Generational Fst estimates remain low despite low Ne and minimal migration

[ojholland]

Hi there,

Thanks for providing such an excellent package. Previously the senior author on the project I am working on has used simuPOP to investigate the degree of migration required to maintain an Fst that supports a panmictic system using a microsatellite dataset. They ran a simulation of varying effective population sizes and migration rates. This produced an expected signature of a sharp increase in Fst, followed by a plateau, which reflects the expected signature of genetic drift effects. The paper can be found here: https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.13734 I am attempting to repeat this analysis in an elasmobranch species using a SNP dataset derived from reduced representation sequencing. While we do see the expected initial increase in Fst, the results begin to jump sharply back and forth at a low level of Fst, and we certainly wouldn't expect reductions in Fst. We expected to see a similar result to the above paper, where the effects of genetic drift eventually take hold (well before 1000 generations!) and plateau Fst, especially when considering quite small Ne values. I have attached the script I am using and would appreciate any suggestions as to if I am utilising the appropriate approach for this. shark_simupop_edit.txt Please let me know if I need to provide more detail. I am new to running simulations of this nature and I may be missing something rather fundamental that is causing this strange output!

Cheers, Owen

[BoPeng]

This looks more like a research question than a simuPOP question (unless you believe there is some bug with simuPOP or your script). I would suggest that you contact experts in the fields directly. On the top of my mind I would recommend Robin Waples (NOAA Fisheries) who happens to know simuPOP as well.