Researchers studying nonmodel organisms have an increasing number of methods available for generating genomic data. However, the applicability of different methods across species, as well as the effect of reference genome choice on population genomic inference, remain difficult to predict in many cases. We evaluated the impact of data type (whole‐genome vs. reduced representation) and reference genome choice on data quality and on population genomic and phylogenomic inference across several species of darters (subfamily Etheostomatinae), a highly diverse radiation of freshwater fish. We generated a high‐quality reference genome and developed a hybrid RADseq/sequence capture (Rapture) protocol for the Arkansas darter (Etheostoma cragini). Rapture data from 1,900 individuals spanning four darter species showed recovery of most loci across darter species at high depth and consistent estimates of heterozygosity regardless of reference genome choice. Loci with baits spanning both sides of the restriction enzyme cut site performed especially well across species. For low‐coverage whole‐genome data, choice of reference genome affected read depth and inferred heterozygosity. For similar amounts of sequence data, Rapture performed better at identifying fine‐scale genetic structure compared to whole‐genome sequencing. Rapture loci also recovered an accurate phylogeny for the study species and demonstrated high phylogenetic informativeness across the evolutionary history of the genus Etheostoma. Low cost and high cross‐species effectiveness regardless of reference genome suggest that Rapture and similar sequence capture methods may be worthwhile choices for studies of diverse species radiations.

中文翻译：

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Rapture-ready darters：参考基因组和基因分型方法（全基因组或序列捕获）的选择影响 Etheostoma 中的种群基因组推断

研究非模式生物的研究人员有越来越多的方法可用于生成基因组数据。然而，不同方法在物种间的适用性，以及参考基因组选择对种群基因组推断的影响，在许多情况下仍然难以预测。我们评估了数据类型（全基因组与减少的表示）和参考基因组选择对数据质量的影响以及对几种镖鱼（亚科 Etheostomatinae）的种群基因组和系统发育推断的影响，这是一种高度多样化的淡水鱼辐射。我们生成了一个高质量的参考基因组，并为阿肯色州镖 ( Etheostoma cragini ) 开发了一个混合 RADseq/序列捕获 (Rapture) 协议）。来自跨越四个镖物种的 1,900 个人的捕获数据显示，无论参考基因组选择如何，在高深度的镖物种中大多数基因座的恢复和杂合性的一致估计。具有跨越限制酶切割位点两侧的诱饵的位点在物种间表现特别好。对于低覆盖率的全基因组数据，参考基因组的选择会影响读取深度和推断的杂合性。对于相似数量的序列数据，与全基因组测序相比，Rapture 在识别精细遗传结构方面表现更好。Rapture 基因座还为研究物种恢复了准确的系统发育，并在整个Etheostoma属的进化历史中展示了高度的系统发育信息. 无论参考基因组如何，低成本和高跨物种有效性表明 Rapture 和类似的序列捕获方法可能是研究不同物种辐射的值得选择。