Problem with running dadi with SNP panel data.

[Suany Quesada]

Hello everyone,

I am running 2D and 3D models with chip sequencing SNPs (SNP panel) of a mammal, however I get a pattern of sfs with empty spaces. The data are filtered in term of LD. Is the obtained pattern normal? Is it due to the sequencing technique? Any suggestions?

I attach two examples (Evaluation of founder effect without migration in a 2D model and evaluation of divergence with migration).

Thank you very much in advance for your suggestions and comments!

[Ryan Gutenkunst]

Hello Suany,

In general, SNP panel data are suitable for use with dadi. The complex ascertainment schemes introduce bias in the frequencies of SNPs that are captured, which is almost impossible to model.

Best,
Ryan

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> <PN_SU_CU_split_nomig_vim01_120905_reducido_miss0.pdf><PS_TF_founder_nomig_vmin01.pdf>

[Suany Quesada]

Hi Ryan

Thank you very much for your quick reply and sorry for the basic questions. About what you say, to know divergence events and changes in the effective population size of my populations, what models should I use? For example, should I use simple models that do not consider migration?

I am very grateful for your response.

[Ryan Gutenkunst]

Hello Suany,

My apologies, I made an important typo. SNP panel data are generally *unsuitable* for use with dadi. I’m not aware of any methods that can straightforwardly give quantitative estimates of demographic history from such data.

Best,
Ryan

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