TY - JOUR
T1 - The laboratory domestication of zebrafish
T2 - From diverse populations to inbred substrains
AU - Suurväli, Jaanus
AU - Whiteley, Andrew R.
AU - Zheng, Yichen
AU - Gharbi, Karim
AU - Leptin, Maria
AU - Wiehe, Thomas
N1 - Publisher Copyright:
© 2019 The Author(s). Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
PY - 2020/4/1
Y1 - 2020/4/1
N2 - 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, behavior, and physiology, for modeling 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 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.
AB - 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, behavior, and physiology, for modeling 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 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.
KW - RAD-seq
KW - genetic differentiation
KW - genetic diversity
KW - inbreeding
KW - laboratory strains
KW - wild populations
KW - zebrafish
UR - http://www.scopus.com/inward/record.url?scp=85082147271&partnerID=8YFLogxK
U2 - 10.1093/molbev/msz289
DO - 10.1093/molbev/msz289
M3 - Article
C2 - 31808937
AN - SCOPUS:85082147271
SN - 0737-4038
VL - 37
SP - 1056
EP - 1069
JO - Molecular Biology and Evolution
JF - Molecular Biology and Evolution
IS - 4
ER -