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

Dan Lahr dlahr at ib.usp.br
Mon Nov 19 07:26:20 CST 2012


I'm sorry John, maybe I did not make myself clear.  I meant character
choice, that is, defining what is are putative states of a homologous
character is always defined by the researcher.  This is primary homology
(sensu de Pinna 1991).  What you mean is secondary homology, that is
putative homology that has been tested and shown not to be homoplastic via
an explicit hypothesis test (a cladogram, again, sensu de Pinna 1991).  We
never test whether character choice was reasonable, and that is where both
molecules and morphology are similar (cf. nixon and Carpenter 2011).

Dan

On Sat, Nov 17, 2012 at 8:36 PM, John Grehan <calabar.john at gmail.com> wrote:

> Dan,
>
> I would disagree that in morphological analyses it comes down to the
> systematist what will be considered homologous or not. That would be like
> making a god out of each systematist! No, my view is that in morphology it
> is the evidence itself that is up for analysis by anyone. That is what
> happened with the morphology of higher primates. Various systematists made
> claims about various characters and it was possible to demonstrate that
> much of the evidence for particular phylogenies either did not exist, or
> was wrong, or ignored other contradictory evidence.
>
>
>
> The main challenge for morphology is not the subjectivity that may
> be invoked  but finding the darned character differences in the first
> place. Its sometimes like looking for a needle in a haystack.
>
>
>
> John Grehan
>
> On Sat, Nov 17, 2012 at 4:36 PM, Dan Lahr <dlahr at ib.usp.br> wrote:
>
> > Hi John,
> >
> > I disagree. Not everything goes in a molecular phylogenetic analyses.
> > There are multiple lines of thought about this, in sum it is all about
> > which sites can be confidently assigned as homologous or not.  There are
> > manual and automated ways of doing this, but in the end, just like in
> > morphological analyses, it comes down to the systematist what will be
> > considered homologous or not. Or at least it should.
> >
> > cheers,
> >
> > Dan
> >
> > On Sat, Nov 17, 2012 at 1:17 PM, John Grehan <calabar.john at gmail.com
> >wrote:
> >
> >> One thing about morphology - the quality lies in the evidence for each
> >> individual character state. One may 'analyse' the characters by any
> number
> >> of algorithms, but in the end it is what goes in that counts. With
> >> sequence
> >> data what seems to go in is 'everything' since there is no way to judge
> >> the
> >> replacement of one base by any other. The data seem to be simply taken
> as
> >> read.
> >>
> >> John Grehan
> >>
> >> On Sat, Nov 17, 2012 at 9:42 AM, Dan Lahr <dlahr at ib.usp.br> wrote:
> >>
> >> > I agree with Dick, that is quite an unusual claim. Similarity methods
> >> are
> >> > the fastest.  If something is so large that it would actually "take
> too
> >> > long" to run UPGMA, then it would probably be impossible to analyze
> >> under
> >> > ML or Bayesian frameworks, and likely parsimony as well.  Just seems
> >> like
> >> > the person confused methods.  I have seen instances where people have
> >> used
> >> > NJ or UPGMA for seriously large datasets, but these are usually
> >> > bioinformatics people asking specific questions, they know the
> pitfalls
> >> (or
> >> > should).  It may also be common practice among genetics labs if they
> are
> >> > looking at very recently diverging entities (pathogenic bacterial
> >> lineages
> >> > perhaps) where using probabilistic models would make very little
> >> difference
> >> > -- lineages have not had time to saturate different substitution
> sites,
> >> but
> >> > you always have the issue of convergent hits.
> >> >
> >> > More interestingly though, you raise an issue that has always bothered
> >> me:
> >> > people using multiple reconstructions methods.  I'll start by saying I
> >> do
> >> > not have a strong stance nor the answers to this question.
> >> >
> >> > In principle, it seems philosophically incoherent -- you should
> choose a
> >> > strategy and stick with it, many of the different analytical methods
> are
> >> > logically incompatible.  It is also naive to think that in some
> >> situations
> >> > different methods would yield different results, provided you do
> things
> >> > correctly.  And if they end up yielding distinct results, what do you
> do
> >> > with them?  For instance, the biggest strength and at the same time
> >> > Achilles heel of Bayesian methods is that you can define "priors",
> which
> >> > are basically distributions of values that you believe, a priori,
> should
> >> > contain your answer.  To simplify, if you were trying to estimate
> which
> >> > exact spot an object would hit after you release it, your prior could
> >> say
> >> > that the general direction it should move is the floor, because we are
> >> > standing on Earth with a gravitational effect.  However, most people
> >> define
> >> > flat priors (meaning they don't believe a priori that any result is
> more
> >> > likely than another), which in practice this makes the analyses
> >> equivalent
> >> > to ML (this is my interpretation, I may be wrong).  I have done this
> >> myself
> >> > many times (the power of editors) but I feel like we need to be more
> >> > explicit in our logical choices.
> >> >
> >> > cheers,
> >> >
> >> > Dan
> >> >
> >> >
> >> > On Thu, Nov 15, 2012 at 1:51 PM, Ashley Nicholas <
> Nicholasa at ukzn.ac.za
> >> > >wrote:
> >> >
> >> > >  Thanks for the insight Dan,
> >> > >
> >> > >
> >> > >
> >> > > Sadly I do know of some labs that still routinely using phenetics
> >> > > particularly Nearest Neighbor. When I queried this, I was told by a
> >> > > colleague  that UPGMA, although the preferred method, took too much
> >> > > computation time!!!! Which I found disturbing given that science is
> >> all
> >> > > about maximizing and not minimizing the uncertainty of results. I
> must
> >> > say
> >> > > though that these labs also routinely run Maximum Likelihood and
> >> Bayesian
> >> > > Analyses using the same gene sequences. I guess they do this to
> >> assess if
> >> > > there is any congruence in the results of all three analytical
> >> methods?
> >> > >
> >> > >
> >> > >
> >> > > Regards
> >> > >
> >> > > Ashley
> >> > >
> >> > > ---------------------------------------------------
> >> > > Ashley Nicholas (PhD)
> >> > > Associate Professor & Curator Ward Herbarium
> >> > > School of Life Science,  Westville Campus
> >> > >
> >> > > University of KwaZulu-Natal,
> >> > >
> >> > > Private Bag X54001,
> >> > > Durban, 4000, South Africa
> >> > > Tel.:+27-31-260 7719 Fax.: +27-31-260 2029
> >> > >
> >> > >
> >> > >
> >> >
> >>
> http://lifesciences.ukzn.ac.za/Staff/Biodiversity/biodiv_evo_staff/Durban/nicholasa.aspx
> >> > > nicholasa at ukzn.ac.za
> >> > >
> >> > > ----------------------------------------------------
> >> > >
> >> > > Empirical scientists do not deal with the truth, we deal with
> >> hypotheses.
> >> > > At their best these hypotheses are insightful and predictive,
> however,
> >> > > nonetheless experience has shown that they are often only a poor
> >> > > approximation of reality and therefor the truth. – Ashley Nicholas
> >> > >
> >> > > —-------------------------------------------------------------------
> >> > >
> >> > >
> >> > >
> >> > > *From:* daniel.lahr at gmail.com [mailto:daniel.lahr at gmail.com] *On
> >> Behalf
> >> > > Of *Dan Lahr
> >> > > *Sent:* 14 November 2012 19:46
> >> > > *To:* Ashley Nicholas
> >> > > *Cc:* taxacom at mailman.nhm.ku.edu
> >> > >
> >> > > *Subject:* Re: [Taxacom] FW: cladistic analysis for morphological
> >> > > characters -- UPGMA is not cladistics
> >> > >
> >> > >
> >> > >
> >> > > Hi Ashley,
> >> > >
> >> > >
> >> > >
> >> > > "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."
> >> > >
> >> > >
> >> > >
> >> > > It is most certainly not.  There are only 4 options for a site
> >> (ATCG), 5
> >> > > if you count indels, and convergent hits are highly likely.
>  Molecular
> >> > > systematists or anyone that cares about molecular evolution cannot
> get
> >> > away
> >> > > with that, and that is why probabilistic methods are used instead of
> >> > > similarity methods.  These assume a model of evolution to infer how
> >> many
> >> > > substitutions actually took place in a specific site, even though
> what
> >> > you
> >> > > may see in modern terminals are the same base pairs for a given
> site.
> >> >  One
> >> > > of the trickiest parts is to flesh apart homology from convergence
> in
> >> > > molecular sequences, and a lot of money and intellect is poured into
> >> that
> >> > > very issue.
> >> > >
> >> > >
> >> > >
> >> > > I am not following this thread, so not sure if this is what you
> >> meant, in
> >> > > which case I apologize. I just wanted to clarify that molecular
> >> > > systematists do NOT rely on similarity methods of historical
> >> > > reconstruction.  If you do see such a case in a paper newer than
> >> 1990´s,
> >> > > then it is a glaring omission from the reviewers and editor.
> >> > >
> >> > >
> >> > >
> >> > > Kind regards,
> >> > >
> >> > >
> >> > >
> >> > > Dan
> >> > >
> >> > >
> >> > >
> >> > > On Tue, Nov 13, 2012 at 10:01 AM, Ashley Nicholas <
> >> Nicholasa at ukzn.ac.za>
> >> > > 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
> >>
> >> > >
> >> > > -----Original Message-----
> >> > > From: taxacom-bounces at mailman.nhm.ku.edu [mailto:
> >> > > taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of John Grehan
> >> > > Sent: 10 November 2012 17:08
> >> > > To: Sami Rabei
> >> > > Cc: TAXACOM
> >> > > Subject: Re: [Taxacom] cladistic analysis for morphological
> characters
> >> > >
> >> > > In my opinion its ok to make a cladistic analysis for any number of
> >> > > characters. It just depends where those characters are clustered
> >> within
> >> > the
> >> > > group analyzed as to the result. I suspect that unless the
> characters
> >> are
> >> > > dispersed throughout the 44 species, there will be some clades that
> >> have
> >> > > some measure of good support, others that do not, and others that
> >> whose
> >> > > relationships are unresolved.
> >> > >
> >> > > I'm a bit out of touch with all methods, but I recall UPGMA is a
> >> phenetic
> >> > > method?
> >> > >
> >> > > John Grehan
> >> > >
> >> > > On Sat, Nov 10, 2012 at 6:45 AM, Sami Rabei <samirabei at mans.edu.eg>
> >> > wrote:
> >> > >
> >> > > > Dear All
> >> > > >
> >> > > > I have 81 morphological characters for 44 species. it is right to
> >> make
> >> > > > a cladistic analysis for them. If it is ok which program I can use
> >> > > > it.On the other hand I did UPGMA .
> >> > > >
> >> > > > Many Thanks in advance
> >> > > >
> >> > > > All the best.
> >> > > >
> >> > > > Sami Rabei
> >> > > >
> >> > > > http://mansoura.academia.edu/SamiRabei
> >> > > >
> >> > > > ----------------------------------
> >> > > > With my Best Wishes
> >> > > > Sami Hussein Rabei, Ph.D.
> >> > > > Botany Department
> >> > > > Faculty of Science,
> >> > > > Damietta University
> >> > > > New Damietta , Post Box 34517
> >> > > > Damietta
> >> > > > Egypt .
> >> > > >
> >> > > > Tel. Mobile:   002 0127 3601618
> >> > > > Tel. Work:     002 057 2403981
> >> > > > Tel. Home:    002 057 2403108
> >> > > > Fax:              002 057 2403868
> >>
> >> > > >
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> >> > > --
> >> > > ___________________
> >> > > Daniel J. G. Lahr, PhD
> >> > > Dept of Zoology, Univ. of Sao Paulo, Brazil
> >> > >  ======= Please find our Email Disclaimer here-->:
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> >> > --
> >> > ___________________
> >> > Daniel J. G. Lahr, PhD
> >> > Dept of Zoology, Univ. of Sao Paulo, Brazil
> >>
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> > Dept of Zoology, Univ. of Sao Paulo, Brazil
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-- 
___________________
Daniel J. G. Lahr, PhD
Dept of Zoology, Univ. of Sao Paulo, Brazil



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