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--- On Mon, 7/21/08, Christopher Rogers wrote:
> From: Christopher Rogers
> Subject: Re: [Aroid-l] Alpha taxonomic drought & molecular meanderings
> To: "'Discussion of aroids'"
> Date: Monday, July 21, 2008, 1:38 PM
> 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
>
>
>
>
>
> D. Christopher Rogers
>
> Senior Invertebrate Ecologist/ Taxonomist
>
> ((,///////////=======<
>
>
>
> EcoAnalysts, Inc.
>
> 1.530.756.4481
>
> 1.530. 383.4798 (cell)
>
> 1307 "L" Street
>
> Davis, CA 95616
>
> USA
>
>
>
> ?Invertebrate Taxonomy
>
> ?Endangered Species
>
> ?Ecological Studies
>
> ?Bioassessment
>
> ?Invasive Species
>
> ?Plankton
>
> ?Phycology
>
>
>
> Moscow, Idaho ? Bozeman, Montana ? Davis, California ?
> Joplin, Missouri
>
> Selinsgrove, Pennsylvania
>
> ecoanalysts.com
>
>
>
> 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_______________________________________________
> Aroid-L mailing list
> Aroid-L at www.gizmoworks.com
> http://www.gizmoworks.com/mailman/listinfo/aroid-l
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