The Extended Specimen Network: A Strategy to Enhance US Biodiversity Collections, Promote Research and Education

Lendemer, James C.; Thiers, Barbara M.; Monfils, Anna; Zaspel, Jennifer M.; Ellwood, Elizabeth R.; Bentley, Andrew; LeVan, Katherine E.; Bates, John M.; Jennings, David; Contreras, Dori L.; Lagomarsino, Laura P.; Mabee, Paula M.; Ford, Linda; Guralnick, Robert; Gropp, Robert E.; Revelez, Marcy; Cobb, Neil S.; Seltmann, Katja C.; Aime, M. Catherine

doi:10.1093/biosci/biz140

Cited by 141 publications

(128 citation statements)

References 26 publications

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“…2 ). Standards for digital representations of specimens are so far lacking, but it is obvious that the cyberspecimen concept, also referred as extended specimens ( Cicero et al 2017 ; Lendemer et al 2020 ), implies digital publication of extensive and diverse data packages connected via unique specimen identifiers.…”

Section: Properties and Diversity Of Alpha-taxonomic Datamentioning

confidence: 99%

Repositories for Taxonomic Data: Where We Are and What is Missing

et al. 2020

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Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000–20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term—ideally perpetual—data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach—linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated $ \le $2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000–40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.]

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Section: Properties and Diversity Of Alpha-taxonomic Datamentioning

confidence: 99%

Repositories for Taxonomic Data: Where We Are and What is Missing

et al. 2020

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“…Progress toward developing robust and comprehensive ecosystem and evosystem models must be achieved by building forward from a historical context, by exploring and querying fossil records, herbaria, botanical and germplasm collections, and seed banks. We recommend maintaining and mobilizing these existing biodiversity resources to amplify dramatically the content and use of the Extended Specimen Network (Lendemer et al., 2020), which enables novel discoveries arising from linking genotypic and phenotypic data on plants and their associated biota to detailed ecosystems data. This information repository needs to be supported by sustained investments in data sciences and ecosystem research such as the Critical Zone Observatories, Long‐Term Ecological Network research sites, and the National Ecological Observatory Network.…”

Section: Recommendationsmentioning

confidence: 99%

Plant science decadal vision 2020–2030: Reimagining the potential of plants for a healthy and sustainable future

et al. 2020

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Plants, and the biological systems around them, are key to the future health of the planet and its inhabitants. The Plant Science Decadal Vision 2020–2030 frames our ability to perform vital and far‐reaching research in plant systems sciences, essential to how we value participants and apply emerging technologies. We outline a comprehensive vision for addressing some of our most pressing global problems through discovery, practical applications, and education. The Decadal Vision was developed by the participants at the Plant Summit 2019, a community event organized by the Plant Science Research Network. The Decadal Vision describes a holistic vision for the next decade of plant science that blends recommendations for research, people, and technology. Going beyond discoveries and applications, we, the plant science community, must implement bold, innovative changes to research cultures and training paradigms in this era of automation, virtualization, and the looming shadow of climate change. Our vision and hopes for the next decade are encapsulated in the phrase reimagining the potential of plants for a healthy and sustainable future. The Decadal Vision recognizes the vital intersection of human and scientific elements and demands an integrated implementation of strategies for research (Goals 1–4), people (Goals 5 and 6), and technology (Goals 7 and 8). This report is intended to help inspire and guide the research community, scientific societies, federal funding agencies, private philanthropies, corporations, educators, entrepreneurs, and early career researchers over the next 10 years. The research encompass experimental and computational approaches to understanding and predicting ecosystem behavior; novel production systems for food, feed, and fiber with greater crop diversity, efficiency, productivity, and resilience that improve ecosystem health; approaches to realize the potential for advances in nutrition, discovery and engineering of plant‐based medicines, and "green infrastructure." Launching the Transparent Plant will use experimental and computational approaches to break down the phytobiome into a "parts store" that supports tinkering and supports query, prediction, and rapid‐response problem solving. Equity, diversity, and inclusion are indispensable cornerstones of realizing our vision. We make recommendations around funding and systems that support customized professional development. Plant systems are frequently taken for granted therefore we make recommendations to improve plant awareness and community science programs to increase understanding of scientific research. We prioritize emerging technologies, focusing on non‐invasive imaging, sensors, and plug‐and‐play portable lab technologies, coupled with enabling computational advances. Plant systems science will benefit from data management and future advances in automation, machine learning, natural language processing, and artificial intelligence‐assisted data integration, pattern identification, and decision making. Implementation of th...

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“…Herbarium samples are an increasingly useful source of DNA for phylogenomic studies, extending the utility of our historic natural history collections (Lendemer et al, 2020), but they are not a panacea. Even high efficiency target capture will fail when DNA is low quality, as is typical in herbarium specimens collected in the wet tropics (Brewer et al, 2019), especially when they are collected in ethanol (Särkinen, Staats, et al, 2012)-a common scenario for Otoba, and likely universal in the herbarium specimens that we sampled.…”

Section: Targeted Sequence Capture Promotes Herbariomics-with Caveatsmentioning

confidence: 99%

“…To facilitate standardized loci that can be combined across studies, the plant systematics community should strive for the development of searchable, long-term repositories for Angiosperms353 datasets. Any such future repository would further benefit from being linked to herbarium vouchers, which would help with reproducibility of research as well as continue to extend the use of herbarium specimens in science (Lendemer et al, 2020).…”

Section: Utility Of Angiosperms353 As Universal Loci For Plant Phylogmentioning

confidence: 99%

Niche evolution of the Neotropical tree genusOtobain the context of global biogeography of the nutmeg family, Myristicaceae

Frost

Santamaría-Aguilar

Singletary

et al. 2020

Preprint

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Abstract•Premise of the studyUniversal probesets for targeted sequence capture have facilitated phylogenomic research into diverse plant groups with limited genomic resources, including from low-quality DNA typical of herbarium specimens. Here, we leverage the Angiosperms353 loci to infer the first phylogeny of Otoba (Myristicaceae), a Neotropical tree genus that is ecologically dominant in low-to-mid elevation wet forests, exclusively from herbarium specimens.•MethodsWe use a combination of Angiosperms353 loci, obtained via targeted sequence capture, and plastid sequences to resolve the phylogeny of Otoba using concatenated and species tree methods. We subsequently use this phylogeny to infer biogeography and trait evolution using phylogenetic comparative methods.•Key resultsRecovery success of loci is correlated with age of herbarium specimens and average annual precipitation. Despite a large amount of missing data, we resolve the phylogeny of Otoba into three major subclades, each structured by geography. We show that Otoba’s crown radiation occurred on the western slopes of the Andes in the late Miocene, and from there, migrated into Central America at least twice; the genus was only able to cross to the eastern slopes of the Andes a single time. Trait evolution has been dynamic across vegetative and reproductive traits, with multiple origins of most discrete traits investigated, including ecologically important aril color.•ConclusionsOtoba is recent, rapid radiation whose evolution is tied to landscape change, including Andean uplift, in the northern Neotropics. Its dynamic morphological evolution is consistent with sorting of ancestral traits during recent speciation events. In one of the first herbariomic studies exclusively using herbarium tissue from specimens collected in the wet tropics, this study demonstrates the promise of Angiosperms353 loci in resolving shallow species-level relationships, even from low-quality DNA.

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The Extended Specimen Network: A Strategy to Enhance US Biodiversity Collections, Promote Research and Education

Cited by 141 publications

References 26 publications

Repositories for Taxonomic Data: Where We Are and What is Missing

Repositories for Taxonomic Data: Where We Are and What is Missing

Plant science decadal vision 2020–2030: Reimagining the potential of plants for a healthy and sustainable future

Niche evolution of the Neotropical tree genusOtobain the context of global biogeography of the nutmeg family, Myristicaceae

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