How can you estimate the Nemf value and/or gene flow value (Nm)?

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--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

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Márcio G Pavan Popular answer

I would not use this formula for gene flow (using Fst), as it is obsolete and unreliable. There are many programs that use bayesian approaches to calculate gene flow between populations. Take a look at the Migrate-n program (http://popgen.sc.fsu.edu/Migrate/Migrate-n.html). Cheers

Ferruccio Maltagliati

Dear Ahasan Habib, you can obtain the expected female gene flow by using a matrilinear genetic marker. Then you can apply, for instance, the classical formula by Hudson, Slatkin & Maddison (1992).

Ahasan Habib

thanks for your reply. I have been using mtDNA Dloop marker, so is it possible to find out the value? i will have a look on your given reference. thanks

If you used Dloop, then you have just to calculate Fst and apply the Hudson et al's (1992) formula. The software DnaSp (http://www.ub.edu/dnasp/) can calculate directly Nmf in a while!

Márcio G Pavan

Thanks. @Ferruccio, could you please write me from which option in DnaSP can find the value of Nmf? i was trying but was not able to do. or sequence data need set up in different way? if can send me a sample file then would be great! thanks

and i need one more assistance to perform Mantel test in Arlequin. i don't know why my data can't read by Arequin!! all seems fine. if anyone has a sample copy please send me via pm. I have been using mtDNA Dloop marker. thanks a lot!

Peter Hondelmann

Arlequin provides several sample files which you can use and copy your data inside....anyway a very close look on the file is necessary then as you can easily forget a bracket or delete something necessary.