[Mesquitelist] maximum likelihood values in ancestral reconstructions?

krushnamegh at mail.utexas.edu krushnamegh at mail.utexas.edu
Tue Aug 19 03:19:16 PDT 2008


i am studying the evolution of mimicry by reconstructing ancestral 
states using the maximum likelihood criterion with one-parameter 
Markov k-state model, implemented in Mesquite. on the phylogeny with 
ancestral reconstructions, when i place the cursor over any of the 
internal nodes, the "trace character" window lists all the character 
states and gives values for each of those. for example, i have six 
character states for a particular character, and a specific internal 
node shows the following in the "trace character" window:

0:0.0002364
1:4.3728954467E-5
2:4.7586737726E-5
3:0.99771091*
4:0.00045689
5:4.7679802321E-5

are these numbers maximum likelihood scores? what do the '*' mean in 
this case? i presume that the '*' denotes some kind of statistical 
significance but i am not very sure. is it a significant value (at p 
< 0.05 or so) from a maximum likelihood model for a particular 
character state (state 3 in the above case) not being the ancestral 
state at that node? i am particularly confused because if any single 
value in a given set of values is below ~0.85 or so, the highest 
values that together make up >0.85 or so all get the *. for example:

0:0.005565657
1:0.71353937*
2:0.00670567
3:0.26246278*
4:0.00614855
5:0.00056387

further, the highest (and single) value i get when i place the cursor 
over any of the extant species is 1, without an asterisk. for 
example, for a particular species:

5:1.0

if these are significant values of some sort, shouldn't the 1's also 
have an asterisk in front of them?

i would appreciate any help with this, and thank you in advance.
-- 
Krushnamegh Kunte

FAS Center for Systems Biology
Harvard University
Cambridge, MA 02138, USA

Office: (617) 384-9920
Cell: (512) 577-1370
Fax: (617) 495-2196
Email: KKunte at cgr.harvard.edu or krushnamegh at gmail.com

Academic Website: 
http://www.bio.utexas.edu/grad/krushnamegh/Moorings/AcademicsHome.htm
General Website: http://www.bio.utexas.edu/grad/krushnamegh/Moorings/index.htm
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