Herbarium specimens have long been a cornerstone of taxonomic research but are only recently being recognized for their potential as a source of spatially and temporally extensive data on plant ...functional traits. Many researchers in trait-based disciplines, including functional ecologists and evolutionary biologists alike, remain surprisingly unaware of this powerful use of herbaria. This review brings together disparate studies to synthesize the past, current, and potential future uses of specimens as functional trait data sources, answering the following questions. First, what insights using specimens (including traits measured, approaches used, and research questions answered) have been made to date? Second, what new trait-based insights (including potential contributions to global trait databases and recent advancements such as machine learning and high-throughput phenotyping) can be made from herbarium specimens? And third, how can inherent limitations and collection biases be addressed when using specimens in unanticipated ways (including new analytical approaches and improved methods for collecting)? I conclude by identifying what is needed to foster the future of herbaria as big data sources of plant traits. Most notably, plant collecting must be continued, expanded beyond predominantly systematists, and intentionally revised with downstream trait measurements in mind. Furthermore, community-wide standards are needed to integrate otherwise disconnected data and directly link newly derived measurements back to specimen records. Specimens serve as reliable (and necessary) sources of phenotypic data, enabling us to answer questions across phylogenetic, temporal, and spatial dimensions that are otherwise not possible to answer. Herbaria should be embraced as centers for functional trait research.
Studies in disturbed, resource-rich environments often show that invasive plants are more productive than co-occurring natives, but with similar physiological tradeoffs. However, in resource-limited ...habitats, it is unclear whether native and invasive plants have similar metabolic constraints or if invasive plants are more productive per unit resource cost – that is, use resources more efficiently.
Using a common garden to control for environment, we compared leaf physiological traits relating to resource investments, carbon returns, and resource-use efficiencies in 14 native and 18 nonnative invasive species of common genera found in Eastern North American (ENA) deciduous forest understories, where growth is constrained by light and nutrient limitation.
Despite greater leaf construction and nitrogen costs, invaders exhibited greater instantaneous photosynthetic energy-use efficiency (PEUE) and marginally greater photosynthetic nitrogen-use efficiency (PNUE). When integrated over leaf lifespan (LL), these differences were magnified. Differences in efficiency were driven by greater productivity per unit leaf investment, as invaders exhibited both greater photosynthetic abilities and longer LL.
Our results indicate that woody understory invaders in ENA forests are not constrained to the same degree by leaf-based metabolic tradeoffs as the native understory flora. These strategy differences could be attributable to pre-adaptation in the native range, although other explanations are possible
Data integration enables global biodiversity synthesis Heberling, J Mason; Miller, Joseph T; Noesgaard, Daniel ...
Proceedings of the National Academy of Sciences - PNAS,
02/2021, Letnik:
118, Številka:
6
Journal Article
Recenzirano
Odprti dostop
The accessibility of global biodiversity information has surged in the past two decades, notably through widespread funding initiatives for museum specimen digitization and emergence of large-scale ...public participation in community science. Effective use of these data requires the integration of disconnected datasets, but the scientific impacts of consolidated biodiversity data networks have not yet been quantified. To determine whether data integration enables novel research, we carried out a quantitative text analysis and bibliographic synthesis of >4,000 studies published from 2003 to 2019 that use data mediated by the world's largest biodiversity data network, the Global Biodiversity Information Facility (GBIF). Data available through GBIF increased 12-fold since 2007, a trend matched by global data use with roughly two publications using GBIF-mediated data per day in 2019. Data-use patterns were diverse by authorship, geographic extent, taxonomic group, and dataset type. Despite facilitating global authorship, legacies of colonial science remain. Studies involving species distribution modeling were most prevalent (31% of literature surveyed) but recently shifted in focus from theory to application. Topic prevalence was stable across the 17-y period for some research areas (e.g., macroecology), yet other topics proportionately declined (e.g., taxonomy) or increased (e.g., species interactions, disease). Although centered on biological subfields, GBIF-enabled research extends surprisingly across all major scientific disciplines. Biodiversity data mobilization through global data aggregation has enabled basic and applied research use at temporal, spatial, and taxonomic scales otherwise not possible, launching biodiversity sciences into a new era.
Widespread specimen digitization has greatly enhanced the use of herbarium data in scientific research. Publications using herbarium data have increased exponentially over the last century. Here, we ...review changing uses of herbaria through time with a computational text analysis of 13,702 articles from 1923 to 2017 that quantitatively complements traditional review approaches. Although maintaining its core contribution to taxonomic knowledge, herbarium use has diversified from a few dominant research topics a century ago (e.g., taxonomic notes, botanical history, local observations), with many topics only recently emerging (e.g., biodiversity informatics, global change biology, DNA analyses). Specimens are now appreciated as temporally and spatially extensive sources of genotypic, phenotypic, and biogeographic data. Specimens are increasingly used in ways that influence our ability to steward future biodiversity. As we enter the Anthropocene, herbaria have likewise entered a new era with enhanced scientific, educational, and societal relevance.
Machine learning (ML) has great potential to drive scientific discovery by harvesting data from images of herbarium specimens—preserved plant material curated in natural history collections—but ML ...techniques have only recently been applied to this rich resource. ML has particularly strong prospects for the study of plant phenological events such as growth and reproduction. As a major indicator of climate change, driver of ecological processes, and critical determinant of plant fitness, plant phenology is an important frontier for the application of ML techniques for science and society. In the present article, we describe a generalized, modular ML workflow for extracting phenological data from images of herbarium specimens, and we discuss the advantages, limitations, and potential future improvements of this workflow. Strategic research and investment in specimen-based ML methods, along with the aggregation of herbarium specimen data, may give rise to a better understanding of life on Earth.
Dead museum specimens are finding new life, providing critical data about otherwise hidden impacts of human-caused environmental change. New research powerfully leverages decades of plant collections ...to uncover global responses in floral pigmentation linked to ozone and climate change.
Dead museum specimens are finding new life, providing critical data about otherwise hidden impacts of human-caused environmental change. New research powerfully leverages decades of plant collections to uncover global responses in floral pigmentation linked to ozone and climate change.
Interacting species can respond differently to climate change, causing unexpected consequences. Many understorey wildflowers in deciduous forests leaf out and flower in the spring when light ...availability is the highest before overstorey canopy closure. Therefore, different phenological responses by understorey and overstorey species to increased spring temperature could have significant ecological implications. Pairing contemporary data with historical observations initiated by Henry David Thoreau (1850s), we found that overstorey tree leaf out is more responsive to increased spring temperature than understorey wildflower phenology, resulting in shorter periods of high light in the understorey before wildflowers are shaded by tree canopies. Because of this overstorey–understorey mismatch, we estimate that wildflower spring carbon budgets in the northeastern United States were 12–26% larger during Thoreau's era and project a 10–48% reduction during this century. This underappreciated phenomenon may have already reduced wildflower fitness and could lead to future population declines in these ecologically important species.
Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via ...digitization—the conversion of specimen data into accessible digital content—has greatly expanded the use of NHC collections across a diversity of disciplines. We broaden the current vision of digitization (Digitization 1.0)—whereby specimens are digitized within NHCs—to include new approaches that rely on digitized products rather than the physical specimen (Digitization 2.0). Digitization 2.0 builds on the data, workflows, and infrastructure produced by Digitization 1.0 to create digital-only workflows that facilitate digitization, curation, and data links, thus returning value to physical specimens by creating new layers of annotation, empowering a global community, and developing automated approaches to advance biodiversity discovery and conservation. These efforts will transform large-scale biodiversity assessments to address fundamental questions including those pertaining to critical issues of global change.
Recent studies have concluded that native and invasive species share a common set of trait relationships. However, native species in isolated regions might be functionally constrained by their unique ...evolutionary histories such that they follow different carbon capture strategies than introduced species. We compared leaf traits relating to resource investment, carbon return, and resource-use efficiency in 16 native (endemic) and three non-native (invasive) species in a temperate forest in Canterbury, South Island, New Zealand. Trait differences were more closely associated with leaf habit than nativity. Deciduous species (including invaders) exhibited greater maximum photosynthetic rates at similar resource costs, which resulted in greater nitrogen- and energy-use efficiencies than evergreen natives. Leaf area was the only trait that differed significantly by nativity (over two-fold larger in invaders). Invaders and deciduous natives both occupied the 'fast return' end of the leaf economics spectrum in contrast to the native evergreens which had comparatively slow return on investment. Dominant woody invaders in this forest are physiologically distinct from many New Zealand endemic species, which are overwhelmingly evergreen. It remains unclear whether these trait differences translate to an ecological divergence in plant strategy, but these results suggest that ecophysiological tradeoffs are likely constrained by biogeography.
Premise
The use of functional traits has surged in recent decades, providing new insights ranging from individual plant fitness to ecosystem processes. Global plant trait databases have advanced our ...understanding of plant functional diversity, but they remain incomplete because of geographic and taxonomic biases. Herbarium specimens may help fill these gaps by providing trait information across space and time. We tested whether herbarium specimen‐derived measurements are reliable estimates of three important, commonly measured functional traits—specific leaf area (SLA), branch wood specific gravity, and leaf thickness.
Methods
Leaves and branches were collected from species cultivated at Fairchild Tropical Botanic Garden and Florida International University in Miami, FL, USA. Fresh components of SLA (area), branch wood specific gravity (volume), and leaf thickness were measured following standard trait measurement protocols. We compared these trait values to corresponding measurements using plant tissues dried in a plant press following standard herbarium plant collecting protocols.
Results
Herbarium‐derived trait measurements (dried tissues) were highly correlated with those measured using fresh tissues following standard protocols (SLA: R2 = 0.72–0.97, p < 0.01; wood specific gravity: R2 = 0.74–0.75, p < 0.01; leaf thickness: R2 = 0.96, p < 0.01). However, except for leaf thickness, linear model slope or intercept coefficients differed from 1, indicating herbarium‐derived trait measurements may provide biased estimates of fresh traits without the use of correction factors.
Conclusions
Herbarium‐derived traits cannot always be used interchangeably with those measured from fresh tissues because of tissue shrinkage. However, herbarium‐derived trait data still have the potential to drastically expand the temporal, geographic, and taxonomic scope of global trait databases.
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