Question on negative Bremer support value and synapomorphies

[lv xiao]

Dear all,

I have been learning TNT recently based on a toy dataset of 55 taxa each with 50 continuous measures (measures of length). I was able to generate results from TNT script. However, I am having some difficulties interpreting the results.

I first generated majority and strict consensus tree as well as the run.tre file containing multiple trees through code below:

I then used code below to estimate Bremer support:

```

log run_Bremer.log;
mxram 4000;
p data.tnt;
hold 100000;
p majority_consensus.tre ;
ttags = ;
naked -;
tplot 0;
sub 100x0.90 ;
bsupp !!+0 0. ;
ttags;
ttags & run_Bremer.svg;
log/;
zzz;

```

The figure below shows that Bremer supports are all negative. Q1: May I ask why this could happen and if there is anything wrong with my data or code? Q2: In above script, should majority_consensus.tre or run.tre which contains multiple best score trees be used? I ask this question since the original TNT paper has an excerpt "When multiple most parsimonious trees are used to calculate consensus trees, the consensus is longer, so that optimizing it for producing synapomorphy lists or studying character evolution is (while possible) inappropriate." This seems to recommend against the use of consensus tree to calculate Bremer support. If this is the case, I am not sure if the run.tre should be used.

Finally, I want to derive plesiomorphic and synapomorphic states by code below:

```

log run_Bremer.log;
mxram 4000;
p data.tnt;
hold 100000;
p majority_consensus.tre ;
apo -;
ttags = ;
naked -;
tplot 0;
sub 100x0.90 ;
bsupp !!+0 0. ;
ttags;
ttags & run_Bremer.svg;
log/;
zzz;

```

The output shows:

    Antecessor :

      Char. 0: 0.478-0.536 --> 0.358

      Char. 40: 0.386 --> 0.000

Q3: How should the numbers before and after --> be interpreted? Plesiomorphic --> Synapomorphic?

I changed apo -; to apo ; and here is the log file:

How to interpret the line 0,40 Antecessor? How does this compare with the output from apo-; ? Both have Char 0 and 40 associated with Antecessor.

Thank you very much.

Xiao