Genome-wide SNP variation reveals genetic structure and high levels of diversity in a global survey of wild and farmed Pacific white shrimp

Domestication and subsequent artificial selection of Pacific white shrimp (Penaeus vannamei) commenced around 1980 and the species is now the most widely farmed crustacean in the world. We documented generally high levels of genetic diversity within 21 globally distributed farmed populations using 44,522 SNP collected using an Illumina SNP chip. The sample set also included 86 wild P. vannamei, facilitating investigation of within population diversity and the extent of divergence between wild shrimp. This revealed weak population structure amongst wild populations from Panama, Honduras, Guatemala and Colombia (FST range 0–3 %) and more significant divergence between those and the wild Mexican animals that should be considered a distinct subpopulation. Comparison between wild and farmed global populations showed low to moderate levels of population differentiation (FST