[Taxacom] Genes Versus Proteins

Kirk Fitzhugh kfitzhugh at nhm.org
Fri Nov 16 05:46:35 CST 2012


I'm curious about your statement,  "I welcome this as years of experimenting with morphology has show that we get more empirically based evolutionary histories from gene sequences." In what way are sequence data any more 'empirical' than other classes of observations? Evolutionary histories of what? The sequences? What about the plethora of other observations one can make that also require evolutionary explanation? Just curious.

Kirk


________________________________________
From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-bounces at mailman.nhm.ku.edu] on behalf of Ashley Nicholas [Nicholasa at ukzn.ac.za]
Sent: Friday, November 16, 2012 12:45 AM
To: Louis Ronse de Craene; John Grehan; taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Genes Versus Proteins

Thanks Louis,

We have the same problem in South Africa -- at Phd level DNA has to be done (and funders will often only fund this type of research). However, I welcome this as years of experimenting with morphology has show that we get more empirically based evolutionary histories from gene sequences. Although we do have emense problems finding fast evolving genes for recent families which have undergone spectaular radiation promoted by glacial and interglacial periods. However, I also insist that my students do lot of fieldwork and morphological studies. I am probably going to be shot for this -- but a gene tree by itself (if uncorrelated with other levels of manifestation especially morphology) gives a rather one dimensional and limited perspective of what is going on.

I still make my PhD students do a morphologically based classification (guided by the gene trees) as part of their PhDs and require all of them to be able to name a new species based on morphology if they have to. Our taxonomies are heavily used by people in the biodiversity industry -- who require keys and discriptions based on morphology.

At present many of our older South African taxonomists are retiring and are not being replaced, leaving many large and complex families without experts and without the expertise to do routine identifications that one can trust. We will suffer in the future because of this imbalance. Fortunately, I am blessed to be in a university that does not suffer from this short sightedness.

Regards Ashley

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Louis Ronse de Craene
Sent: 15 November 2012 19:15
To: John Grehan; taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Genes Versus Proteins

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
>>
>> Department of Biology
>>
>> Saint Mary's College
>>
>> Notre Dame, IN 46556
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>> Tel: 574-284-4674
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