[Taxacom] FW: cladistic analysis for morphological characters -- UPGMA is not cladistics

Tue Nov 13 12:30:49 CST 2012

"All morphology is genetic"?  This seems a rather extreme position and 
not even in the same sense as DNA. No allowance for phenotypic 
plasticity, etc.

Dick J

On 11/13/2012 12:19 PM, John Grehan wrote:
> I would agree with Richard that a phylogeny only explains what it 
> explains.
> Ashley makes the important point that both morphological and molecular 
> methods have their challenges and none is a silver bullet, but the 
> predominent view is that molecular methods are more reliable. As those 
> who have been on this list for some time already know that in the 
> systematics of higher primates molecular methods have been elevated to 
> the status of infaliability and an absolute falsifier of any 
> contradictory morphology.
> I would beg to differ with Ashley's characterization of morphology and 
> genetics. All morphology is genetic in the same sense that DNA 
> molecules are genetic. However, systematic analysis of DNA molecules 
> is not genetics (in the sense of inheritance), is is a comparative 
> morphology of DNA molecular composition.
> John Grehan
>
>
> On Wed, Nov 14, 2012 at 3:39 AM, Ashley Nicholas <Nicholasa at ukzn.ac.za 
> <mailto:Nicholasa at ukzn.ac.za>> wrote:
>
>     Agreed -- if it is acknowledge that the reulting phenogram is
>     assummed to be an approximation of an evolutionary tree then I
>     have no problem. The words assummed and approximation are
>     important. Many paper do not acknowledge the uncertainty that
>     surrounds their phenetically produced hypotheses because of these
>     assumtions and approximations. I am not saying don't use these
>     analyses, but I do feel we should own up to the flaws inherent in
>     all methodologies.
>
>     Classifications produced using only morphology are always treated
>     as too subjective (and I agree -- they are) however, many other
>     methods especially those that are use for molecular systematics
>     ignore the assummtions they also make. Such as evolution always
>     being parsimonious, that molecular sequences are never analagous,
>     that evolution is only cladogenic (ignoring anagenic evolution,
>     hybridization [esp. in plants], tokogeny and polygenic evolution
>     [where metapopulations of a widespread species is undergoing
>     multiple divergence and synchronised but quite separate episodes
>     of isolation]). Monospecific genera are automatically nested into
>     the clade below -- and any unique feature on any other level of
>     manifestation is just ignored. I know of labs that don't bother to
>     run control lanes when running gels. So called evolutionary trees
>     based on one gene (usually a plastid gene) are regarded as
>     representing the evolution of those organisms when in fact they
>     are just an evolutionary tree of that gene. Horizontal gene
>     transfer and epigenetics are also ignored. And, then, there is the
>     problem of sample size with large genera that may have as many as
>     300 species being used to generate cladograms/hypotheses based on
>      1% to 2% sample size.
>
>     I embrace both morphology and genetics (and other levels of
>     manifestation) -- but it is getting just a little annoying that
>     some disciplines are acting more eletist than others; especially
>     when a close examination of their fields shows them to also be
>     flawed in some ways. Not that we want funding bodies to know this
>     of course.
>
>     Cladograms, in the end, are also just hypotheses.
>
>     Regards
>     Ashley
>
>     -----Original Message-----
>     From: taxacom-bounces at mailman.nhm.ku.edu
>     <mailto:taxacom-bounces at mailman.nhm.ku.edu>
>     [mailto:taxacom-bounces at mailman.nhm.ku.edu
>     <mailto:taxacom-bounces at mailman.nhm.ku.edu>] On Behalf Of Richard
>     Jensen
>     Sent: 13 November 2012 15:46
>     To: taxacom at mailman.nhm.ku.edu <mailto:taxacom at mailman.nhm.ku.edu>
>     Subject: Re: [Taxacom] FW: cladistic analysis for morphological
>     characters -- UPGMA is not cladistics
>
>     Ashley's comments are clearly reminiscent of what Sneath & Sokal
>     wrote in their seminal texts (Sokal & Sneath 1963; Sneath & Sokal,
>     1973) on numerical taxonomy.  They referred to the 60 character
>     minimum as well as to the "matches asymptote" - as the number of
>     characters increases, the measure of similarity (or dissimilarity)
>     among OTUs is likely to stabilize.  They were also explicit in
>     stating that, while phenograms are not intended to reflect
>     evolutionary history, they will, in many cases, be a good first
>     approximation of such.
>
>     UPGMA phenograms are based on (dis)similarity matrices, and there
>     are a number of choices for determining  pairwise OTU
>     relationships.  If one wishes to use a UPGMA phenogram as an
>     approximation of evolutionary relationships, then one can choose a
>     measure that is consistent with the kinds of data and a clustering
>     algorithm appropriate both for the similarity measure used and the
>     relative numbers of OTUs in different subsets of the "ingroup".
>     Colless, Estabrook and others discussed various approaches that
>     may yield good approximations.
>
>     Cheers,
>
>     Dick J
>
>     On 11/13/2012 7:01 AM, Ashley Nicholas wrote:
>     > John you are right,
>     >
>     > UPGMA is a phenetics method and is not eplicitly evolutionary.
>     It only measures similarity, and similarity is not always a good
>     indicator of descent from a common ancestor. This is especially
>     true in flowering plants where convergent evolution/homoplasy is rife.
>     >
>     > Analogous (rather than homologous) base pair sequences are
>     probably less common than in morphology -- so maybe molecular
>     systematists can get away with approximating it to an evolutionary
>     tree. However, in the end it is not an explicit evolutionary tree
>     -- and this needs to be acknowledged rather than ignored (which is
>     what usually happens). However, no matter what, the resulting
>     phenogram is a hypothesis. This hypothesis is as valid as any
>     other hypothesis (until falsified) -- and probably carries some
>     interesting insightes and may generate some interesting questions
>     for further explorations.
>     >
>     > The text books say a minum of 60 characters is needed but I
>     would think the number of characters needed would depend on the
>     size of the group being analysed. Some statistician has probably
>     established this??
>     >
>     > Regards
>     > Ashley
>     >
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-- 
Richard J. Jensen, Professor
Department of Biology
Saint Mary's College
Notre Dame, IN 46556
Tel: 574-284-4674