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long-branch attraction



George,
I read about some software that is basically Maximum Parsimony with some tinkering to reduce the effect of long-branch attraction. It was called Higher Order Parsimony (or maybe it was High Order Parsimony). I have no idea if it works or not, but at least someone thinks they have something that helps.
-------Cheers, Ken
********************************************************
From: Dinogeorge@aol.com
Reply-To: Dinogeorge@aol.com
To: dinosaur@usc.edu
Subject: Re: Triassic Sauropods
Date: Fri, 6 Apr 2001 19:06:43 EDT

In a message dated 4/6/01 2:29:51 PM EST, twilliams_alpha@hotmail.com writes:

<< Perhaps in overall form, but the devil's in the detail.
_Opisthocoelicaudia_ shows a *lot* of titanosaurian characters, and I don't
think they can be discarded just be invoking the specter of "convergence".
("Convergence is an insidious and treacherous trap, baited and waiting for
the unsuspecting worker... etc etc) >>


Here's how long-branch convergence works. Suppose you and a friend play a
game of heads and tails. He tosses a coin, you toss a coin. If the coins come
up alike (heads-heads or tails-tails), you win; if the coins come up unalike
(heads-tails or tails-heads) he wins. After a couple of hundred tosses,
you'll both be about even, usually. His string of tosses will match your
string of losses about 50% of the time. Your tosses and his tosses are random
and completely unrelated, yet they share about fifty "similarities."


Now replace each pair of coin tosses by a different bistate character in two
related taxa being analyzed cladistically. Let the taxa evolve for a few
million years to give the characters some time to shake out (a "long branch";
this amounts to playing the game with a few score coin tosses). What happens?
Quite a few characters, just by chance, are going to shake out the same way,
just like your coin tosses being alike 50% of the time. This is the "noise"
in cladistic analysis. How many characters have to shake out alike before you
have a genuine phyletic relationship? Take a look at the character lists for
oviraptorosaurs and segnosaurs listed in the Alxasaurus article (for
example). The similarities are all over the map, no system to them. Does this
amount to relationship, or is this just long-branch noise? Likewise with the
sauropods. Are the similarities between Opisthocoelicaudia and titanosaurs
noise, or are they indicative of some kind of close phyletic relationship?


Euhelopus has a similar problem in Sereno's analysis.

And this long-branch problem afflicts molecular analyses perhaps even worse
than it afflicts morphological analyses, since amino-acid sequences and DNA
sequences are more like discrete coin tosses than are morphological
characters.

I'd like to hear comments about how cladistic analyses might get around this
problem.
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