Bayesian Coalescent model and the number of populations

[Jared Lamy]

Hello,

I'm new to using MIGRATE and am trying to follow the methods of a published study (Kazyak et al. 2016). There MIGRATE procedure is as follows

"To quantify long-term rates of genetic exchange among groups inferred using STRUCTURE, we implemented a Bayesian coalescent model in MIGRATE and estimated θ and M, where θ represents the mutation-scaled effective population size(4Neμ)and M represents the mutation-scaled immigration rate(m/μ),where m is the proportion of migrants per generation and μ is the mutation rate per locus per generation [41],[42].Migration rates were allowed to be asymmetric and to vary between groups. A preliminary examination of allele frequencies found little support for the stepwise mutation model,so we used the Brownian motion option within MIGRATE and assumed a constant mutation rate across all loci.We used uniform prior distributions for θ (0–20) and M (0–600). The model ran with an initial burn-in of 50,000 steps, followed by data collection for 200,000 MCMC replicates every 20 steps. Static heating was used(four chains) and the chains were allowed to swap.Modal values from posterior distributions were used for parameter estimates.To calculate long-term genetic exchange rates in units of effective migrants per generation from group j to group i [43],we used the relationship described by Eq1 that is independent of the mutation rate. We also examined the skyline plots produced by MIGRATE to determine if the observed genetic differences were the result of recent divergence or historic departure with continued genetic exchange."

The only difference is I have 7 sampling locations (tributaries along a mainstem river) and Kazyak et al. 2016 only has 2. I have the data in the proper format (I'm using 12 microsatellite loci) and am trying to create a parameter file. When I try to set the number of populations to 7 under option 5 in the parameter settings I am then prompted to give "49 nine more values out of 49". What should these values be? Any tips on creating a parameter file for 7 populations with the above procedure would be appreciated.

Thanks,

Jared

[Peter Beerli]

Jared,

I suggest to look at the manual, the section about migration models will help,

there are also tutorials that deal with these type of issues, too look at https://peterbeerli.com/migrate-html5/tutorials.html

[the tutorials for version 4 discuss both changing the migration model.]

The easiest to construct complex migration models is to use the a texteditor and edit the parmfile, search for the option

custom-migration,

Peter

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