ArticleApplications in plant sciences2021
High-throughput methods for efficiently building massive phylogenies from natural history collections.
Article in Applications in plant sciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Resolving relationships in the radiation of Australia's largest pea clade (Fabaceae tribe Mirbelieae) with target-capture sequencing.Annals of botany · 2025Article
- An integrative framework reveals widespread gene flow during the early radiation of oaks and relatives in Quercoideae (Fagaceae).Journal of integrative plant biology · 2025Article
- Article
- Phylogenomics, reticulation, and biogeographical history of Elaeagnaceae.Plant diversity · 2024Article
- Herbarium collections remain essential in the age of community science.Nature communications · 2024Article
- Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants.Nature communications · 2024Article
- Retrieval of long DNA reads from herbarium specimens.AoB PLANTS · 2023Review
- Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections.Biodiversity data journal · 2023Article
- Green plant genomes: What we know in an era of rapidly expanding opportunities.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Structural and evolutionary insights into astacin metallopeptidases.Frontiers in molecular biosciences · 2022Article
- Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics.Applications in plant sciences · 2021Article
- High-throughput methods for efficiently building massive phylogenies from natural history collections.Applications in plant sciences · 2021Article
- The Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing Success.Frontiers in plant science · 2021Article
- PhyloHerb: A high-throughput phylogenomic pipeline for processing genome skimming data.Applications in plant sciencesArticle
- Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections.Applications in plant sciencesArticle
- FieldPrism: A system for creating snapshot vouchers from field images using photogrammetric markers and QR codes.Applications in plant sciencesArticle
- HybSuite: An integrated pipeline for hybrid capture phylogenomics from reads to trees.Applications in plant sciencesArticle
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
premiseLarge phylogenetic data sets have often been restricted to small numbers of loci from GenBank, and a vetted sampling-to-sequencing phylogenomic protocol scaling to thousands of species is not yet available. Here, we report a high-throughput collections-based approach that empowers researchers to explore more branches of the tree of life with numerous loci.
methodsWe developed an integrated Specimen-to-Laboratory Information Management System (SLIMS), connecting sampling and wet lab efforts with progress tracking at each stage. Using unique identifiers encoded in QR codes and a taxonomic database, a research team can sample herbarium specimens, efficiently record the sampling event, and capture specimen images. After sampling in herbaria, images are uploaded to a citizen science platform for metadata generation, and tissue samples are moved through a simple, high-throughput, plate-based herbarium DNA extraction and sequencing protocol.
resultsWe applied this sampling-to-sequencing workflow to ~15,000 species, producing for the first time a data set with ~50% taxonomic representation of the "nitrogen-fixing clade" of angiosperms. DISCUSSION: The approach we present is appropriate at any taxonomic scale and is extensible to other collection types. The widespread use of large-scale sampling strategies repositions herbaria as accessible but largely untapped resources for broad taxonomic sampling with thousands of species.
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