Migrate Analysis Diagnosis

[Dandára Yasmim Bonfim De Oliveira Silva]

Dear Professor Peter and all MIGRATE users,

I started my interaction with MIGRATE about 4 months ago, using version 3.7.2. My goal is to estimate the values of Theta and gene flow among six populations.

Data summary: I have six populations, 33 SNPs, and a variable number of individuals per population. However, my main concern is determining which parameter in the output file I should rely on to identify the right moment to stop – that is, the number of iterations necessary to obtain reliable data. Is there a specific "Stop Diagnostic" value?

For instance, we might reach a point where further iterations don't significantly improve the parameters. Identifying this "stopping point" as the "ideal number of iterations" is crucial (see the graph below).

Attached is the result of a recent analysis I did.
Thank you
Best regards,

Dandara Yasmim B. O. Silva

Doutoranda em Ciência Florestal (Unesp/FCA)

Mestre em Ciência Florestal (Unesp/FCA)

Engenharia Florestal  (UFPI/CPCE)

Contato: (89) 999156915

Lattes e Linkedin

   

[Peter Beerli]

Dandara,

Your graph suggests that you want to run more than 200,000 iterations without heating,

but I suggest that you repeat your experiment with heating

You also want to consider whether the n-island model is really the model that you want to run, also may want to consider to use 

use the 5.0 version of migrate, which is a Bayesian inference instead of maximum likelihood (using 3.7 is fine, but lack capability such as model selection among different evolutionary models).

Peter

On Jan 18, 2024, at 8:26 PM, Dandára Yasmim Bonfim De Oliveira Silva <dandara...@unesp.br> wrote:

Dear Professor Peter and all MIGRATE users,

I started my interaction with MIGRATE about 4 months ago, using version 3.7.2. My goal is to estimate the values of Theta and gene flow among six populations.

Data summary: I have six populations, 33 SNPs, and a variable number of individuals per population. However, my main concern is determining which parameter in the output file I should rely on to identify the right moment to stop – that is, the number of iterations necessary to obtain reliable data. Is there a specific "Stop Diagnostic" value?

<image.png>

For instance, we might reach a point where further iterations don't significantly improve the parameters. Identifying this "stopping point" as the "ideal number of iterations" is crucial (see the graph below).

Attached is the result of a recent analysis I did.
Thank you
Best regards,

Dandara Yasmim B. O. Silva

Doutoranda em Ciência Florestal (Unesp/FCA)

Mestre em Ciência Florestal (Unesp/FCA)

Engenharia Florestal  (UFPI/CPCE)

Contato: (89) 999156915

Lattes e Linkedin

   

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