[Taxacom] Congruence of gene trees

[Richard Zander]

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
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richard.zander at mobot.org
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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.