> Second, the bootstrap values will not change for a maximum parsimony
> analysis when you add invariable characters; although they can change a
> little using some other methods, like maximum likelihood. For maximum
> likelihood, the result is not predictable; sometimes the bootstrap values
> will increase, sometimes they will decrease.
>
Guy,
Just to take issue with one point in your otherwise impeccable answer.
Bootstrap values can be affected by the inclusion or exclusion of
constant characters for a parsimony analysis. This will affect the
sampling process. If you consider this alignment:
species1 acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgttag
species2 acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtaga
species3 acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtaga
species4 acgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgtacgttag
There are three parsimony-informative sites, all supporting the same
topology. By removing the 60 constant sites you will get a bootstrap
value for the internal branch that is 100%. If you include the constant
sites, you will only get a bootstrap value of 95.4% (you should do about
one million replicates to get a reasonably accurate estimate of the
b'strap value).
So, the inclusion or exclusion of these sites can affect the bootstrap
values. There are probably better cases, this is just a quick alignment
I put together.
Kindest regards,
James
---
