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.

借助对经典实验室模式生物的生态学与进化学研究，我们能够更全面地解析基因型-表型关联（genotype-phenotype association）的多样类型。本研究首次针对分布于尼泊尔、印度与孟加拉国的野生斑马鱼（Danio rerio）种群内部及种群间的遗传变异开展大规模地理分析，并将野生种群与数种常用实验室品系进行了遗传学比对。我们对13个野生种群与3个实验室品系的1832个基于表达序列标签（Expressed Sequence Tag, EST）的多态性单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点以及线粒体细胞色素b（cytb）基因的遗传变异进行了检测。野生种群可被划分为3个主要的线粒体DNA（mtDNA）进化枝，各进化枝间的序列平均分化水平为5.8%。SNP分型结果揭示了5个在进化与遗传层面均显著分化的主要类群，整体遗传分化指数（Fixation Index, FST）为0.170（95%置信区间（Confidence Interval, CI）：0.105~0.254）。这些遗传分化类群对应于独立的地理区域，推测其形成与古气候周期中种群在避难所内的隔离分化过程相关。本研究共检测到71个显著分化的异常位点（占总位点数的3.4%）以及9个FST值显著偏低的位点（占总位点数的0.5%）。在显著分化的异常位点周围，存在长度可达10 Mb的变异降低谷，该特征与选择性清除（selective sweep）的理论预期相符。本次分析的实验室品系形成了另外两个类群，且在遗传学层面与所有野生种群均存在显著分化。另有部分异常位点的特征与实验室品系的人工驯化选择过程相符。本次分析的实验室品系丢失了斑马鱼整个物种天然种群中存在的大量遗传变异。结合实验室研究与野外调查，并纳入来自不同分化野生种群的遗传变异，将是全面解析该物种遗传变异对表型变异的全部影响的必要前提。