BEAST time trees with equal branch lengths - is this/are these equivalent to an ultrametric tree(s)

[John Morathy]

Dear All,

 

    I have what may be a beginner's question, but here goes:  I am using a program that requests an ultrametric tree as input to determine, among other things, the informativeness of certain loci.  Since the dendrogram-like tree produced by BEAST (labeled time) has equal lengths, is this in fact an ultrametric tree?  I've been scouring the web but have not found a satisfactory answer.  My tree was built using:  GTR + Gamma + Inv, a relaxed log normal clock, and a Yule process prior.  If my assumption is incorrect, would anyone know a program that can accomplish the task, perhaps using a BEAST subst. tree as input.

 

Cheers

[Santiago Sánchez]

Hi John,

The answer to your question is is yes, BEAST does output ultrametric trees. However in BEAST you can make use of different clock models to estimate the amount time since the last common ancestor of each of your sampled terminals. Each clock model has different underlying assumptions and parameters, but in general you have strict (assumes a global rate across the tree), relaxed clocks (branch rates drawn from lognormal or exponential distributions), which can accommodate for among-branch rate heterogeneity (some genes evolving faster in some lineages than in others), and local clocks which allow different clocks in different parts of the tree. Also, BEAST outputs a sample of trees from the posterior distribution, which can be condensed into a summary tree (e.g. MCC tree) including mean or median values (plus 95% Hights Posterior Density intervals) for node heights, branch rates, branch lenghts, and clade posterior probabilities. This summary tree is also ultrametric. If no  prior information is known about time scales in divergence (e.g. Fossil data, molecular clock rates) analyses can still be performed by fixing rate estimates to 1 in BEAuti.

Hope it helps.

Cheers,

Santiago

--
You received this message because you are subscribed to the Google Groups "beast-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to beast-users...@googlegroups.com.
To post to this group, send email to beast...@googlegroups.com.
Visit this group at http://groups.google.com/group/beast-users.
For more options, visit https://groups.google.com/d/optout.

--
Santiago Sánchez-Ramírez

Department of Ecology and Evolutionary Biology, University of Toronto

Department of Natural History (Mycology), Royal Ontario Museum

100 Queen's Park

Toronto, ON

M5S 2C6

Canada

Other email: santiago...@mail.utoronto.ca

Tel. 416-586-8025