Data from: 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 outlier loci (3.4 %) and nine loci (0.5%) with
significantly low FST values. Valleys of reduced variation of up to 10 Mb
in size surrounding divergent outliers were consistent with selective
sweeps. The lab strains formed two additional groups that were genetically
distinct from all wild populations. An additional subset of outlier loci
was consistent with domestication selection within lab strains.
Substantial genetic variation that exists in zebrafish as a whole is
missing from lab strains that we analyzed. A combination of laboratory and
field studies that incorporates genetic variation from divergent wild
populations will be essential to understand the full range of genetic
influences on phenotypic variation in this species.