[Taxacom] Congruence of gene trees

Sat Aug 15 11:26:38 CDT 2009

Michael:

Interesting. So you are saying that an ancestor that is morphologically
polymorphic gives rise to multiple descendants that reflect those
polymorphisms variously. AND are you also saying that an ancestor that
is molecularly polymorphic also gives rise to multiple descendants with
various distributions of those molecular polymorphisms? 

THUS are you also saying that any group of, say, three exemplars that
are supported in three different ways by different gene lineages are all
derived from that same ancestor. SO if there is evidence that there is
differential lineage sorting, then molecular analysis cannot be used to
distinguish a correct species tree for the taxa involved because there
is no one correct species tree and all the taxa are derived from a joint
ancestor with polymorphic genes? 

So if John Grehan can find differential lineage sorting with
well-supported but different gene trees for configurations of orang,
man, chimp and gorilla, then the molecular evidence cannot be used to
disprove or decide against a morphological analysis of relationships? 

Are you implying this? Are you saying that if there are many gene trees
supporting one tree and only are few supporting other configurations,
then we should not choose the configuration (topology) of the one
supported by the most or the overwhelming number of gene trees from
different genes?

This is NOT following dogma, Michael! Doubtless one of the excellent
phylogeneticists among us will explain why my take (above) on your
message is totally wrong.

R.

*****************************
Richard H. Zander 
Voice: 314-577-0276
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166-0299 USA
richard.zander at mobot.org
Web sites: http://www.mobot.org/plantscience/resbot/
and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Non-post deliveries to:
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________________________________

From: Michael Heads [mailto:michael.heads at yahoo.com] 
Sent: Friday, August 14, 2009 7:11 PM
To: Richard Zander
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Congruence of gene trees

Hi Richard,

Ancestors may be polymorphic (cf. Heads, M. 1985. On the nature of
ancestors. Systematic Zoology 34: 205-215.). If lineage sorting in the
ancestor is incomplete there is no 'clean slate' (pure monomorphism) in
the ancestor before a new round of differentiation begins. The old
polymorphism may be inherited and may have a spatial distribution quite
different from the new break. The end result of incomplete lineage
sorting in the ancestor - the incongruence - is similar to that of
hybridism, but ILS occurred before the differentiation of the new
subclades, hybridism after.  ILS explains incongruence in any character
tree, molecular or morphological. See also: Heads, M. 2009.  Darwin's
changing ideas on evolution: from centres of origin and teleology to
vicariance and incomplete lineage sorting. Journal of Biogeography 36:
1018-1026.

Michael Heads

Wellington, New Zealand.

My papers on biogeography are at: http://tiny.cc/RiUE0

--- On Sat, 8/15/09, Richard Zander <Richard.Zander at mobot.org> wrote:

	From: Richard Zander <Richard.Zander at mobot.org>
	Subject: [Taxacom] Congruence of gene trees
	To: "Jason Mate" <jfmate at hotmail.com>, "Taxacom"
<taxacom at mailman.nhm.ku.edu>
	Date: Saturday, August 15, 2009, 11:18 AM

	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 
	Voice: 314-577-0276
	Missouri Botanical Garden
	PO Box 299
	St. Louis, MO 63166-0299 USA
	richard.zander at mobot.org
<http://us.mc383.mail.yahoo.com/mc/compose?to=richard.zander@mobot.org> 
	Web sites: http://www.mobot.org/plantscience/resbot/
	and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
	Non-post deliveries to:
	Missouri Botanical Garden, 4344 Shaw Blvd., St. Louis, MO 63110
	*****************************

	-----Original Message-----
	From: taxacom-bounces at mailman.nhm.ku.edu
<http://us.mc383.mail.yahoo.com/mc/compose?to=taxacom-bounces@mailman.nh
m.ku.edu> 
	[mailto:taxacom-bounces at mailman.nhm.ku.edu
<http://us.mc383.mail.yahoo.com/mc/compose?to=taxacom-bounces@mailman.nh
m.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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