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.

中文翻译：

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斑马鱼的实验室驯化：从不同种群到近交亚种。

从人类遗传学研究中我们知道，生物学的几乎所有方面都受到遗传背景的强烈影响，这体现在“个性化医学”的出现上。但是，几乎没有例外，在将实验室种群用作这些领域研究的动物模型系统时，没有考虑到这一点。斑马鱼的实验室菌株（Danio rerio）被广泛用于脊椎动物发育生物学，行为和生理学的研究，疾病建模以及体内测试药物化合物。但是，所有这些菌株均来自人工瓶颈事件，因此很可能仅代表该物种内存在的遗传多样性的一小部分。在这里，我们使用限制性酶切位点相关的DNA测序技术对印度，尼泊尔和孟加拉国的斑马鱼野生种群进行遗传学表征，并将其与先前发表的关于四种常见实验室菌株的数据进行比较。我们测量了核苷酸多样性，杂合性和等位基因频谱，发现野生斑马鱼比实验室菌株更具多样性。此外，在野生斑马鱼中，有明显的GC偏向基因转换信号，而实验室菌株中却没有。我们还发现，尼泊尔和孟加拉国的斑马鱼种群与所研究的所有其他菌株最为不同，这使其成为今后斑马鱼种群遗传学和分子生态学研究的一个有吸引力的主题。最后，保存在不同实验室中的同一菌株的分离株显示出持续分化为遗传上不同的亚菌株的模式。总之，我们的发现为以后的遗传，生理，药学和进化研究奠定了基础。达尼奥·雷里奥（Danio rerio）。