Digital accessible knowledge of biodiversity data is an increasingly important source of information in studies of biogeography and conservation. These databases can also reveal temporal, spatial and ...taxonomical gaps in biodiversity documentation, even in areas that have been intensively studied and from where accurate species lists are available. Therefore, revealing these gaps may help allocating collecting efforts, conservation priorities and strategies for improving database curation. Here, we evaluate potential shortfalls for flowering plants in a tropical hotspot, the Brazilian Atlantic Forest, by cross-referencing two online repositories of biodiversity data (the Global Biodiversity Information Facility – GBIF – and the Brazilian Flora 2020 floristic database – BFG). We aimed to evaluate the congruence between those repositories, highlighting tendencies in current documentation for this area. We found that from the 7220 reported flowering plant species endemics to the Atlantic Forest, 1573 (22%) have no valid spatial data in GBIF, and 75% of all of the 605,951 records do not present valid spatial information. Most of the missing information is related to species known only from few and old collections with absent or inaccurately georeferenced data. This lack of information may cause a large impact in spatial studies, especially for rare and threatened species. Nevertheless, our analysis also shows that spatial information for the filtered data is highly congruent between GBIF and BFG data, indicating relatively high availability of quality data in large repositories after standard and automatized cleaning procedures. Still, good practices to decrease the impact of losing data are recommended, including more investment in field collections, targeting poorly known species and returning cleaned spatial datasets to online repositories after taxonomic revisions.
As herbaria move to digitize their collections, the question remains of how to efficiently digitize collections other than standard herbarium sheets, such as wood slide collections. Beginning in ...September 2018, the Harvard University Herbaria began a project to image and digitize the wood slides contained in the Bailey-Wetmore Wood Collection. The primary goal of this project was to produce images of the wood tissue that could be used for specimen-level research and to make them available on the internet for remote scholarship. A secondary goal was to establish best practices for digitizing and imaging a microscope slide collection of tissue sections. Due to the size of the wood slide collection (approximately 30,000 slides), a medical histology scanner and virtual microscopy software were used to image these slides. This article outlines the workflow used to create these images and compares the results with digital resources currently available for wood anatomy research. Prior to this project, the very little of the Bailey-Wetmore Wood Collection was cataloged digitally and none of it was imaged, which made access to this unique collection difficult. By imaging and digitizing 6605 slides in the collection, this project has demonstrated how other institutions can make similar slide collections available to the broader scientific community.
Bioregionalisation partitions diversity so that similarity of the selected biological and ecological variables is higher within regions than it is outside those regions. The classic approach ...partitions an area based on species composition, whereas more recent methods based on remotely sensed data classify biogeographic regions on biophysical and structural variables of vegetation. Another, yet to be explored opportunity, is offered by identifying distinct ecological strategies of plants inhabiting a given area, that is, a functional trait‐based bioregionalisation. Here, we propose such a bioregionalisation using trait hypervolumes. We also compare the proposed functional bioregionalisation with established classifications based on species composition or on remotely sensed data to identify spatial congruence among them, and suggest possible reasons behind observed patterns.
Natural history collections represent an underexploited resource, despite holding both trait and locality information and being taxonomically comprehensive. We compile values of traits (leaf size, plant height, seed number per fruit, seed volume) derived from natural history collections for a random sample of African angiosperm species (~1% of the continental flora) to estimate a trait hypervolume. We use hierarchical clustering to divide the hypervolume into four segments (each representing a distinct ecological strategy), whose spatial intersections produced 12 putative biogeographic regions, each containing one or more of these strategies. We spatially map the hypervolume segments onto the entire African continent and calculate the spatial congruence of the putative functional biogeographic regions with previous bioregionalisations.
We identify values and combinations of traits that can be indicative of biogeographic regions. This functional bioregionalisation shows greater spatial congruence with that derived from species composition than from remote sensing. However, spatial congruence is low at the continent scale (19%–37%), and varies greatly among regions and in pairwise comparisons between bioregionalisations.
Synthesis. Plant traits from natural history collections offer an underused source of information for biogeographic analyses. We demonstrate potential applications of trait hypervolumes in functional biogeography, and outline strengths and drawbacks of the different bioregionalisation methods. Finally, we suggest that key ecological strategies could be used in future models as proxies to anticipate shifts of species assemblages and biogeographic regions.
Plant trait values from natural history collections are underused within functional ecology, but we rely on them to establish trait‐space as a hypervolume, in which different plant ecological strategies can be identified. Using this trait‐space hypervolume, and a spatial projection of trait values, we propose functional biogeographic regions and compare them with regions derived using different methodological approaches.
•Herbarium materials provide enough fata to recover the change of vascular plants.•Distributional change of the orchids is estimated from 1880th to the present time.•Orchids of Russia reveal ...consistent change throughout Russia.•Widely distributed orchid display the strongest decrease.
Monitoring the distributional changes of native vascular plants over time is an important task both from the scientific and conservation point. However, numerical data for such studies are often missing, especially for countries lacking national biodiversity datasets, such as Russia. The main aim of this study was to assess whether direct data from herbarium collections are sufficient to recover the distributional changes effectively. The object of this study was the orchid family, a conservationally important group of plants, in the Flora of Russia and Crimea. Primary source of the data were georeferenced herbarium labels from 59 herbarium collections. The distributional changes were assessed by comparisons between the numbers of grid cells with records in different time intervals, taking into account the variation of recording intensity with time.
The method proved to be applicable to 108 out of 135 species of orchids occurring within the studied territory. For many of them, reliable changes in the number of localities were confirmed. Among widely distributed orchid species constant negative change was detected for Anacamptis coriophora, Calypso bulbosa, Coeloglossum viride, Cypripedium guttatum, C. macranthos, Gymnadenia conopsea, Herminium monorchis, Neotinea ustulata, Orchis militaris, Platanthera hologlottis; constant positive change was recovered for Dactylorhiza baltica and D. fuchsii only. In many species, trends over time were uneven. The direction of change proved to be generally consistent for a given species across the whole studied territory, suggesting the principal influence of general factors, such as climate change and general eutrophication of the environment. The direction of change is consistent with type of geographic distribution of plants.
Although the method used in the current study for recovering distributional changes has limitations, it may be further recommended for use with other taxa.
Premise
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.
Methods
We utilized a resurrection ecology approach, leveraging dormant seeds from herbarium collections to assess whether populations of Plantago patagonica 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.
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.
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.
Advances in DNA extraction and next‐generation sequencing have made a vast number of historical herbarium specimens available for genomic investigation. These specimens contain not only genomic ...information from the individual plants themselves, but also from associated microorganisms such as bacteria and fungi. These microorganisms may have colonized the living plant (e.g., pathogens or host‐associated commensal taxa) or may result from postmortem colonization that may include decomposition processes or contamination during sample handling. Here we characterize the metagenomic profile from shotgun sequencing data from herbarium specimens of two widespread plant species (Ambrosia artemisiifolia and Arabidopsis thaliana) collected up to 180 years ago. We used blast searching in combination with megan and were able to infer the metagenomic community even from the oldest herbarium sample. Through comparison with contemporary plant collections, we identify three microbial species that are nearly exclusive to herbarium specimens, including the fungus Alternaria alternata, which can comprise up to 7% of the total sequencing reads. This species probably colonizes the herbarium specimens during preparation for mounting or during storage. By removing the probable contaminating taxa, we observe a temporal shift in the metagenomic composition of the invasive weed Am. artemisiifolia. Our findings demonstrate that it is generally possible to use herbarium specimens for metagenomic analyses, but that the results should be treated with caution, as some of the identified species may be herbarium contaminants rather than representing the natural metagenomic community of the host plant.
Aim
We analyse the oldest available data on the high‐elevation vegetation on Tenerife's Mt. Teide, namely the species shown in A. von Humboldt's (1817) Tableau Physique des Iles Canaries (TPIC), ...which is based on his own 1799 visit and an 1815 visit by L. von Buch and C. Smith. The analysis is of interest in the context of climate change and biotic changes, such as the eradication of non‐native goats from the Teide National Park. Between 1944 and 2010, the summit region of Mt. Teide has warmed at a rate of 0.14°C/decade.
Location
Mt. Teide on Tenerife, Canary Islands.
Taxon
Vascular plants.
Methods
We updated the taxonomy of the 197 species shown in the TPIC, data‐mined publications and letters, searched relevant herbaria for surviving collections, and compared historic and modern species presence, absence and elevational ranges.
Results
Both Humboldt and Buch had to use formulas to convert barometer readings into elevations above sea level, and none of Humboldt's collections and few of Buch's are linked to precise elevations. The upper range limits of all 23 species for which we found data have shifted upward, with the average shift being 36.4 m per decade (1799/1815–2021). Four species that today are abundant were not recorded in 1815, suggesting population expansion, probably due to goat eradication.
Main conclusions
While our data cannot disentangle the effects of climate change and changing herbivory, they provide the earliest available record on the vegetation on Mt. Teide and illustrate the magnitude of change.
More than ever, ecologists seek to employ herbarium collections to estimate plant functional traits from the past and across biomes. However, many trait measurements are destructive, which may ...preclude their use on valuable specimens. Researchers increasingly use reflectance spectroscopy to estimate traits from fresh or ground leaves, and to delimit or identify taxa. Here, we extend this body of work to non‐destructive measurements on pressed, intact leaves, like those in herbarium collections.
Using 618 samples from 68 species, we used partial least‐squares regression to build models linking pressed‐leaf reflectance spectra to a broad suite of traits, including leaf mass per area (LMA), leaf dry matter content (LDMC), equivalent water thickness, carbon fractions, pigments, and twelve elements. We compared these models to those trained on fresh‐ or ground‐leaf spectra of the same samples.
The traits our pressed‐leaf models could estimate best were LMA (R2 = 0.932; %RMSE = 6.56), C (R2 = 0.855; %RMSE = 9.03), and cellulose (R2 = 0.803; %RMSE = 12.2), followed by water‐related traits, certain nutrients (Ca, Mg, N, and P), other carbon fractions, and pigments (all R2 = 0.514–0.790; %RMSE = 12.8–19.6). Remaining elements were predicted poorly (R2 < 0.5, %RMSE > 20). For most chemical traits, pressed‐leaf models performed better than fresh‐leaf models, but worse than ground‐leaf models. Pressed‐leaf models were worse than fresh‐leaf models for estimating LMA and LDMC, but better than ground‐leaf models for LMA. Finally, in a subset of samples, we used partial least‐squares discriminant analysis to classify specimens among 10 species with near‐perfect accuracy (>97%) from pressed‐ and ground‐leaf spectra, and slightly lower accuracy (>93%) from fresh‐leaf spectra.
These results show that applying spectroscopy to pressed leaves is a promising way to estimate leaf functional traits and identify species without destructive analysis. Pressed‐leaf spectra might combine advantages of fresh and ground leaves: like fresh leaves, they retain some of the spectral expression of leaf structure; but like ground leaves, they circumvent the masking effect of water absorption. Our study has far‐reaching implications for capturing the wide range of functional and taxonomic information in the world’s preserved plant collections.
Résumé
Plus que jamais, les écologistes cherchent à utiliser des collections d'herbiers pour estimer les traits fonctionnels des plantes dans le passé et à travers des biomes. Cependant, plusieurs mesures de traits sont destructives et pourraient ne pas être effectuées sur des spécimens de grande valeur. De plus en plus, les chercheuses et chercheurs utilisent la spectroscopie de réflectance pour estimer des traits des feuilles fraîches ou broyées, et pour délimiter ou identifier les espèces. Nous étendons ici ces travaux en réalisant des mesures non‐destructives avec des feuilles entières et pressées.
À partir de 618 échantillons provenant de 68 espèces, nous avons utilisé la régression des moindres carrés partiels pour construire des modèles liant les spectres de réflectance des feuilles pressées avec un large ensemble de traits, incluant la masse foliaire spécifique (‘leaf mass per area,’ LMA), la teneur en matière sèche des feuilles (‘leaf dry matter content,’ LDMC), l'épaisseur d'eau équivalente, les fractions de carbone, des pigments et douze éléments. Nous avons comparé ces modèles à ceux entraînés sur les spectres des feuilles fraîches ou broyées provenant des mêmes échantillons.
Les traits les mieux estimés par nos modèles sur des feuilles pressées étaient la LMA (R2 = 0.932; %REQM = 6.56), le carbone (R2 = 0.855; %REQM = 9.03) et la cellulose (R2 = 0.803; %REQM = 12.2), suivis des traits liés à l'eau, de certains éléments nutritifs (Ca, Mg, N et P), des autres fractions de carbone et des pigments (tous les R2 = 0.514–0.790; %REQM = 12.8–19.6). Les autres éléments nutritifs ne pouvaient pas être bien estimés (R2 < 0.5, %RMSE >20). Pour la plupart des traits chimiques, les modèles sur des feuilles pressées étaient plus performants que ceux de feuilles fraîches, mais moins performants que ceux à partir de feuilles broyées. Les modèles sur des feuilles pressées performaient moins bien que ceux sur des feuilles fraîches pour estimer la LMA et la LDMC, mais performaient mieux que ceux sur des feuilles broyées pour la LMA. Finalement, pour un sous‐ensemble d'échantillons, nous avons utilisé l'analyse discriminante des moindres carrés partiels et réussi à classifier les spécimens parmi 10 espèces avec une précision presque parfaite (>97%) à partir des spectres des feuilles pressées ou broyées, et avec une précision légèrement plus basse (>93%) à partir de feuilles fraîches.
Nos résultats démontrent que l'application de la spectroscopie sur des feuilles pressées est une approche non‐destructive prometteuse pour estimer des traits fonctionnels et pour identifier des espèces. Les spectres des feuilles pressées semblent combiner les avantages des feuilles fraîches et de celles broyées: comme les feuilles fraîches, elles conservent une partie de l'expression spectrale de la structure foliaire; comme les feuilles broyées, elles contournent l'effet masquant de l'absorption par l'eau. Notre étude a des implications importantes pour l'acquisition de données fonctionnelles et taxonomiques à partir des collections de plantes préservées à travers le monde.
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