[Taxacom] Genes Versus Proteins

John Grehan calabar.john at gmail.com
Thu Nov 15 10:51:37 CST 2012


To clarify (or muddy the waters further), all morphology is genetic and all
morphology is environmental. In systematics one is concenred with
hertitable features that are consistent for taxa, whatever they are called.
My previous comments were directed at the false dichotomy between
morphology and (molecular) genetics.

Over time there has been a quest for the holy grail in molecular
systematics, and at the same time variouis theorist would claim the truth
of one particular source of molecules (protiens, amino acids, 'genes' etc)
as the refutation of morphology, another group of theorists would come
along and denounce them and claim to have found the new holy grail (e.g.
SINE's), and so it goes on. Same for analytical methods.

John Grehan

On Thu, Nov 15, 2012 at 8:44 AM, Ashley Nicholas <Nicholasa at ukzn.ac.za>wrote:

> Discounting epigenetic variation, I agree that all morphology is probably
> genetically controlled (although I feel uncomfortable about saying this -
> there goes that feeling of uncertainty again). I stand to be corrected
> here, and would like feedback on this. My impression is that the
> genes/genome expresses the potential of what can possibly be expressed  --
> however, in reality not all of that potential is actually expressed. If we
> want to know what is actually being expressed we really need to look at the
> proteins (the direct result of genetic expression). In consequence, I have
> been toying with the idea of returning to proteomics - especially for
> trying to understand diversification in metapopulations and species
> complexes in which divergence is very recent. However, the idea of carting
> liquid nitrogen into remote areas on almost non-existent roads is a barrier
> that has put me off. I am also told that proteomics is much more expensive
> to do than gene sequences. Micro-satellites seems the next best thing to do
> - although many years ago I found RAPIDs a good way to explore the
> diversity existing in gene pools of a single species. I guess most journals
> though would no longer be prepared to publish papers using RAPIDs?
>
> My question then to people reading this thread is "is it better to look at
> genes or proteins when trying to understand recent divergence (which would
> give a better indication of the possible causal events guiding divergence)
> in metapopulations or species complexes?"
>
> Ashley
>
> From: Richard Jensen [mailto:rjensen at saintmarys.edu]
> Sent: 13 November 2012 20:31
> To: John Grehan
> Cc: Ashley Nicholas; taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] FW: cladistic analysis for morphological characters
> -- UPGMA is not cladistics
>
> "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
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> Tel: 574-284-4674
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