[From Brian Farrell's webpage http://insects.oeb.harvard.edu/farrell_lab/techniques/phylogenetics.html#clock
Once the appropriate likelihood model has been selected by ModelTest, one can test for a clock.
Copy the lscores line corresponding to ModelTest's chosen model from the modelblock file and paste this over the
[LSCORES] lines in the following batch file:]
#nexus
begin paup;
set criterion=distance;
log file=clocktest.log;
[********change outgroup**********]
outgroup 2;
DSet distance=JC objective=ME base=equal rates=equal pinv=0
subst=all negbrlen=setzero;
NJ showtree=no breakties=random;
set criterion=likelihood;
lset clock=no;
[**********INSERT MODELTEST CHOSEN MODEL BELOW********]
Lset Base=(0.2685 0.3063 0.1395) Nst=6 Rmat=(1.0000 35.0183 1.0000 1.0000 8.4463)
Rates=gamma Shape=1.3225 Pinvar=0.5689;
lscores [!Non-clock score above, clock score below]/scorefile=molecular_clock_test.txt append;
roottrees;
lset clock=yes;
[***************INSERT MODELTEST CHOSEN MODEL BELOW************]
Lset Base=(0.2685 0.3063 0.1395) Nst=6 Rmat=(1.0000 35.0183 1.0000 1.0000 8.4463)
Rates=gamma Shape=1.3225 Pinvar=0.5689;
lscores [!Clock score above]/scorefile=molecular_clock_test.txt append;
tstatus;
log stop;
end;
[This will result in two ln likelihood scores. Take the difference between the scores and double it.
This is your test statistic for a chi-squared test; the number of taxa minus 2 is the degrees of freedom.
You can use a program such as Microsoft Excel (the chidist function) or this web site to compute the p-value.
Significant p-values mean that the clock is rejected. People generally try each locus independently;
if you have time, you could use ModelTest to determine the correct likelihood model for each locus,
or just use the model chosen for all the loci combined.
From http://workshop.molecularevolution.org/resources/lrt.php
Testing the Molecular Clock: Often, one is interested whether a DNA segment evolves along all branches in a phylogeny at a homogeneous rate.
That is, one wants to test whether the assumption of a molecular clock is a valid one. Since a molecular clock only allows a single rate, this is the simpler,
hierarchically nested, null model. In testing a molecular clock, the degrees of freedom work out to be s-2, where s is the number of taxa in the
phylogeny (Felsenstein 1981). Here after determining the best likelihood model (similar to Example 1 above), we calculate the likelihood scores for a
5 taxon statement with and without a molecular clock:
HKY85 + clock -lnL = 7573.81
HKY85 -lnL = 7568.56
Then,
LR = 2 (7573.81 - 7568.56) = 10.50
degrees of freedom = s-2 = 5-2 = 3
critical value (P = 0.05) = 7.82
A Web site to determine the critical values for the chi-square distribution is available.
The null hypothesis, that the rate of evolution is homogeneous among all branches in the phylogeny, is rejected.
Rates of substitution significantly vary among branches and a molecular clock is inappropriate.
]