[R-sig-phylo] diversification analysis for non ultrametric trees

ppiras at uniroma3.it ppiras at uniroma3.it
Wed Nov 9 03:54:22 CET 2011

Hi Emmanuel,
Thankyou very much for your reply. In fact the rwb()
function (library paleoPhylo; thanks to Thomas Ezard
for some extra code) does much of the things I need.
Some other methods are not yet implemented for non
ultrametric trees. For now...

Hi Paolo,

The methods you cite (and many others in several
packages) have been developed to analyse trees without
fossils, so these trees are ultrametric by nature, not
by necessity. A tree with fossils should be analysed
with appropriate methods, some of them are available
in packages paleoPhylo and paleoTS.


-----Original Message-----
From: ppiras at uniroma3.it
Date: Tue, 8 Nov 2011 15:03:37
To: <emmanuel.paradis at ird.fr>
Cc: Joe Felsenstein<joe at gs.washington.edu>;
<r-sig-phylo-bounces at r-project.org>; R-phylo
Mailing-list<r-sig-phylo at r-project.org>
Subject: diversification analysis for non ultrametric

Hi all,
I would like to try some diversification analyses
using medusa or related methods(gamma stat, Quasse,
However, my tree is highly NOT ultrametric as it
includes many extinct (and sometimes very old) taxa.
>From literature it seems that these methods are not
applicable to non ultrametric trees.
I write to ask you if some branch length adjustments
to make the tree ultramteric (i.e. grafen method,
etc.) are acceptable in order to explore patterns of
diversification among my taxa using existing methods.

Thankyou in advance for suggestions

Paolo Piras

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