How to explain the results of bPTP

[王贺崐元]

Hi

I am very interested in the species delimitation analyses by bptp model.

I input my ML tree for bptp analysis and got a result. The attached file is the tree output by bptp. 

I am asking that 1) what is the colors red and blue in the tree refer to? 2) how does it tell if a species involves only one lineage or multiple lineages in the output tree of the bPTP analysis?  3) why do the terminal branches have posterior probabilities? For example, terminal branches A5 and A6 are the same species sampled in the same location, but the posterior probabilities = 0.28. Is the model delimiting A5 and A6 to two different species?

Thanks very much for your help.

Kunyuan Wanghe

[Alexandros Stamatakis]

Dear Kunyuuan,

The support values are posterior probabilities of the respective
delimitations, that is that the split defined by the respective branch
splits the tree into two distinct species.

The Bayesian version samples alternative delimitations.

So the blue and red colors show you the most plausible delimitation into
species and individuals from the same species.

Hope this helps,

Alexis

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Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Affiliated Scientist, Evolutionary Genetics and Paleogenomics (EGP) lab,
Institute of Molecular Biology and Biotechnology, Foundation for
Research and Technology Hellas

www.exelixis-lab.org