weird consensus tree

[T. Xu]

Hi TNTers,

I am running TNT by traditional search with the parameters setting like below:

log run.log ;  
mxram 1024;
taxname = ;
p 9.tnt;
hold 10000 ;  
mult=tbr repl 1000 hold 10;
bbreak = tbr ;
nelsen * ;
tchoose { strict } ;
ttags = ;
blength *;
ttags );
export - consensus_tree.tre ;
ttags -;
ttags = ;
resample boot replications 1000;
keep 1 ;
ttags );
ttags ;
export - XXX9.tre;
proc/;

The topology of the consensus tree is super weird, while the retained trees look good. I would appreciate it if some one knows why?

                 

Cheers,

Tao

[Santiago Catalano]

Hi Tao, 

This is a completely unresolved consensus. This can be caused by: (i) presence of wildcard taxa (ii) high incongruence among characters (iii) dataset that is not much informative. (iv) a combination of the previous causes.

bests

Santi

 

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Dr. Santiago A. Catalano

Investigador Independiente CONICET

Unidad Ejecutora Lillo (UEL FML-CONICET)

FCNeIML-UNT

SM Tucumán - Tucumán
Argentina

Research Associate - Division of Anthropology at the American Museum of

Natural History. 

New York - USA 

[Dimitri Forero]

Hi Tao,

Is not a matter of having a rogue taxon? I mean, a taxon that is "floating" around, so that when making the consensus you get a full comb.

cheers,

Dimitri

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DIMITRI FORERO, PhD

Instituto de Ciencias Naturales

Universidad Nacional de Colombia

Bogotá - COLOMBIA

E-mail: id...@cornell.edu; ifor...@unal.edu.co
https://sites.google.com/a/cornell.edu/dimitriforero/home
https://www.researchgate.net/profile/Dimitri_Forero

[Xu, T.]

Hi Dimitri,

Thanks for your reply. After checking the raw data, it may not be the rogue taxon. I tried different parameters, but still do not know. 

I have attached my .tnt data, I wuold appreciate it if you can also have a check!!!!

Cheers,

Tao

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[Martín Ramírez]

Hi Tao,

It is probably because you have taxa without any data in common,

e.g.,

Palaemon_concinnus        0010000...00000...???????...????????????...
Macrobrachium_jelskii    ???????...?????...???????...????00000000...

Their relative positions in the tree may be undetermined because of that, hence collapsing everything in between.

Best wishes,

Martin J. Ramirez Curador y Jefe, División Aracnología / Curator & Head, Division of Arachnology Museo Argentino de Ciencias Naturales - CONICET Av. Angel Gallardo 470 C1405DJR Buenos Aires Argentina