How to set Locus and Theta value error

[winky Luo]

Dear Peter and migrate-support users,

 

I'm new to Migrate - N and I'd like to ask you some questions.

The research object of my project is Dipterocarcinaceae tree species, which has three wild populations (POP1 80 individuals, POP2 94, POP3 55), and 13148 loci were obtained by RADseq sequencing of its leaves. Here are the questions:

 

Q1: Should these data be treated as one locus or two locus? Or is either one ok?

Q2: Why did I set Theta=FST on Linux with Migrate-n version 4.4.4, the output file shows Theta value is error?

Q3: How to deal with this warning: Genealogies 10: Effective sample size of run seems too short!

 

I could run perfect results (outfile_one locus) with one locus and 50 individuals per pop, but I ended up with multiple peaks and right wing with two locus (outfile_two locus) , more Increment and all individuals. I tried adding Theta Prior Maximum to 50 with 10 individuals, but the results were also disappointing (outfile_POP1toPOP2&3_10i).

 

Looking forward to your reply, thank you.

 

Winky

[Alison Wee]

Hi Peter and migrate-support users,

I just want to echo Winky's query (I'm on the same project). Basically, we're trying to run migrate analysis on RADseq SNP data, and we just need to double confirm if we are doing it right: 

Q1. For RADseq SNP data, we should organize the input file as two loci, right? 

Q2. We tried setting estimating Theta based on the FST (Theta=FST), but the output pdf showed "ERROR" for the Theta value. We're not sure how to resolve this issue and cannot find a satisfactory suggestion online. 

Q3. Does the warning "Genealogies 10: Effective sample size of run seems too short!" mean anything? What can we do to resolve this issue? 

The outfiles and parmfiles that we obtained are as attached in Winky's post above. 

ANY advice is much appreciated! Please help! 

Thank you. 

Cheers,

Alison