Roger Doyle This py project file tags the record of every individual in a simulated evolution with its ID, parentage and subpopulation membership along with genotype. I am greatly indebted to Bo Peng for advice on how to do this tagging, which helps in monitoring genetic changes in small populations that are fluctuating haphazardly in census number, effective population number and mating system.

The general objective of this simuPOP simulation project is to find indicators of genetic erosion and other genetic problems in small-holder aquaculture farms and hatcheries that, mostly for financial reasons, are unable to manage their broodstocks in any of the approved ways. None of the Fisher-Wright assumptions fit the demographies of such populations even approximately, hence the simulation.

For background/context, two recent papers are available free on the web: Doyle, R.W., 2016. Inbreeding and disease in tropical shrimp aquaculture: a reappraisal and caution. Aquaculture Research. 47, 21-35; Doyle, R.W., 2014. ‘Big Picture’ Connects Shrimp Disease, Inbreeding. Global Aquaculture Advocate. 17 (Sept/Oct), 45-46.