[Evolution_RU] Journal Club in Evolution, Jan 26: Long Branch Attraction in Bayesian Analysis
struwe at AESOP.Rutgers.edu
Wed Jan 20 14:54:04 EST 2010
Journal Club in Evolution for Spring 2010 starts on Tuesday Jan 26, 2 PM
in 262 Foran Hall on Cook Campus, and the first subject will be a recent
paper highlighted by Dana Price (thanks, Dana!). We will discuss the
pros and cons of different phylogenetic methods as it relates to the
long branch attraction problem.
The paper is:
Long-Branch Attraction Bias and Inconsistency in Bayesian Phylogenetics,
by Bryan Kolaczkowski & Joseph W. Thornton, 2009, PLoS ONE 4(12): e7891.
Short background: Long branch attraction (LBA) is a known problem in
maximum parsimony analysis when you use highly divergent taxa, which can
result in monophyletic clades in groups that are really paraphyletic.
Maximum likelihood (ML) is less susceptible to this problem. This paper
shows the LBA effect in Bayesian Analysis.
A good introduction to the LBA and the "Felsenstein zone" is in the
lecture notes by Delwiche, available here:
Links: Wikipedia, LBA: http://en.wikipedia.org/wiki/Long_branch_attraction
Journal Club in Evolution is open to all students and faculty interested
in organismal evolution at any level (individual to phyla, genes to
morphology) and is arranged by Lena Struwe and Karl Kjer. To get all
journal club announcements and other evolution-related information
campus-wide, sign up for the Mailing list in Evolution at Rutgers:
-------- Original Message --------
Subject: [Evolution_RU] LBA and bayes
Date: Thu, 07 Jan 2010 11:02:14 -0500
From: Dana Price <d.price at rutgers.edu>
To: evolution_ru at email.rutgers.edu
In a nutshell, bayes' ability to integrate over parameter uncertainty
(i.e branch lengths) does counterintuitive things when your datasets get
bigger and bigger. The attached shows it to be hugely susceptible to
long branch attraction with posteriors converging to 1.0 on incorrect
trees, and a weakness of likelihood that may now be a strength.
Dr. Lena Struwe
Dept. of Ecology, Evolution, & Natural Resources/ Dept. of Plant Biology & Pathology
237 Foran Hall, 59 Dudley Road
New Brunswick, NJ 08901-8551, USA
phone: (732) 932-9711 ext. 235, fax: (732) 932-9441
e-mail: struwe at aesop.rutgers.edu
home page: www.rci.rutgers.edu/~struwe
GENTIAN RESEARCH NETWORK: http://gentian.rutgers.edu
Director, CHRYSLER HERBARIUM: http://herbarium.rutgers.edu
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