The ancient DNA revolution of the past 35 years has driven an explosion in the breadth, nuance, and diversity of questions that are approachable using ancient biomolecules, and plant research has ...been a constant, indispensable facet of these developments. Using archaeological, paleontological, and herbarium plant tissues, researchers have probed plant domestication and dispersal, plant evolution and ecology, paleoenvironmental composition and dynamics, and other topics across related disciplines. Here, we review the development of the ancient DNA discipline and the role of plant research in its progress and refinement. We summarize our understanding of long-term plant DNA preservation and the characteristics of degraded DNA. In addition, we discuss challenges in ancient DNA recovery and analysis and the laboratory and bioinformatic strategies used to mitigate them. Finally, we review recent applications of ancient plant genomic research.
Abstract Tagetes dombeyi (Asteraceae, Tageteae), a new species from the Central Andes first collected in the 18th century. A new annual species of Tagetes from the Central Andes of Peru and Bolivia, ...T. dombeyi, is described and illustrated based on herbarium collections and photographs of the plants in their habitat. Tagetes dombeyi is closely related to Tagetes imbricata, Tagetes multiflora - both of which can occasionally be found mixed with the former on the same herbarium sheet - and Tagetes iltisiana. However, they can be distinguished by diagnostic characters of leaf, corolla, and pappus. A morphological description is provided along with an illustration, a range map, and a key to differentiating the Tagetes species that inhabit Peru and Bolivia.
Resumo Tagetes dombeyi (Asteraceae, Tageteae), una especie nueva de los Andes Centrales coleccionada por primera vez en el Siglo XVIII. Una especie anual de Tagetes de los Andes Centrales de Perú y Bolivia, T. dombeyi, es descrita e ilustrada por primera vez a partir de colecciones de herbario y fotografías de las plantas en su hábitat. Tagetes dombeyi se asemeja a Tagetes imbricata, Tagetes multiflora - siendo éstas dos ocasionalmente halladas montadas en la misma cartulina de herbario junto con la primera - y Tagetes iltisiana. Sin embargo, estas especies estrechamente relacionadas pueden ser distinguidas a partir de caracteres diagnóstico de hoja, corola y papus. Se provee una descripción morfológica de la nueva especie junto con una ilustración, un mapa de distribución geográfica y una clave para diferenciar las especies de Tagetes que habitan en Perú y Bolivia.
Global herbarium collections house a vast number of plant specimens stretching back over centuries. They include rare and extinct species, important historical collections, and valuable type ...specimens that could help to resolve long-standing taxonomic issues. Historical plant collections also provide unique windows into past evolutionary processes and population histories that do not exist with modern data alone. However, because the DNA in such specimens is often degraded and scarce, manipulation and analysis of their genetic material can be challenging. Recent developments in non-destructive genetic sampling and working with very small quantities of genomic DNA, especially in next-generation sequencing and bioinformatic analysis of ancient DNA, now make the majority of herbarium specimens potentially accessible to phylogenetic, population genetic, and barcoding studies. For example, studies of DNA from long time series of Ipomoea batatas and Anacamptis palustris collections revealed linkages between anthropogenic activity and changes in haplotype distribution. These time series also enable the identification of genes under recent selection in the genomes of both the plants and their pathogens, as was shown for Phytophthora infestans, a microbial pathogen of Solanum tuberosum. Here, we summarize the major challenges in using historical plant DNA in evolutionary studies and review genetic studies integrating herbarium specimens. We expect future genetic studies of historical herbarium specimens to use genomic, metagenomic, and population genetic approaches to: investigate how plant populations respond to environmental change; infer temporal changes in genetic diversity; identify genes under recent selection; and investigate past plant pathogen epidemics.
Here we describe Cryptogamic Russian Information System (CRIS), a web service cataloguing the biodiversity of cryptogams: cyanobacteria, fungi (including lichens), and bryophytes. CRIS incorporates a ...wide spectrum of data types, allowing for greater ease of use. It is possible to print the labels for herbarium collections, to input literature references, media files, etc., using CRIS which has a flexible interface and specific technical abilities. Currently, CRIS contains ~ 90,000 herbarium records, including 67,861 records of bryophytes, 12,486 records of lichens and 3,800 records of cyanobacteria. Data analysis of the different taxonomic groups is provided below. Perspectives and directions for the future development of CRIS are discussed.
Recent evidence suggests that community science and herbarium datasets yield similar estimates of species' phenological sensitivities to temperature. Despite this, two recent studies by Alecrim ...et al. (2023) and Miller et al. (2022) found very different results when using different data sources (community science and herbarium specimens, respectively) to investigate whether warming threatens wildflowers with phenological mismatch in relation to shading by deciduous trees.
Here, we investigated whether differences between the two studies' results could be reconciled by testing four hypotheses related to model design, species, spatiotemporal data extent and phenophase.
Hybrid model structures brought results from the two datasets closer together but did not fully reconcile the differences between the studies. Neither the species nor the phenophase selected for analysis seemed to be responsible for differences in results. Cropping the datasets to match spatial and temporal extents appeared to reconcile most differences but only at the cost of much higher uncertainty associated with reduced sample size.
Synthesis: Our analysis suggests that although species‐level estimates of phenological sensitivity may be similar between community science and herbarium datasets, inherent differences in the types and extent of data may lead to contradictory inference about complex biotic interactions. We conclude that, until community science data repositories expand to match the range of climate conditions present in herbarium collections or until herbarium collections match the spatial extent and temporal frequency of community science repositories, ecological studies should ideally be evaluated using both datasets to test the possibility of biased results from either.
Résumé
Des preuves récentes suggèrent que les ensembles de données de la science communautaire et des herbiers produisent des estimations similaires des sensibilités phénologiques des espèces à la température. Malgré cela, deux études récentes menées par Alecrim et al. (2023) et Miller et al. (2022) ont obtenu des résultats très différents en utilisant des sources de données différentes (science communautaire et spécimens d'herbier, respectivement) pour déterminer si le réchauffement menace les fleurs sauvages avec un décalage phénologique par rapport à l'ombrage des arbres à feuilles caduques.
Ici, nous avons cherché à savoir si les différences entre les résultats des deux études pouvaient être conciliées en testant quatre hypothèses liées à la conception du modèle, aux espèces, à l'étendue spatio‐temporelle des données et à la phénophase.
Les structures de modèles hybrides ont rapproché les résultats des deux ensembles de données, mais n'ont pas permis de réconcilier complètement les différences entre les études. Ni les espèces ni la phénophase sélectionnées pour l'analyse ne semblent être responsables des différences de résultats. Le recadrage des ensembles de données pour faire correspondre les étendues spatiales et temporelles a semblé concilier la plupart des différences, mais seulement au prix d'une incertitude beaucoup plus élevée associée à la taille réduite de l'échantillon.
Synthèse : Notre analyse suggère que, bien que les estimations de la sensibilité phénologique au niveau des espèces puissent être similaires entre les ensembles de données de la science communautaire et des herbiers, les différences inhérentes aux types et à l'étendue des données peuvent conduire à des déductions contradictoires sur des interactions biotiques complexes. Nous concluons que, jusqu'à ce que les banques de données de la science communautaire s'étendent pour correspondre à la gamme des conditions climatiques présentes dans les collections d'herbiers ou jusqu'à ce que les collections d'herbiers correspondent à l'étendue spatiale et à la fréquence temporelle des dépôts de données de la science communautaire, les études écologiques devraient idéalement être évaluées en utilisant les deux ensembles de données pour tester la possibilité de résultats biaisés de l'un ou de l'autre.
This analysis suggests that although species‐level estimates of phenological sensitivity may be similar between community science and herbarium datasets, inherent differences in the types and extent of data may lead to contradictory inference about complex biotic interactions. The authors conclude that, until community science data repositories expand to match the range of climate conditions present in herbarium collections or until herbarium collections match the spatial extent and temporal frequency of community science repositories, ecological studies should ideally be evaluated using both datasets to test the possibility of biased results from either.
The Arabian Peninsula is known to have a comprehensive and rich endowment of unique and genetically diverse plant genetic resources. Analysis and conservation of biological diversity is a crucial ...issue to the whole Arabian Peninsula. The rapid and accurate delimitation and identification of a species is crucial to genetic diversity analysis and the first critical step in the assessment of distribution, population abundance and threats related to a particular target species. During the last two decades, classical strategies of evaluating genetic variability, such as morphology and physiology, have been greatly complemented by phylogenetic, taxonomic, genetic diversity and breeding research molecular studies. At present, initiatives are taking place around the world to generate DNA barcode libraries for vascular plant flora and to make these data available in order to better understand, conserve and utilize biodiversity. The number of herbarium collection-based plant evolutionary genetics and genomics studies being conducted has been increasing worldwide. The herbaria provide a rich resource of already preserved and identified material, and these as well as freshly collected samples from the wild can be used for creating a reference DNA barcode library for the vascular plant flora of a region. This review discusses the main molecular and genomic techniques used in plant identification and biodiversity analysis. Hence, we highlight studies emphasizing various molecular techniques undertaken during the last 10 years to study the plant biodiversity of the Arabian Peninsula. Special emphasis on the role of DNA barcoding as a powerful tool for plant biodiversity analysis is provided, along with the crucial role of herbaria in creating a DNA barcode library.
Summary
Species delimitation is challenging in lineages that exhibit both high plasticity and introgression. This challenge can be compounded by collection biases, which may downweight specimens ...morphologically intermediate between traditional species. Additionally, mismatch between named species and observable phenotypes can compromise species conservation.
We studied the species boundaries of Quercus acerifolia, a tree endemic to Arkansas, U.S. We performed morphometric analyses of leaves and acorns from 527 field and 138 herbarium samples of Q. acerifolia and its close relatives, Q. shumardii and Q. rubra. We employed two novel approaches: sampling ex situ collections to detect phenotypic plasticity caused by environmental variation and comparing random field samples with historical herbarium samples to identify collection biases that might undermine species delimitation. To provide genetic evidence, we also performed molecular analyses on genome‐wide SNPs.
Quercus acerifolia shows distinctive morphological, ecological, and genomic characteristics, rejecting the hypothesis that Q. acerifolia is a phenotypic variant of Q. shumardii. We found mismatches between traditional taxonomy and phenotypic clusters. We detected underrepresentation of morphological intermediates in herbarium collections, which may bias species discovery and recognition.
Rare species conservation requires considering and addressing taxonomic problems related to phenotypic plasticity, mismatch between taxonomy and morphological clusters, and collection biases.
Aim
Trees need to avoid frost damage to their young leaves by leafing out after the occurrence of the last frost, yet they also need to start photosynthesis early in the season to achieve sufficient ...growth. This trade‐off leads to the hypothesis that ‘safety margins’ against spring frost should become shorter, the longer the winter duration, perhaps reaching an asymptotic limit where frost damage would occur in most years. Physiologically, shorter safety margins in high‐latitude ecotypes might be achieved by lower degree‐day requirements for leaf‐out, compared to low‐latitude ecotypes.
Location
Europe.
Time period
1902–2009.
Major taxa studied
Temperate trees.
Methods
Using herbarium collections of Acer platanoides, Carpinus betulus, Fagus sylvatica and Prunus spinosa made over 108 years at 40° to 60° N latitude, we related historic leaf‐out dates to winter and spring temperatures (chilling and degree‐days), winter duration, and date of last frost occurrence in the relevant years and locations.
Results
In all species, frost safety margins decreased towards high‐latitude regions with long winters, with each day increase in winter duration reducing frost safety margins by 0.48 days in Fagus and 0.32–0.21 days in Prunus, Acer and Carpinus. These latitudinal differences correlate with northern ecotypes’ shorter degree‐day requirements for leaf‐out.
Main conclusions
The decline in spring frost safety margins in regions with long winters supports the new hypothesis that species may reach their geographic range limit where they ‘bump up’ against experiencing regular frost injury to their young leaves. Larger datasets are necessary to further corroborate our hypothesis and future efforts should thus be directed toward increasing the latitudinal range of existing phenological databases.
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.
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