{[ promptMessage ]}

Bookmark it

{[ promptMessage ]}


Info iconThis preview shows pages 1–2. Sign up to view the full content.

View Full Document Right Arrow Icon
"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION" Integrative Biology 200a Spring 2008 University of California, Berkeley B.D. Mishler Dating in the 21st Century: putting dates on nodes, characters, and events This is an area of intense recent interest, yet in need of much further thought and research. There are two fundamental steps in the process of putting time onto a node or a branch of a tree: 1. Establishing the clock What is ultrametricity? Ultrametric matrix and its tree: A non-ultrametric tree: from: http://www.diku.dk/~pawel/comp-bio/ev_trees/intro/intro/ultrametric.html A. Determining whether your data fit a clock model i. relative rate tests comparing three taxa at a time, in rooted context: ii. likelihood ratio test Testing the Molecular Clock using a likelihood ratio test (courtesy of John Huelsenbeck) Under the null hypothesis, the phylogeny is ultrametric (i.e., rooted and the branch lengths are constrained such that all of the tips can be drawn at a single time plane). Under the alternative hypothesis, each branch is allowed to vary independently. The alternative hypothesis invokes s - 2 additional parameters, where s is the number of sequences. The likelihood ratio test statistic is -2logL = 2(logL0 - logL1), where L0 and L1 are the likelihoods under the null and alternative hypotheses, respectively.
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
Image of page 2
This is the end of the preview. Sign up to access the rest of the document.
  • Spring '08
  • Null hypothesis, Statistical hypothesis testing, Likelihood function, Phylogenetics, likelihood ratio test, Berkeley B.D. Mishler Dating

{[ snackBarMessage ]}