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31 results for “herbarium specimen data”
Data from Herbarium Specimens Reveal Delays in Autumn Maple Coloration in the Northeastern United States Over the Past 150 Years
Data from "Herbarium Specimens Reveal Delays in Autumn Maple Coloration in the Northeastern United States Over the Past 150 Years". Herbarium specimens annotated for damage and phenological status paired with climate and locality information to investigate long-term trends in species-interactions and autumn phenology.
A benchmark dataset of herbarium specimen images with label data: Summary
<p>This landing page contains a CSV file compiling all data associated with herbarium specimens that are part of this dataset, as they could be found on GBIF, JACQ or FinBIF. A CSV file with and without Darwin Core extension data is available, as some CSV readers have trouble with the JSON format that is used for those extensions.</p> <p>In addition, DOI's of the individual specimens uploaded to Zenodo and direct links to the different files (JPEG, TIFF, JSON, PNG) are also included. Index of these added variables:</p> <p>- persistentID: Persistent Identifier of the collection specimen. Data uploaded as part of this dataset will not be kept in sync with changes at the collection's repository. Hence, this URI will always point to the most up to date information known about the herbarium specimen.</p> <p>- jpegURL, tiffURL, jsonURL: URL's pointing straight to the respective image and data files themselves, to facilitate (selective) batch downloads.</p> <p>- pngSegAllURL and pngSegSelURL: Segmented overlays of the herbarium specimens indicating the location of different labels and reference material on the sheet ("All") and their content ("Sel"). More information can be found in the paper (in prep) associated with this data publication and the individual depositions themselves.</p> <p>- DOI: The DOI of the deposition of images and data of these specimens on Zenodo. DOI's point to the most up-to-date version of these depositions at the time of the publication of this CSV file. As a rule, this CSV file will be updated should any changes happen to any of the depositions.</p> <p>- jpegURL2, tiffURL2: A few herbarium sheets had labels on the back and consisted therefore of two scans. As a rule, the label scans are in this category.</p>
Phenological and climate data for herbarium specimens of Streptanthus tortuosus (Brasicaceae)
<p>These data represent phenological data derived from herbarium specimens of Streptanthus tortuous collected between 1903 and 2013 in California. The associated temperature and precipitation related climate data during the year of specimen collection at the location of collection are also included.</p>
Data from: Resurrected seeds from herbarium specimens reveal rapid evolution of drought resistance in a selfing annual
<p>Premise of study: Increased aridity and drought associated with climate change are exerting unprecedented selection pressures on plant populations. Whether populations can rapidly adapt, and which life history traits might confer increased fitness under drought, remain outstanding questions. </p> <p>Methods: We utilized a resurrection ecology approach, leveraging dormant seeds from herbarium collections to assess whether populations of <em>Plantago patagonica</em> from the semi-arid Colorado Plateau have rapidly evolved in response to approximately ten years of intense drought in the region. We quantified multiple traits associated with drought escape and drought resistance and assessed the survival of ancestors and descendants under simulated drought. </p> <p>Key Results: Descendant populations displayed a significant shift in resource allocation, in which they invested less in reproductive tissues and relatively more in both above- and below-ground vegetative tissues. Plants with greater leaf biomass survived longer under terminal drought; moreover, even after accounting for the effect of increased leaf biomass, descendant seedlings survived drought longer than their ancestors. </p> <p>Conclusions: Our results document rapid adaptive evolution in response to climate change in a selfing annual and suggest that shifts in tissue allocation strategies may underlie adaptive responses to drought in arid or semi-arid environments. This work also illustrates a novel approach, documenting that under specific circumstances, seeds from herbarium specimens may provide an untapped source of dormant propagules for future resurrection experiments.</p>
Simulated Herbarium data for testing the accuracy with which specimen data can predict the timing and duration of population-level flowering displays
<p>This dataset provides code and example data for simulating specimen collections of flowering plants across North America, and for developing phenological predictions of population-level flowering onset and termination for these data. It further presents code for assessing the accuracy of these predictions relaticve to known (simulated) population-level flowering dates at the location of each collection.</p>
Morphological and DNA sequence data generated by Sanger sequencing and target capture methods for moss plants in the genus Fissidens from herbarium specimens
<p><span>Morphological evolution in mosses has long been hypothesized to accompany shifts in microhabitats and can be tested using comparative phylogenetics. These lines of inquiry have developed substantially, in part, by target capture sequencing allowing for phylogenomic scale data generated from herbarium specimens. In the present study, we test the relationship between taxonomically important morphological characters in the moss genus <em>Fissidens</em>, using both a 400-locus dataset generated using a target-capture approach as well as a three-locus phylogeny generated using sanger sequencing. Phylogenetic trees were generated using ASTRAL and Bayesian Inference and used to test the monophyly of subgenera/sections and provided the basis for ancestral character reconstruction and phylogenetic correlation analyses among five morphological characters as well as habitat moisture scored from literature. The characters <em>axillary hyaline nodules</em>, <em>limbidium</em>, <em>costa</em>, and <em>peristome morphology</em> as well as <em>sexual system</em>, <em>minimum habitat moisture</em>, <em>average habitat moisture</em>, <em>maximum habitat moisture</em>, and <em>habitat moisture niche breadth</em> each exhibit statistically significant phylogenetic signal. Significant correlations were found between the limbidium (phyllid/leaf border) and habitat moisture niche breadth, which could be interpreted as a more extensive <em>limbidium</em> enabling species to survive across a wider variety of habitats. Correlations were also found between <em>costa anatomy</em> and the <em>limbidum</em> of the gametophyte and sporophyte <em>peristome</em> <em>morphology</em>, as well as <em>average habitat moisture</em> and <em>sexual system</em>. Continued exploration of the relationships between morphological evolution, life history, and habitat will enable us to expand our understanding of functional morphology in mosses.</span></p>
Linked collectors and determiners for: Flora Sumatra: Digitizing and data basing specimens of the Sumatran Flora deposited at Herbarium Universitas Andalas (ANDA)-Part 2.
Natural history specimen data linked to collectors and determiners held within, "Flora Sumatra: Digitizing and data basing specimens of the Sumatran Flora deposited at Herbarium Universitas Andalas (ANDA)-Part 2". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/39e85504-1ebe-4671-be65-19ccdc1d7c7d">https://bionomia.net/dataset/39e85504-1ebe-4671-be65-19ccdc1d7c7d</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/39e85504-1ebe-4671-be65-19ccdc1d7c7d">https://gbif.org/dataset/39e85504-1ebe-4671-be65-19ccdc1d7c7d</a>. Formatted as a Frictionless Data package.
Data For: Herbarium specimens provide reliable estimates of phenological responsiveness to climate at unparalleled taxonomic and spatiotemporal scales
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Data from: Phenological patterns of tropical mountain forest trees across the neotropics: Evidence from herbarium specimens
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Data from: Resurrected seeds from herbarium specimens reveal rapid evolution of drought resistance in a selfing annual
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Simulated Herbarium data for testing the accuracy with which specimen data can predict the timing and duration of population-level flowering displays
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Morphological and DNA sequence data generated by Sanger sequencing and target capture methods for moss plants in the genus Fissidens from herbarium specimens
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Data from: Specimen-based analysis of morphology and the environment in ecologically dominant grasses: the power of the herbarium
Herbaria contain a cumulative sample of the world's flora, assembled by thousands of people over several hundred years. Recent advances in computation, DNA sequencing, and image manipulation have allowed us to capitalize on this resource. Using herbarium material, we conducted a species-level analysis of a major clade in the grass tribe Andropogoneae, which includes the dominant species of the world's grasslands, from the genera Andropogon, Schizachyrium, Hyparrhenia, and other groups. We imaged 188 of the 250 available species of the clade, georeferenced the specimens, and extracted climatic variables for each. Using semiand fully automated image analysis techniques, we extracted spikelet morphological characters and correlated these with environmental variables. We are currently generating chloroplast genome sequences to correct for phylogenetic covariance and here present an analysis of a subset of 81 species, representing the power of this approach. In addition to taxonomic/phylogenetic observations, we find all morphological and ecological characters are homoplasious but variable among clades. For example, sessile spikelet length is positively correlated with awn length when all accessions are considered, but when separated by clade, the relationship is positive for five sub-clades and negative for three others. Macrohair density and pedicel length were negatively correlated with precipitation.
Data from: Herbarium specimens reveal increasing herbivory over the past century
Predicting how ecological interactions will respond to global change is a major challenge. Plants and their associated insect herbivores compose much of macroscopic diversity, yet how their interactions have been altered by recent environmental change remains underexplored. To address this gap, we quantified herbivory on herbarium specimens of four plant species with records extending back 112 years. Our study focused on the northeastern US, where temperatures have increased rapidly over the last few decades. This region also represents a range of urban development, a form of global change that has shown variable effects on herbivores in the past studies. Herbarium specimens collected in the early 2000s were 23% more likely to be damaged by herbivores than those collected in the early 1900s. Herbivory was greater following warmer winters and at low latitudes, suggesting that climate warming may drive increasing insect damage over time. In contrast, human population densities were negatively associated with herbivore damage. To explore whether changes in insect occurrence or abundance might explain shifts in herbivory, we used insect observational records to build climate occupancy models for lepidopteran herbivores (butterflies and moths) of our focal plant species. These models show that higher winter temperatures were associated with higher probability of insect herbivore presence, while urbanization was associated with reduced probability of herbivore presence, supporting a link between insect herbivore occurrence and herbivory mediated through environment. Synthesis. Using a temporal record of plant herbivory that spans over a century, we show that both temperature and urbanization influence insect damage to plants, but in very different ways. Our results indicate that damage to plants by insect herbivores will likely continue to increase through time in the northeastern US as global temperatures rise, but that urbanization may disrupt local effects of winter warming on herbivory by excluding certain herbivores. These changes may scale to shape ecosystem processes that are driven by herbivory, including plant productivity.
Data from: Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance
Invasive plants provide ample opportunity to study evolutionary shifts that occur after introduction to novel environments. However, although genetic characters pre-dating introduction can be important determinants of later success, large-scale investigations of historical genetic structure have not been feasible. Common ragweed (Ambrosia artemisiifolia L.) is an invasive weed native to North America that is known for its allergenic pollen. Palynological records from sediment cores indicate that this species was uncommon before European colonization of North America, and ragweed populations expanded rapidly as settlers deforested the landscape on a massive scale, later becoming an aggressive invasive with populations established globally. Toward a direct comparison of genetic structure now and during intense anthropogenic disturbance of the late 19th century, we sampled 45 natural populations of common ragweed across its native range as well as historical herbarium specimens collected up to 140 years ago. Bayesian clustering analyses of 453 modern and 473 historical samples genotyped at three chloroplast spacer regions and six nuclear microsatellite loci reveal that historical ragweed's spatial-genetic structure mirrors both the paleo-record of Ambrosia pollen deposition and the historical pattern of agricultural density across the landscape. Furthermore, for unknown reasons this spatial-genetic pattern has changed substantially in the intervening years. Following on previous work relating morphology and and genetic expression between plants collected from eastern North America and Western Europe, we speculate that the cluster associated with humans' rapid transformation of the landscape is a likely source of these aggressive invasive populations.
Data from: Tracking population genetic signatures of local extinction with herbarium specimens
<p><strong><span>Background and Aims </span></strong><span>Habitat degradation and landscape fragmentation dramatically lower population sizes of rare plant species. Decreasing population sizes may, in turn, negatively affect genetic diversity and reproductive fitness which can ultimately lead to local extinction of populations. Although such extinction vortex dynamics have been postulated in theory and modelling for decades, empirical evidence from local extinctions of plant populations is scarce. In particular, comparisons between current vs. historical genetic diversity and differentiation are lacking despite their potential to guide conservation management.</span></p> <p><strong><span>Methods </span></strong><span>We studied the population genetic signatures of the local extinction of <em>Biscutella laevigata</em> subsp. <em>gracilis </em>populations in Central Germany. We used microsatellites to genotype individuals from 15 current populations, one ex-situ population, and 81 herbarium samples from five extant and 22 extinct populations. In the current populations, we recorded population size and fitness proxies, collected seeds for a germination trial and conducted a vegetation survey. The latter served as surrogate for habitat conditions to study how habitat dissimilarity affects functional connectivity among the current populations. </span></p> <p><strong><span>Key Results </span></strong><span>Bayesian clustering revealed similar gene pool distribution in current and historical samples but also indicated that a distinct genetic cluster was significantly associated with extinction probability. Gene flow was affected by both spatial distance and floristic composition of population sites, highlighting the potential of floristic composition as powerful predictor of functional connectivity which may promote decision making for reintroduction measures. For an extinct population, we found a negative relationship between sampling year and heterozygosity. Inbreeding negatively affected germination. </span></p> <p><strong><span>Conclusions</span></strong><span> Our study illustrates the usefulness of historical DNA to study extinction vortices in threatened species. Our novel combination of classical population genetics together with data from herbarium specimens, an ex-situ population and a germination trial underscores the need for genetic rescue measures to prevent extinction of <em>B. laevigata</em> in Central Germany. </span></p>
Data from: Carbon isotope trends across a century of herbarium specimens suggest CO2 fertilization of C4 grasses
<p>Increasing atmospheric CO<sub>2</sub> is changing the dynamics of tropical savanna vegetation. C<sub>3</sub> trees and grasses are known to experience CO<sub>2</sub> fertilization, whereas responses to CO<sub>2</sub> by C<sub>4</sub> grasses are more ambiguous. Here, we sample stable carbon isotope trends in herbarium collections of South African C<sub>4</sub> and C<sub>3</sub> grasses to reconstruct <sup>13</sup>C discrimination. We found that C<sub>3</sub> grasses showed no trends in <sup>13</sup>C discrimination over the past century but that C<sub>4</sub> grasses increased their <sup>13</sup>C discrimination through time, especially since 1950. These changes were most strongly linked to changes in atmospheric CO<sub>2</sub> rather than to trends in rainfall climatology or temperature. Combined with previously published evidence that grass biomass has increased in C<sub>4</sub>-dominated savannas, these trends suggest that increasing water use efficiency due to CO<sub>2</sub> fertilization may be changing C<sub>4</sub> plant-water relations. CO<sub>2</sub> fertilization of C<sub>4</sub> grasses may thus be a neglected pathway for anthropogenic global change in tropical savanna ecosystems.</p>
Data from: Pollen on stigmas of herbarium specimens: a window into the impacts of a century of environmental disturbance on pollen transfer
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Data from: Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance
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Data from: Specimen-based analysis of morphology and the environment in ecologically dominant grasses: the power of the herbarium
Open the record for dataset details and reuse information.
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