Question: Outgroup And Tree Display In Phylogenetic Analysis
gravatar for Yongjie Zhang
6.5 years ago by
UC Berkeley, USA/ Shanxi Univ, China
Yongjie Zhang80 wrote:

Hello all,

I have two questions concerning parsimony phylogenetic analysis in PAUP.

1) When to define outgroups, before or after heuristic searches? I noticed someone stated that do not use the entire out-group as the root, as this forces the putative in-group to form a monophyletic group. I have two outgroup taxa in my dataset, what's the correct practice for me?

2) I had more than 1 trees retained after heuristic search. Which tree should I use to display? Someone said "When multiple MP trees were produced, the tree chosen for display in a figure was the one determined to be most likely using substitution models suggested by ModelTest". But how to know which tree is most compatible with the suggested model?

Any comments are welcome. Thanks.


ADD COMMENTlink modified 5.2 years ago by Biostar ♦♦ 20 • written 6.5 years ago by Yongjie Zhang80
gravatar for Joseph Hughes
6.5 years ago by
Joseph Hughes2.8k
Scotland, UK
Joseph Hughes2.8k wrote:

1) To select one of your outgroup taxa and state clearly that that taxa was used as an outgroup to root the tree for visualisation, perhaps choose the one with the longest branch

2) In PAUP, set the criterion to likelihood, using the command it would be

set criterion=likelihood;

Specify the best substitution model according to ModelTest, for example HKY:

lset nst=2 basefreq=empirical variant=hky;

Obtain the likelihood score under that model for the trees retained after the Maximum parsimony heurist search:

lscores all;

Sorry, I am not familiar with the GUI interface but it must be something rather similar.

ADD COMMENTlink written 6.5 years ago by Joseph Hughes2.8k

Thanks, Joseph. Could you please explain more on the first question? Do you know if there is difference if I define the two outgroup taxa before the implementation of heuristic search, or use the the outgroup taxa to root the tree after heuristic search?

I know from a paper that "do not use the entire out-group as the root, as this forces the putative in-group to form a monophyletic group." Does that mean I have to use only one outgroup taxon to root the tree?

ADD REPLYlink modified 6.5 years ago • written 6.5 years ago by Yongjie Zhang80
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