This sounded wrong to me, as the OU process should be agnostic to the dataset: 
There are no restrictions inherent in the OU process that apply particularly to 
phylogenetic data, whether the tree is ultrametric or not. I re-read Slater 
2014 and it is clear that you can use branch length transformations with OU, so 
long as you use the (correct) Hansen formula, not the Butler-king formula, 
which does indeed require an ultrametric tree.



Sent from my iPhone

> On 12 Jun 2018, at 8:01 am, David Bapst <> wrote:
> Just to follow off what Lucas said, but please note you cannot rescale
> branches of a phylogeny using an OU model when the tree is
> non-ultrametric (such as when it contains extinct, fossil taxa as
> tips). Slater (2014, MEE) discusses this more in a brief correction to
> Slater (2013).
> I don't know if anyone in this conversation has a non-ultrametric
> tree, but I wanted to make that clear for anyone who stumbles on this
> thread n the future using a google search.
> -Dave
>> On Sun, Jun 10, 2018 at 12:25 PM, Lucas Jardim <> 
>> wrote:
>> Hi Bruno,
>> You can transform the branches of your phylogeny using the estimated
>> parameters of OU models. Then, if those models describe the observed data
>> adequatly, the transformed tree should model the observed data as a
>> Brownian motion model. So you can use an ancestral state reconstruction
>> based on Brownian motion model. However, I do not know if that is the best
>> approach as optimum values would not be included into the reconstruction
>> process.
>> Best,
>> --
>> Lucas Jardim
>> Doutor em Ecologia e Evolução
>> Bolsista do INCT-EECBio (Ecologia, Evolução e Conservação da
>> Biodiversidade)
>> Instituto de Ciências Biológicas
>> Laboratório de Ecologia Teórica e Síntese
>> Universidade Federal de Goiás
>>        [[alternative HTML version deleted]]
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> -- 
> David W. Bapst, PhD
> Asst Research Professor, Geology & Geophysics, Texas A & M University
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