us with the means
of understanding the ecology of the habitats we study. Certain orders,
families, genera and species in my quantitative samples have certain
ecological meaning. I can take a one square meter sample from a river, for
example, and depending on what taxa are there, I can tell you what metals
and pollutants are present, what nutrients, what the dissolved oxygen levels
are, what the flow regime is, how long an impacted site will take to
recover, or if a restored habitat is beginning to function naturally, how
clean the water is, etcetera. Different species, genera, and families of
invertebrates mean very different things ecologically. I could give dozens
of general, and hundreds of specific examples. Certain subfamilies of flies
in the family Dixidae will tell you different things than others. Different
mayfly genera will give you different information concerning heavy metals.
Different midge genera will tell you what type of nutrient loading (if any)
is occurring in a given site. My beloved crustaceans at order level can tell
me about pesticide contamination in certain areas. Most larval insects
cannot be identified beyond family or genus level, yet they are important
ecological indicators of water quality! Furthermore, I need dichotomous keys
to orders, families, genera and species to identify the organisms in my
samples, and some of these samples may harbor more than 10,000 individual
organisms. I need taxonomical hierarchy to identify my specimens. There is
an international bioassessment industry (I work all over the world), borne
of the desire for clean water, clean soil and clean air, as well as natural
and restored wildlife habitat, that relies on Linnaean taxonomy. Therefore,
to those of us who work in this field much of phyllocode, barcoding and
least inclusive taxonomic units are of little use, and to some of us in this
industry represent "ivory tower thinking". Organisms are a function of their
environment. Their taxonomy, in terms of their biology and ecology, are of
far greater significance to the general public who wants clean water, clean
air, and a healthy environment. If you take an organism out of its
environment, and reduce it to a mere terminus on a line, you may risk losing
everything that made it what it is.
Just my two cents worth! I hope that I have not strayed! But why do we
collect these amazing plant? For their genes or to appreciate their beauty
and complexity?
Happy days,
Christopher
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D. Christopher Rogers
Senior Invertebrate Ecologist/ Taxonomist
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EcoAnalysts, Inc.
1.530.756.4481
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Davis, CA 95616
USA
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From: aroid-l-bounces at gizmoworks.com [mailto:aroid-l-bounces at gizmoworks.com]
On Behalf Of Peter Boyce
Sent: Wednesday, July 16, 2008 10:34 PM
To: Discussion of aroids
Subject: [Aroid-l] Alpha taxonomic drought & molecular meanderings
Dear Leland,
Well, where I live unless there is a change in education policy to imbue
those few (and it is FEW) students with some botanical aptitude, to gain
knowledge of the basic building blocks of botany, notably comparative
morphology, ecology & geomorphology, the spectre of no wide-experience field
botanists, already a fact in many parts of Asia, will become a region-wide
problem. In fact the whole of taxonomy, let alone systematics, is in danger
of slipping off the curriculum in universities throughout the region such
that only the minute hard-core (essentially botanically hard-wired) folks
will make it through and continue. The problem then will be that there are
increasingly fewer jobs that call for taxonomic expertise such that those
few that wish to remain in the field usually end up earning a living doing
something at the best only tangentially associated with their passion. Of
course the irony is that there has never been a greater need for taxonomic
expertise in order to make the rational decisions required to protect the
remaining tropical habitats.
Curiously, I am not anywhere near as doubtful or indeed pessimistic about
the increasing use of molecular data and also don't altogether agree with
the total genome argument. Regarding the function of various parts of the
molecular code, in recent years there has been made enormous strides in
understanding what various coding regions 'do' such that the link with this
and evo-devo is now a well established area of scientific exploration. Of
course some of these areas are ferociously expensive but with molecular
extraction methodologies and analyses programmes increasingly simplified
costs are dropping such that even quite sophisticated extraction and
analyses methodologies are well within the budget of even quite modest
research establishments.
Regarding the usefulness of molecular data, especially vis-a-vis the ability
of the molecular practitioners to actually identify the organisms they are
studying, yes, I agree, that still far too many molecular research outputs
are the product of lab rats without any practical field training and worse
are oftentimes undertaken without or with only minimal taxonomic cross
fertilization. However, that situation is fast becoming history as more and
more multi-author research outputs based on sound alpha-taxonomy, with the
molecular toolbox being opened only once a decent 'traditional' taxonomy is
established and is testable. This is much the approach we are using, with a
multi-stranded project that is investigating alpha-tax. and then
phylogentics and then using the phylogenies to investigate spatial
evolution, etc. We have been very fotunate to find good students who are
willing to spend the necessary field time as part of their molecular-based
research and as a result have a much more complete biological research
toolbox.
Cheers
Peter
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