[Taxacom] (no subject)

[John Grehan]

I agree with Richard about gene trees not necessarily matching species
trees. I don't know what the answer will be for the
molecular-morphological incongruence.

I have never had the time to quantify molecular-morphological
correspondence in primates so I do not know if 'most' of the ape/monkey
molecular tree matches what is expected from morphology. But there is
quite a lot of incongruence, and some other primate morphological
groupings have been overturned on the basis of molecular similarity. On
the other hand, there are good morphological studies and bad
morphological studies (we argued, for example, that the morphological
studies supporting the chimpanzee theory of human origins were bad -
many characters that were incorrect, undocumented, unsubstantiated) so
sometimes the molecular result is later found to agree with further
morphological research. 

Some groups, such as tarsiers, seem to be forever in molecular limbo. 

I don't think it is for me to figure out what might be wrong with
molecular similarity (although we do provide some possibilities). Its
for the molecular folk to figure out, just as much as it was for us, and
not the molecular folk, to figure out the morphological argument.

John Grehan


> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Richard Zander
> Sent: Monday, July 27, 2009 11:26 AM
> To: taxacom at mailman.nhm.ku.edu
> Subject: [Taxacom] (no subject)
> 
> Taxacom is where we can share curiosities and problems. Some of us
lurk
> and learn, some lock and load, others get entertained, and we switch
> places depending on the topic. In honor of John Grehan's return to
> Taxacom, I submit an idea of what he might possibly mean when he says
> molecular data could be wrong and the true tree is ((man, orang)
chimp,
> gorilla) or somthing on that order. Bear with me on this, since this
has
> to do with self-taught statistics, which could be a good thing because
it
> frees one from the competing schools, but is probably bad.
> 
> Different genes give different gene histories when their time of
> divergence is different from speciation events. Some genes seem to
track
> species trees better than others, but given any three taxa terminal on
a
> molecular cladogram, of say 40 DNA sequences analysed, maybe half or
2/3
> support one of the three possible resolved trees, and the other two
trees
> are supported about half and half by the other DNA sequences. IF the
null
> hypothesis is that different trees have an equal chance of appearing
given
> equal chance of gene trees, then a superfluity of one gene tree would
tend
> to support that gene tree as the species tree.
> 
> E.g. In the meta-analysis by Satta et al. (2000) of 39 hominoid loci,
23
> supported the ((Homo Pan) Gorilla) gene tree, 8 supported ((Homo
Gorilla)
> Pan), and 8 supported ((Gorilla Pan) Homo).
> 
> This works fine if one assumes all apes have a similar distribution of
> right (matches to species tree) and wrong gene trees. The mechanism of
> delayed gene history is understood, and one should be able to do a
> calculation that chi-square indicates the above distribution would
occur
> by chance alone only 2 percent of the time (null proportion of 1/3).
You
> can try this yourself:
> http://faculty.vassar.edu/lowry/csfit.html
> 
> But the number of terminals on the tree are small, and the null may be
> wrong. Do other apes have this kind of distribution of more right gene
> trees than wrong? How do you tell? One way is to examine more than 30
gene
> sequences and see what kind of distribution we have? Is it much
skewed?
> 
> E.g. the magic number 30 is apparently that minimum number of
observations
> that allow calculations without prior assumptions of distribtuion. For
> instance, we test if a coin is loaded by flipping it. Given a binomial
> distribution (two equal columns of observations to match the normal
curve)
> each should appear 50% of the time. But coins are not binomially
> distributed, since the head side is heavier, and the actual
distribution
> (small as it is) requires not small number analysis (with assumptions
of
> binomial distribution) but large number analysis (to see if there is a
> difference between expected number of heads from a coin naturally
slightly
> loaded on the heads side and the number of heads from the particular
coin
> you are flipping to see if it is additionally loaded and unlike other
> coins.
> 
> Thus, gene tree histories may be different from species tree histories
by
> (1) chance alone, and (2) gene histories different from species
histories
> in each taxon that may be due to linkage, selection, and whatnot that
may
> confound analysis of shared ancestry.
> 
> As to (1), it could be that by chance alone the most common gene tree
is
> not the species tree in the great ape complex. How might we tell this?
A
> broad survey of lots of gene sequences might do it so we can maybe
> postulate a poisson distribution which would never demonstrate
anything as
> wrong as that which we see in great apes, but we don't have this.
> 
> Another way is to see if the gene tree of many sequences but
> parsimoniously reflecting the most common approximates a tree from a
> different class of data. Grehan suggests or implies or could imply, I
> think, that most of the ape/monkey molecular tree matches what is
expected
> from morphology, but not with the great apes, and this difference is
> statistically to be expected (an occasional wrong inference because
such
> occurs by chance alone, say 2% of the time). Is this right? Anybody
who
> knows this kind of statistics better than me (doubtless anyone who has
> actually taken a course) have an opinion?
> 
> As to (2), there may be a mechanism that warps the null of all
different
> gene tree histories being equally likely. This could be selection,
> linkage, mistaken orthology, or maybe cussedness. Then, the most
unlikely
> gene tree might match the species tree in great apes. Grehan has to at
> least demonstrate what these mechanisms might be and how they work to
make
> his point better.
> 
> _______________________
> Richard H. Zander
> Missouri Botanical Garden
> PO Box 299
> St. Louis, MO 63166 U.S.A.
> richard.zander at mobot.org
> 
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