Data from: The laboratory domestication of zebrafish: from diverse populations to inbred substrains

We know from human genetic studies that practically all aspects of biology
are strongly influenced by the genetic background, as reflected in the
advent of ‘personalized medicine’. Yet, with few exceptions, this is not
taken into account when using laboratory populations as animal model
systems for research in these fields. Laboratory strains of zebrafish
(Danio rerio) are widely used for research in vertebrate developmental
biology, behaviour and physiology, for modelling diseases, and for testing
pharmaceutic compounds in vivo. However, all of these strains are derived
from artificial bottleneck events and therefore are likely to represent
only a fraction of the genetic diversity present within the species. Here
we use Restriction site-Associated DNA sequencing (RAD-seq) to genetically
characterize wild populations of zebrafish from India, Nepal and
Bangladesh, and to compare them to previously published data on four
common laboratory strains. We measured nucleotide diversity,
heterozygosity and allele frequency spectra, and find that wild zebrafish
are much more diverse than laboratory strains. Further, in wild zebrafish
there is a clear signal of GC-biased gene conversion that is missing in
laboratory strains. We also find that zebrafish populations in Nepal and
Bangladesh are most distinct from all other strains studied, making them
an attractive subject for future studies of zebrafish population genetics
and molecular ecology. Finally, isolates of the same strains kept in
different laboratories show a pattern of ongoing differentiation into
genetically distinct substrains. Together, our findings broaden the basis
for future genetic, physiological, pharmaceutic and evolutionary studies
in Danio rerio.