Looking to the past to inform the future: What eDNA from herbarium specimens can tell us about plant–animal interactions

IF 2.7 3区生物学 Q2 PLANT SCIENCES

Applications in Plant Sciences Pub Date : 2025-02-05 DOI:10.1002/aps3.11633

Christopher Waters, Carla Hurt, Shawn Krosnick

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引用次数: 0

Abstract

Premise

The importance of natural history collections in modern ecological and genetic research cannot be overstated. Herbarium specimens provide historical information that can be used to investigate community ecology, phenology, and population genetics. In this study, environmental DNA (eDNA) metabarcoding and next-generation sequencing were used to test the efficacy of detecting historical plant–animal interactions from herbarium specimen flowers.

Methods

A modified eDNA isolation method and standard Illumina sequencing protocols were used. Animal eDNA was amplified using both cytochrome c oxidase subunit I (COI) and 16S primers to increase detection probability. The relationship between specimen age (0–69 years) and target taxa read depth was also investigated.

Results

We generated and identified over 1.5 million sequences of animal taxa belonging to 29 clades (families or orders). These methods enabled the detection of taxa including birds, mammals, hymenopterans, lepidopterans, coleopterans, and taxa belonging to “intrafloral” communities. While herbarium specimens overall yielded less identifiable eDNA compared to fresh material, the age of the herbarium specimen negligibly affected the amount of target and/or non-target eDNA detected in flowers.

Discussion

With careful consideration of the types of data that may be obtained through sampling eDNA from herbarium specimens, these methods could prove valuable to future research on plant–animal interactions.

Abstract Image

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回顾过去，展望未来：植物标本中的eDNA可以告诉我们植物与动物之间的相互作用

自然历史收藏在现代生态学和遗传学研究中的重要性怎么强调都不为过。植物标本室标本提供了可用于调查群落生态学、物候学和群体遗传学的历史信息。本研究利用环境DNA （eDNA）元条形码技术和新一代测序技术，对植物标本花中植物-动物相互作用的检测效果进行了验证。方法采用改良的eDNA分离方法和标准Illumina测序方案。利用细胞色素c氧化酶亚基I （COI）和16S引物扩增动物eDNA，提高检测概率。研究了标本年龄（0 ~ 69岁）与目标分类群阅读深度的关系。结果生成并鉴定了29个进化支（科或目）的150多万个动物分类群序列。这些方法可以检测到鸟类、哺乳动物、膜翅目、鳞翅目、鞘翅目以及属于“花内”群落的分类群。虽然与新鲜材料相比，植物标本馆标本总体上产生的可识别eDNA较少，但植物标本馆标本的年龄对花中检测到的目标和/或非目标eDNA的数量影响很小。仔细考虑从植物标本室标本中取样eDNA可能获得的数据类型，这些方法可能对未来植物与动物相互作用的研究有价值。

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来源期刊

Applications in Plant Sciences PLANT SCIENCES-

CiteScore

7.30

自引率

0.00%

发文量

审稿时长

12 weeks

期刊介绍： Applications in Plant Sciences (APPS) is a monthly, peer-reviewed, open access journal promoting the rapid dissemination of newly developed, innovative tools and protocols in all areas of the plant sciences, including genetics, structure, function, development, evolution, systematics, and ecology. Given the rapid progress today in technology and its application in the plant sciences, the goal of APPS is to foster communication within the plant science community to advance scientific research. APPS is a publication of the Botanical Society of America, originating in 2009 as the American Journal of Botany''s online-only section, AJB Primer Notes & Protocols in the Plant Sciences. APPS publishes the following types of articles: (1) Protocol Notes describe new methods and technological advancements; (2) Genomic Resources Articles characterize the development and demonstrate the usefulness of newly developed genomic resources, including transcriptomes; (3) Software Notes detail new software applications; (4) Application Articles illustrate the application of a new protocol, method, or software application within the context of a larger study; (5) Review Articles evaluate available techniques, methods, or protocols; (6) Primer Notes report novel genetic markers with evidence of wide applicability.