[Taxacom] Genes Versus Proteins

John Grehan calabar.john at gmail.com
Fri Nov 16 05:39:09 CST 2012


The point of view expressed by Loius is extremely rare nowadays (and in the
world of higher primate systematics there would be a call for the straight
jacket). There was a posting for a PhD project in the last week that did
indeed give an 'and/or' possibility for the systematic project being
morphological or molecular, but this is rare and one wonders if any go for
morphological given the career opportunities. In US I suspect that the only
places where morphological systematics has survived to any degree at all is
in museums, but in many of those institutions the support for morphological
research has declined or has been eliminated altogether.

The ignorance of morphology is perhaps nowhere better illustrated than for
higher primates where comparative morphology remains largely stuck in the
1960's when the progress made over the preceding decades, much of it from
German researchers, came to a screaming halt. Since then there have been
various morphological studies, but often superficial and taxon limited and
often poorer quality than the earlier works. Even for human anatomy there
is little known about the precise morphology of many anatomic features (you
would think it would be otherwise), especially for variability. As for the
apes the situation is a catastrophic disgrace. Now we are supposed to
believe in the truth that chimpanzees are our nearest relative even thought
here is virtually nothing in morphology to support that. And we are
supposed to believe the orangutan is our most distant great ape relative
even though it shares specialized, and often unique (within primates)
similarities in anatomy, behavior, and physiology - including aspects of
reproductive biology that most people think of as almost defining what is
to be human. The state of comparative morphology in higher primates is so
pathetic that it was an entomologist (my wife), who first discovered that
our external ear is uniquely most like that of an orangutan. Imagine all
those primate biologists being so blind as not to be able to see the
obvious.

I would again repeat my caution about contrasting morphology and genetics.
DNA comparisons for systematics analysis is not genetics in the sense
of studying inheritance and development, but a morphological study of the
positional distribution of DNA base pairs (either singly or in groups).

John Grehan

On Thu, Nov 15, 2012 at 12:15 PM, Louis Ronse de Craene <
L.RonsedeCraene at rbge.ac.uk> wrote:

> The problem nowadays is that almost all emphasis and funding is going to
> genetic research and not to morphology.
> For students it is not possible anymore to get funding fora purely
> morphology-based PhD without any genetic tail attached to it.
>
> Although each approach has its significance and merits, the tilting of the
> balance to genetic research is dangerous, as morphological expertise is
> lost with unforeseeable consequences.
> One knows often more about the genetics of organisms than about their
> morphology and several organisms remain poorly described.
> However, biology becomes particularly exciting when one studies
> morphological evolution in the framework of a good phylogeny, which is
> mainly based on molecular data.
>
> Louis RDC
>
> Dr. Louis Ronse De Craene
> Director of the MSc course
> Royal Botanic Garden Edinburgh
> 20A Inverleith Row, Edinburgh EH3 5LR, U.K.
> Tel. +44 131 248 2804
> Fax  +44 131 248 2901
> url: www.rbge.org.uk/msctaxonomy
>
>
>
>
>
> On 15/11/2012 16:51, "John Grehan" <calabar.john at gmail.com> wrote:
>
> >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
> >>
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