AU test query

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张东

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Jun 29, 2019, 9:15:40 PM6/29/19
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Dear all,

I have two different topologies generated from 28S (tree-28S) and mitogenome (tree-MT), respectively, and I tried to conduct AU test on them using both datasets. The results (as shown below) showed that the tree-MT was rejected in the AU test using 28S dataset (28S AU test), whereas the tree-28S was rejected in the AU test using MT dataset (MT AU test). Therefore, I wanna to know how AU test compare the topologies? Does it first selects a tree with highest logL, and then compares each of the user trees to this tree? If take the my results (below) as example, I am comparing tree-MT to tree-28S in 28S AU test, and comparing tree-28S to tree-MT in MT AU test. 

If I am wrong, what is tree-28S comparing to in 28S AU test? and what is tree-MT comparing to in MT AU test? 


AU test based on 28S dataset (iqtree -s 28S.phy -m GTR+G -z trees.treels -n 0 -zb 10000 -au).

Tree      logL    deltaL  bp-RELL    p-KH     p-SH       c-ELW       p-AU
-------------------------------------------------------------------------
 MT -22822.25152  30.811  0.0005 -  0.001 -  0.001 -  0.000702 - 0.000633 - 
28S -22791.44054       0       1 +  0.999 +      1 +     0.999 +    0.999 + 


AU test based on mitochondrial genome dataset (iqtree -s mitogenome.phy -m mtZOA+F+I+G4 -z trees.treels -n 0 -zb 10000 -au).

Tree      logL    deltaL  bp-RELL    p-KH     p-SH       c-ELW       p-AU
-------------------------------------------------------------------------
 MT -54731.89675       0       1 +      1 +      1 +         1 +        1 +
28S -59255.35408  4523.5       0 -      0 -      0 -         0 - 4.61e-05 - 

Thank you for your help!

Minh Bui

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Jun 30, 2019, 3:47:11 PM6/30/19
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Hi there,

Heiko can better answer your question. I suggest that you have a look at his book chapter on Tree Topology Tests in "The Phylogenetic Handbook: A practical approach to phylogenetic analysis and hypothesis testing”: 


This provides a much better explanation than the original Shimodaira’s paper.

Cheers,
Minh

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张东

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Jun 30, 2019, 9:59:04 PM6/30/19
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Hi Minh,

Thank you for your help. I am going to look into that book chapter.

Sincerely,

Dong Zhang

在 2019年7月1日星期一 UTC+8上午3:47:11,Minh Bui写道:
Hi there,

Heiko can better answer your question. I suggest that you have a look at his book chapter on Tree Topology Tests in "The Phylogenetic Handbook: A practical approach to phylogenetic analysis and hypothesis testing”: 


This provides a much better explanation than the original Shimodaira’s paper.

Cheers,
Minh
On 30 Jun 2019, at 11:15 am, 张东 <dongzh...@gmail.com> wrote:

Dear all,

I have two different topologies generated from 28S (tree-28S) and mitogenome (tree-MT), respectively, and I tried to conduct AU test on them using both datasets. The results (as shown below) showed that the tree-MT was rejected in the AU test using 28S dataset (28S AU test), whereas the tree-28S was rejected in the AU test using MT dataset (MT AU test). Therefore, I wanna to know how AU test compare the topologies? Does it first selects a tree with highest logL, and then compares each of the user trees to this tree? If take the my results (below) as example, I am comparing tree-MT to tree-28S in 28S AU test, and comparing tree-28S to tree-MT in MT AU test. 

If I am wrong, what is tree-28S comparing to in 28S AU test? and what is tree-MT comparing to in MT AU test? 


AU test based on 28S dataset (iqtree -s 28S.phy -m GTR+G -z trees.treels -n 0 -zb 10000 -au).

Tree      logL    deltaL  bp-RELL    p-KH     p-SH       c-ELW       p-AU
-------------------------------------------------------------------------
 MT -22822.25152  30.811  0.0005 -  0.001 -  0.001 -  0.000702 - 0.000633 - 
28S -22791.44054       0       1 +  0.999 +      1 +     0.999 +    0.999 + 


AU test based on mitochondrial genome dataset (iqtree -s mitogenome.phy -m mtZOA+F+I+G4 -z trees.treels -n 0 -zb 10000 -au).

Tree      logL    deltaL  bp-RELL    p-KH     p-SH       c-ELW       p-AU
-------------------------------------------------------------------------
 MT -54731.89675       0       1 +      1 +      1 +         1 +        1 +
28S -59255.35408  4523.5       0 -      0 -      0 -         0 - 4.61e-05 - 

Thank you for your help!

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