Population genomics of wild and laboratory zebrafish (Danio rerio)

Understanding a wider range of genotype-phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large-scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1,832 polymorphic EST-based SNPs and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mtDNA clades with an average of 5.8% among-clade sequence divergence. SNPs revealed five major evolutionarily and genetically distinct groups with an overall FST of 0.170 (95% CI 0.105 - 0.254). Evolutionarily distinct groups corresponded to discrete geographic regions and appear to reflect isolation in refugia during past climate cycles. We detected 71 significantly divergent ou...