Restriction‐site associated DNA sequencing (RADseq) has become a powerful and versatile tool in modern population genomics, enabling large‐scale evolutionary and genomic analyses in otherwise inaccessible biological systems. With its widespread use, different variants on the protocol have been developed to suit specific experimental needs. Researchers face the challenge of choosing the optimal molecular and sequencing protocols for their reduced representation experimental design, an often‐complicated process. Strategic errors can lead to biased data generation that has reduced power to answer biological questions. Here, we present RADinitio, simulation software for the selection and optimization of RADseq experiments via the generation of sequencing data that behave similarly to empirical sources. RADinitio provides an evolutionary simulation of populations, implementation of various RADseq protocols with customizable parameters, and thorough assessment of missing data. We test the efficacy of the software using different RAD protocols across several organisms, highlighting the importance of protocol selection on the magnitude and quality of data acquired. Additionally, we test the effects of RAD library preparation and sequencing on allelic dropout, observing that library preparation and sequencing often contributes more to missing alleles than population‐level variation.

中文翻译：

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使用 RADinitio 进行仿真改进了 RADseq 实验设计并揭示了缺失数据的来源。

限制性位点相关 DNA 测序 (RADseq) 已成为现代群体基因组学中强大而通用的工具，能够在其他方式无法访问的生物系统中进行大规模进化和基因组分析。随着其广泛使用，该协议的不同变体已经开发出来，以满足特定的实验需求。研究人员面临着为减少代表性的实验设计选择最佳分子和测序方案的挑战，这是一个经常复杂的过程。战略错误会导致生成有偏见的数据，从而降低回答生物学问题的能力。在这里，我们展示了 RADinitio，这是一种模拟软件，用于通过生成与经验来源类似的测序数据来选择和优化 RADseq 实验。RADinitio 提供了种群的进化模拟、具有可定制参数的各种 RADseq 协议的实施，以及对缺失数据的彻底评估。我们在多个生物体中使用不同的 RAD 协议来测试软件的功效，强调了协议选择对获取的数据的数量和质量的重要性。此外，我们测试了 RAD 文库制备和测序对等位基因丢失的影响，观察到文库制备和测序通常比群体水平变异对缺失等位基因的贡献更大。强调协议选择对获取的数据的数量和质量的重要性。此外，我们测试了 RAD 文库制备和测序对等位基因丢失的影响，观察到文库制备和测序通常比群体水平变异对缺失等位基因的贡献更大。强调协议选择对获取的数据的数量和质量的重要性。此外，我们测试了 RAD 文库制备和测序对等位基因丢失的影响，观察到文库制备和测序通常比群体水平变异对缺失等位基因的贡献更大。