[Taxacom] Genes Versus Proteins

Ashley Nicholas Nicholasa at ukzn.ac.za
Thu Nov 15 10:44:22 CST 2012


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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