Species’ responses at the genetic level are key to understanding the long‐term consequences of anthropogenic global change. Herbaria document such responses, and, with contemporary sampling, provide high‐resolution time‐series of plant evolutionary change. Characterizing genetic diversity is straightforward for model species with small genomes and a reference sequence. For nonmodel species—with small or large genomes—diversity is traditionally assessed using restriction‐enzyme‐based sequencing. However, age‐related DNA damage and fragmentation preclude the use of this approach for ancient herbarium DNA. Here, we combine reduced‐representation sequencing and hybridization‐capture to overcome this challenge and efficiently compare contemporary and historical specimens. Specifically, we describe how homemade DNA baits can be produced from reduced‐representation libraries of fresh samples, and used to efficiently enrich historical libraries for the same fraction of the genome to produce compatible sets of sequence data from both types of material. Applying this approach to both Arabidopsis thaliana and the nonmodel plant Cardamine bulbifera, we discovered polymorphisms de novo in an unbiased, reference‐free manner. We show that the recovered genetic variation recapitulates known genetic diversity in A. thaliana, and recovers geographical origin in both species and over time, independent of bait diversity. Hence, our method enables fast, cost‐efficient, large‐scale integration of contemporary and historical specimens for assessment of genome‐wide genetic trends over time, independent of genome size and presence of a reference genome.

中文翻译：

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使用高度降解的历史样本 DNA 进行非模式植物种群基因组学的杂交 ddRAD 测序。

物种在遗传水平上的反应是了解人为全球变化长期后果的关键。Herbaria 记录了这些反应，并通过现代采样提供了植物进化变化的高分辨率时间序列。对于具有小基因组和参考序列的模型物种，表征遗传多样性很简单。对于具有小型或大型基因组的非模型物种，传统上使用基于限制酶的测序来评估多样性。然而，与年龄相关的 DNA 损伤和片段化阻止了这种方法用于古代植物标本馆 DNA。在这里，我们结合减少表征测序和杂交捕获来克服这一挑战并有效地比较当代和历史标本。具体来说，我们描述了如何从新鲜样本的减少代表性文库中生产自制 DNA 诱饵，并用于有效地丰富基因组相同部分的历史文库，以从两种类型的材料中产生兼容的序列数据集。将此方法应用于两者拟南芥和nonmodel植物碎米黄药子，我们在一个不带偏见，无参考的方式发现多态性从头。我们表明，恢复的遗传变异概括了拟南芥中已知的遗传多样性，并随着时间的推移恢复了物种的地理起源，与诱饵多样性无关。因此，我们的方法能够快速、经济、大规模地整合当代和历史标本，以评估全基因组遗传趋势随时间的推移，独立于基因组大小和参考基因组的存在。