>>I'm interested in using ITS rDNA sequences to estimate gene flow among
>>>different populations of nematodes and would like to know 1) if this can
>>>provide a satisfactory estimate, and 2) if there are any programs
>>available >which will help me do this.
>On Fri I found what I was looking for at
>http://evolution.genetics.washington.edu/index.html
To (2): You can find programs for estimating
population parameters like population size, exponential growth rate,
and migration rates through the above URL,
but the more appropriate URL is
http://evolution.genetics.washington.edu/lamarc.html
To (1): I do not really know how variable ITS rDNA is, but
my simulations show that if Theta (4 * N_e * mu: N_e = effective population
size, mu = mutation rate per site and generation) is very small, the power
to estimate any migration rate gets rather small, you can see that this is
related to the number of variable sites in your datasets:
if there is no variation in the dataset migration
rate estimates are huge and Theta will approach 0.
For a good estimation of 4N_e m (m = migrate rate per generation) you need
either a fairly variable locus, a long stretch of DNA (to catch some
variability), more individuals (ditto), or (the best) more unlinked loci
(and for the currently available methods based on coalescent theory
you need also non-recombining loci).
Peter
-----
Peter Beerli <beerli at genetics.washington.edu>
University of Washington, GENETICS, Box 357360, Seattle,
WA 98195-7360, USA. Work:(206) 543-8751,
Home:(206) 527-9906, Fax:(206) 543-0754; GMT+0800.
http://evolution.genetics.washington.edu/PBhtmls/beerli.html
