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 ( F ST 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 ( F ST < 6 %) with farmed Asian populations most divergent. Interestingly, SNP chip data documented a marked absence of widespread reduction in the diversity in farmed populations when compared with their wild relatives. To ensure the results were not influenced by ascertainment bias, whole genome sequencing was used to identify 4.13 M SNP in a subset of both farmed and wild shrimp. Observed levels of nucleotide diversity in wild (π = 1.95 × 10 −4 ) and farmed animals (π = 2.05 × 10 −4 ) were similar, suggesting that broad and repeated introductions of wild shrimp have likely contributed to the domestication process. A search for selection sweeps identified a small collection of outlier regions (38 intervals spanning 2.1 Mb) and 20 protein coding genes. The results represent a broad snapshot of the genetic diversity and divergence that exists within this important aquaculture species. • Genetic diversity compared between wild and farmed Pacific white shrimp populations. • SNP array revealed generally high diversity has persisted in farmed shrimp. • Allele frequencies shifts have occurred since domestication. • Wild shrimp appear to carry diversity not captured in the farmed animals tested.