ArticleMolecular ecology2011
Population genomics of wild and laboratory zebrafish (Danio rerio).
Article in Molecular ecology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Genomic and genetic insights into speciation and pigment pattern diversification inbioRxiv : the preprint server for biology · 2025Article
- Zebrafishology, study design guidelines for rigorous and reproducible data using zebrafish.Communications biology · 2025Review
- Genes and crystals are not so separate.Nature chemical biology · 2025Article
- Lampbrush chromosomes of Danio rerio.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2025Article
- Genomic Signatures of Domestication in European Seabass (Ecology and evolution · 2024Article
- Fisheries-induced life-history changes recover in experimentally harvested fish populations.Biology letters · 2024Article
- Comparative study of the growth, stress status and reproductive capabilities of four wild-type zebrafish (Danio rerio) lines.Biological research · 2024Article
- Individual differences in the boldness of female zebrafish are associated with alterations in serotonin function.The Journal of experimental biology · 2024Article
- Copy number variation and population-specific immune genes in the model vertebrate zebrafish.eLife · 2024Article
- Key HPI axis receptors facilitate light adaptive behavior in larval zebrafish.Scientific reports · 2024Article
- River zebrafish combine behavioral plasticity and generalized morphology with specialized sensory and metabolic physiology to survive in a challenging environment.Scientific reports · 2023Article
- Correlations begin at home: drivers of co-occurrence patterns in personality and cognitive ability in wild populations of zebrafish.Animal cognition · 2023Article
- Genomic basis of fishing-associated selection varies with population density.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Density influences the heritability and genetic correlations of fish behaviour under trawling-associated selection.Evolutionary applications · 2021Article
- Wild Zebrafish Sentinels: Biological Monitoring of Site Differences Using Behavior and Morphology.Toxics · 2021Article
- Thermal tolerance and routine oxygen consumption of convict cichlid, Archocentrus nigrofasciatus, acclimated to constant temperatures (20 °C and 30 °C) and a daily temperature cycle (20 °C → 30 °C).Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology · 2021Article
- A fish is not a mouse: understanding differences in background genetics is critical for reproducibility.Lab animal · 2021Review
- Article
- Low potential for evolutionary rescue from climate change in a tropical fish.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Shedding new light on early sex determination in zebrafish.Archives of toxicology · 2020Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 1832 polymorphic EST-based single nucleotide polymorphisms (SNPs) and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mitochondrial DNA clades with an average among-clade sequence divergence of 5.8%. SNPs revealed five major evolutionarily and genetically distinct groups with an overall FST of 0.170 (95% CI 0.105-0.254). These genetic 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 heterozygosity, consistent with selective sweeps, surrounded six of the 71 outliers (8.5%). 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 analysed. A combination of laboratory and field studies that incorporates genetic variation from divergent wild populations along with the wealth of molecular information available for this model organism provides an opportunity to advance our understanding of genetic influences on phenotypic variation for a vertebrate species.
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