Fwd: Re: [TAXACOM] genetic vs morphological trace o f phylogeny

[Richard.Zander at MOBOT.ORG]

The Batzler study, although using SINEs (apparently the dernier cri of
molecular methods), is an example of Reciprocal Obfuscation.

Oh, (((H,P)G)O) is probably correct, but the Batzler study does not nail it
down.

Reciprocal Obfuscation works like this. You go into a magician's supply
store to buy, for good and sufficient reasons, a loaded coin. There are two
glass jars of quarters labeled Loaded on Heads, and Loaded on Tails, $5.00
each. You ask for one loaded on heads and pull out your wallet. The sales
persons removes one from the Loaded on Heads jar and says, "Let's check it,
just so I didn't mix them up" and flips the coin, once, and it falls heads
up. "There ya go," he says.

What do you do? Well, you ask for more flips since it may not be loaded
strongly and a Loaded on Tails coin may have been mistakenly dropped into
the Loaded on Heads jar. Thus, more info that supports a hypothesis, if
dubious, may cause a perception of decreased reliability.

The Batzler study is really, really impressive, but there are some lacunae:

1. Sequence alignment is a consensus. Parsimony is often used during
sequencing when alignment by eye is difficult. Gap costs are often involved
and they are rather arbitrary. Is the final cladogram robust to different,
less parsimonious alignments, or different but reasonable gap costs? No
info.

2. Dollo parsimony is reasonable given the sequence over time of insertions.
But that is somewhat circular and is allowable only if a different sequence
over time is unreasonable. How to demonstrate that? Is the cladogram robust
to non-Dollo parsimony? Are Alu insertions definitely random in place of
insertion in a sequence and can they be lost and regained in place?

3. Are Alu traits independent? Certainly they can be identified with unique
sequences, so are they affected by the rest of the genome and by adaptive
pressures? Are they to some extent inherited as a block? No lineage sorting?
How does one tell except by (a) comparison with other gene behavior, and (2)
the reasonableness of accepting no alternative to viewing the data set as
evidence of increasing number of insertions over time.

The phylogenetic coin is doubtless loaded, but would pay $5.00 or bet your
science on the results? Remember that to attain a 95% or 99% confidence
interval, you only have 5% or 1% wriggle room for doubt.

That said, it looks black for (((H O)P)G).



______________________
Richard H. Zander
Bryology Group
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166-0299
richard.zander at mobot.org <mailto:richard.zander at mobot.org>
Voice: 314-577-5180
Fax: 314-577-9595
Websites
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-----Original Message-----
From: A.P. Jason de Koning [mailto:apjdk at ALBANY.EDU]
Sent: Thursday, April 08, 2004 10:01 AM
To: TAXACOM at LISTSERV.NHM.KU.EDU
Subject: Re: [TAXACOM] Fwd: Re: [TAXACOM] genetic vs morphological trace
of phylogeny

SNIP

Apropos to John's crusade for a Schwartz-orang sister relationship, a recent
study by Mark Batzer's lab scored the presence/absence of 153 known Alu Ye
subfamily members across multiple individuals from 8 primate species (human,
5 apes, 2 monkeys), by PCR-amplification using primers designed against the
human genome and against primate DNAs in GenBank.  Their analysis
unambiguously resolved the conventional ((H,C),G),O) relationship.  For
John's edification, I also reanalysed their dataset as follows:

Performing an unconstrained, exhaustive search on their dataset, the
conventional relationship is resolved by a tree with 124 steps using Dollo
parsimony.  The consistency index was something like 0.999.  With John in
mind, I forced a human-orang sister relationship and performed an exhaustive
search with that constraint.  The shortest tree supporting this hypothesis
was 166 steps, and was strongly excluded by all relevant statistical
comparisons against the optimal unconstrained tree, with P < 0.0001.  (I can
post details or data if anyone wants.)

While their dataset cannot be exhaustive, and could possibly be complicated
by ascertainment bias because of using mostly human-designed primers, there
doesn't appear to be any reason to infer directional bias.

You can find a link to the source paper at:
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Ab
stract&list_uids=14561894

Cheers,
- Jason

__________________________________________________________________________
  A.P. Jason de Koning, Doctoral student        Email: apjdk at albany.edu
    Department of Biological Sciences             Lab:  (518) 442-4347
    University at Albany, SUNY                    FAX:  (518) 442-4767
    1400 Washington Ave., Albany NY 12222, USA  Mobil:  (518) 210-4504
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