PE (Phylogenetic endemism) question

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Julio A

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May 15, 2020, 11:31:22 AM5/15/20
to Biodiverse Users
Hi everyone!

I continue thinking that Biodiverse is a very useful tool. Each time I need to use it I find out something new and it´s amazing, but unfortunately I also find some troubles.

I  calculated the PE index, but some days ago I was having a look at this publication   https://doi.org/10.1111/j.1365-294X.2009.04311.x. I found it in the Biodiverse web in the section of indexes. In that publication the authors show a figure called  Figure 1 that makes me wonder some questions. 

Reading that publication and seeing that Figure I understand that it´s necessary to use a special phylogenetic tree. With a special phylogenetic tree I mean a phylogram, a tree that doesn´t have the same lenght in every branch as a cladogram.

I used a cladogram, every branch in my tree have the same lenght and I don´t know if it´s necessary a phylogram or something like a tree with the exchange rate in his branches (it would mean that every branch could have a different lenght as it´s shown at that paper in Figure 1).

I hope I have explained well. It´s an important question for me because I have to know it to continue working.

Thank you so much.

Shawn Laffan

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May 18, 2020, 1:58:55 AM5/18/20
to biodiver...@googlegroups.com, Julio A
Hello Julio,

The nature of the phylogenetic tree determines how you interpret the results of the analyses. 

A phylogram has branch lengths measured in units of features used to build the tree, for example base pairs or morphological characters.  A chronogram is calibrated so the branches are in units of time. 

If you calculate PD using a cladogram then the value for a location will be the number of branches.  If you use a phylogram then it is the number of features, while for a chronogram it is the sum of evolutionary time.

PE is simply a range weighted PD measure (See Laffan et al. 2016, https://doi.org/10.1111/2041-210X.12513 ), so for a cladogram it is the sum of range weighted branches.

A phylogenetic analysis would typically use a a phylogram or chronogram, but the cladogram can still be useful. It is actually what is used as the alternate tree in the CANAPE analyses.  (See http://biodiverse-analysis-software.blogspot.com.au/search/label/CANAPE ).

The above is not a definitive answer, but hopefully is useful.

There are also some members on the list who have experience accessing and/or building phyogenetic trees, so hopefully they can shed some light for you in that regard.


Regards,
Shawn.
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