[Taxacom] Congruence of gene trees

[John Grehan]

As Michael Heads has pointed out, ancestral polymorphism may explain
incongruence, not only between genes, but also morphological characters.
I've never counted the number of genes that are more similar between
particular primate taxa, but it can be tricky as the analyses may be
different, and the number of outgroup samples (when used) vary widely -
although in all cases concerning human origins are laughably small.

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: Friday, August 14, 2009 7:19 PM
To: Jason Mate; Taxacom
Subject: [Taxacom] Congruence of gene trees

Disparate congruence of results of different genes (sequences) between
the sequences has long been known. Many gene trees have apparently
different histories (differential lineage sorting). Some trios (like
man, chimp, gorilla) have most genes supporting one tree (man, chimp
terminal) and about equal but fewer numbers of genes supporting two
alternative full resolutions (man, gorilla terminal) and (chimp, gorilla
terminal). All or many gene trees may be well supported, which supports
their discrepant histories. But then the distributions become governed
by small sample statistics (requiring assumed distributions) in most
cases but a few.

The explanation is fairly well-known, but the functional basis as it
affects statistics is not understood at least by me. Okay, the null is
not that all three trees are equal in probability, but instead the null
is that only one tree is possible given shared ancestry. The null is
that some process forces some gene trees into wrong configurations, and
this process is equiprobable in the two alternative wrong
configurations. We then assume that the two least common configurations
are probably the wrong ones. I think that works okay. 

So what is the process that makes some trees wrong? Why is it
equiprobable for all possible trees? Is it "oh, I'm late homogenizing in
the population" and two polymorphisms are fixed during speciation
instead of one? Or some selection might be involved such that
equiprobable wrong configurations are not to be expected?

Someone enlighten us?

*****************************
Richard H. Zander
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Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166-0299 USA
richard.zander at mobot.org
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and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
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*****************************

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Jason Mate
Sent: Friday, August 14, 2009 5:31 PM
To: Taxacom
Subject: Re: [Taxacom] Molecules vs Morphology I am somewhat confused by
this. If evolution does not act on every aspect of the organism equally
all the time and lineages are independent why would you expect
congruence throughout? You can  have local incongruence between any two
particular datasets simply out of chance or because the gene-tree of one
molecular dataset is different from the other due to the speciation
process. It is the average of many datasets that you want as your
best-available-hypothesis.


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