Science Enabled by Specimen Data

Roberts, J., and S. Florentine. 2025. Current and future management challenges for globally invasive grasses, with special reference to Echinochloa crus‐galli, Panicum capillare and Sorghum halepense. Weed Research 65. https://doi.org/10.1111/wre.70005

Without appropriate and ongoing management interventions, weeds will continue to economically and environmentally disadvantage agricultural and natural ecosystems. For these management strategies to have long‐term sustained success, they need to carefully consider the biological aspects of the targeted weed. These strategies will also need to consider potential adaptations evolved by the targeted weed in response to a range of selection pressures imposed by anthropogenetic factors, climate change, changing environmental conditions, and inappropriate or unsuccessful management regimes. One group of weeds that has been observed to readily adapt to a wide range of conditions and has shown considerable challenges in their management is invasive grasses. Adding to these challenges is that several invasive grasses have also developed resistance to a range of herbicide modes of action, which, to date, has been one of the most commonly used methods of control. To address these challenges, this review explores the biology and ecology of the globally invasive annuals Echinochloa crus‐galli (Barnyard grass) and Panicum capillare (Witchgrass), and the perennial Sorghum halepense (Johnson grass) to identify (i) the most suitable management options for their control and (ii) potential research gaps that may assist in the future management direction of these species. Based on the findings of this review, it is clear that an integrated management approach that targets different aspects of the plant's biology, in combination with early detection and treatment and ongoing surveillance, is necessary for the long‐term control of these species. Although a combination of methods appears promising, further investigation still is required to evaluate their efficiency and long‐term success in a changing environment, all of which are further discussed within this review.

Wenk, E., T. Mesaglio, D. Keith, and W. Cornwell. 2024. Curating protected area-level species lists in an era of diverse and dynamic data sources. Ecological Informatics 84: 102921. https://doi.org/10.1016/j.ecoinf.2024.102921

Dynamic yet accurate species lists for protected areas are essential for conservation and biodiversity research. Even when such lists exist, changing taxonomy, ongoing species migrations and invasions, and new discoveries of historically overlooked species mean static lists can become rapidly outdated. Biodiversity databases such as the Global Biodiversity Information Facility, and citizen science platforms such as iNaturalist, offer rapidly accessible, georeferenced data, but their accuracy is rarely tested. Here we compare species lists generated for two of the world's oldest, more famous protected areas – Yosemite National Park in California, United States and Royal National Park in New South Wales, Australia – using both automated data extraction techniques and extensive manual curation steps. We show that automated list creation without manual curation offers inflated measures of species diversity. Lists generated from herbarium vouchers required more curation than lists generated from iNaturalist, with both incorrect coordinates attached to vouchers and long-outdated names inflating voucher-based species lists. In comparison, iNaturalist data had relatively few errors, in part due to continual curation by a large community, including many botanical experts, and the frequent and automatic implementation of taxonomic updates. As such, iNaturalist will become an increasingly accurate supplementary source for automated biodiversity lists over time, but currently offers poor coverage of graminoid species and introduced species relative to showier, native taxa, and relies on continued expert contributions to identifications. At this point, researchers must manually curate lists extracted from herbarium vouchers or static park lists, and integrate these data with records from iNaturalist, to produce the most robust and taxonomically up-to-date species lists for protected areas.

Uehira, K., and Y. Shimono. 2024. Evaluation of climate conditions and ecological traits that limit the distribution expansion of alien Lolium rigidum in Japan. NeoBiota 96: 89–104. https://doi.org/10.3897/neobiota.96.122752

AbstractInvasive alien plants cause severe global problems; therefore, determining the factors that lead to the success or failure of invasion is a critical question in the field of invasion ecology. In this study, we aimed to determine the factors underlying differences in the distribution range of alien plants in Japan by investigating why Loliummultiflorum thrives in a wide range of habitats while L.rigidum is mainly distributed on sandy beaches. We initially evaluated environmental niche suitability through species distribution modelling and subsequently examined whether species traits influence the differences in range expansion between the two species. We used MaxEnt modelling to identify potential environmental niches for both species. The analysis revealed that L.rigidum was considerably less suited to the Japanese climate compared to L.multiflorum, with high summer precipitation in Japan identified as one of the climatic factors limiting the distribution of L.rigidum. Given that these winter annual plants remain dormant as seeds during summer, in subsequent experiments, we buried seeds in paddy field soil and sandy beach sand during summer and evaluated their survival rate in autumn. The survival rate of L.rigidum seeds was significantly lower than that of L.multiflorum, particularly in paddy soil. Factors contributing to seed mortality may include the decay or early germination of L.rigidum seeds under Japan’s high rainfall conditions. This study emphasises the importance of considering local environmental factors alongside climate niche modelling in the risk assessment of invasive species. Moreover, the integration of species distribution modelling for large-scale evaluations and manipulation experiments for fine-scale assessments proved effective in identifying climatic conditions and species traits influencing the success or failure of alien species invasion.

Bradshaw, C. D., D. L. Hemming, T. Mona, W. Thurston, M. K. Seier, D. P. Hodson, J. W. Smith, et al. 2024. Transmission pathways for the stem rust pathogen into Central and East Asia and the role of the alternate host, barberry. Environmental Research Letters 19: 114097. https://doi.org/10.1088/1748-9326/ad7ee3

Abstract After many decades of effective control of stem rust caused by the Puccinia graminis f.sp. tritici, (hereafter Pgt) the reported emergence of race TTKSK/Ug99 of Pgt in Uganda reignited concerns about epidemics worldwide because ∼90% of world wheat cultivars had no resistance to the new race. Since it was initially detected in Uganda in 1998, Ug99 variants have now been identified in thirteen countries in Africa and the Middle East. Stem rust has been a major problem in the past, and concern is increasing about the risk of return to Central and East Asia. Whilst control programs in North America and Europe relied on the use of resistant cultivars in combination with eradication of barberry (Berberis spp.), the alternate host required for the stem rust pathogen to complete its full lifecycle, the focus in East Asia was principally on the use of resistant wheat cultivars. Here, we investigate potential airborne transmission pathways for stem rust outbreaks in the Middle East to reach East Asia using an integrated modelling framework combining estimates of fungal spore deposition from an atmospheric dispersion model, environmental suitability for spore germination, and crop calendar information. We consider the role of mountain ranges in restricting transmission pathways, and we incorporate a representation of a generic barberry species into the lifecycle. We find viable transmission pathways to East Asia from the Middle East to the north via Central Asia and to the south via South Asia and that an initial infection in the Middle East could persist in East Asia for up to three years due to the presence of the alternate host. Our results indicate the need for further assessment of barberry species distributions in East Asia and appropriate methods for targeted surveillance and mitigation strategies should stem rust incidence increase in the Middle East region.

Xu, L., Z. Song, T. Li, Z. Jin, B. Zhang, S. Du, S. Liao, et al. 2024. New insights into the phylogeny and infrageneric taxonomy of Saussurea based on hybrid capture phylogenomics (Hyb-Seq). Plant Diversity. https://doi.org/10.1016/j.pld.2024.10.003

Saussurea is one of the largest and most rapidly evolving genera within the Asteraceae, comprising approximately 520 species from the Northern Hemisphere. A comprehensive infrageneric classification, supported by robust phylogenetic trees and corroborated by morphological and other data, has not yet been published. For the first time, we recovered a well-resolved nuclear phylogeny of Saussurea consisting of four main clades, which was also supported by morphological data. Our analyses show that ancient hybridization is the most likely source of deep cytoplasmic-nuclear conflict in Saussurea, and a phylogeny based on nuclear data is more suitable than one based on chloroplast data for exploring the infrageneric classification of Saussurea. Based on the nuclear phylogeny obtained and morphological characters, we proposed a revised infrageneric taxonomy of Saussurea, which includes four subgenera and 13 sections. Specifically, 1) S. sect. Cincta, S. sect. Gymnocline, S. sect. Lagurostemon, and S. sect. Strictae were moved from S. subg. Saussurea to S. subg. Amphilaena, 2) S. sect. Pseudoeriocoryne was moved from S. subg. Eriocoryne to S. subg. Amphilaena, and 3) S. sect. Laguranthera was moved from S. subg. Saussurea to S. subg. Theodorea.

Marchuk, E. A., A. K. Kvitchenko, L. A. Kameneva, A. A. Yuferova, and D. E. Kislov. 2024. East Asian forest-steppe outpost in the Khanka Lowland (Russia) and its conservation. Journal of Plant Research 137: 997–1018. https://doi.org/10.1007/s10265-024-01570-z

The Khanka Lowland forest-steppe is the most eastern outpost of the Eurasian steppe biome. It includes unique grassland plant communities with rare steppe species. These coenosis have changed under the influence of anthropogenic activity, especially during the last 100 years and included both typical steppe species and nemoral mesophytic species. To distinguish these ecological groups of plants the random forest method with three datasets of environmental variables was applied. Specifically, a model of classification with the most important bioindices to predict a mesophytic ecological group of plants with a sensitivity greater than 80% was constructed. The data demonstrated the presence of steppe species that arrived at different times in the Primorye Territory. Most of these species are associated with the Mongolian-Daurian relict steppe complex and habit in the Khanka Lowland. Other species occur only in mountains in Primorye Territory and do not persist in the Khanka Lowland. These findings emphasize the presence of relict steppe communities with a complex of true steppe species in the Khanka Lowland. Steppe communities exhibit features of anthropogenic influence definitely through the long land use period but are not anthropogenic in origin. The most steppe species are located at the eastern border of distribution in the Khanka Lowlands and are valuable in terms of conservation and sources of information about steppe species origin and the emergence of the steppe biome as a whole.

Gan, Z., X. Fang, C. Yin, Y. Tian, L. Zhang, X. Zhong, G. Jiang, and A. Tao. 2024. Extraction, purification, structural characterization, and bioactivities of the genus Rhodiola L. polysaccharides: A review. International Journal of Biological Macromolecules 276: 133614. https://doi.org/10.1016/j.ijbiomac.2024.133614

The genus Rhodiola L., an integral part of traditional Chinese medicine and Tibetan medicine in China, exhibits a broad spectrum of applications. This genus contains key compounds such as ginsenosides, polysaccharides, and flavonoids, which possess anti-inflammatory, antioxidant, hypoglycaemic, immune-enhancing, and anti-hypoxic properties. As a vital raw material, Rhodiola L. contributes to twenty-four kinds of Chinese patent medicines and 481 health food products in China, finding extensive application in the health food sector. Recently, polysaccharides have emerged as a focal point in natural product research, with applications spanning the medicine, food, and materials sectors. Despite this, a comprehensive and systematic review of polysaccharides from the genus Rhodiola L. polysaccharides (TGRPs) is warranted. This study undertakes a systematic review of both domestic and international literature, assessing the research advancements and chemical functional values of polysaccharides derived from Rhodiola rosea. It involves the isolation, purification, and identification of a variety of homogeneous polysaccharides, followed by a detailed analysis of their chemical structures, pharmacological activities, and molecular mechanisms, structure-activity relationship (SAR) of TGRPs. The discussion includes the influence of molecular weight, monosaccharide composition, and glycosidic bonds on their biological activities, such as sulfation and carboxymethylation et al. Such analyses are crucial for deepening the understanding of Rhodiola rosea and for fostering the development and exploitation of TGRPs, offering a reference point for further investigations into TGRPs and their resource utilization.

Hämälä, T., C. Moore, L. Cowan, M. Carlile, D. Gopaulchan, M. K. Brandrud, S. Birkeland, et al. 2024. Impact of whole-genome duplications on structural variant evolution in Cochlearia. Nature Communications 15. https://doi.org/10.1038/s41467-024-49679-y

Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in greater diversity of genomic structural variants (SVs) and how they influence evolutionary dynamics in a plant genus, Cochlearia (Brassicaceae). By using long-read sequencing and a graph-based pangenome, we find both negative and positive interactions between WGDs and SVs. Masking of recessive mutations due to WGDs leads to a progressive accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), likely reducing the adaptive potential of polyploid populations. However, we also discover putative benefits arising from SV accumulation, as more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids. Together, our results suggest that SVs play diverse and contrasting roles in the evolutionary trajectories of young polyploids. Cochlearia is an evolutionarily dynamic genus with different base chromosome numbers and ploidal levels. Here, the authors construct a graph-based pangenome for Cochlearia and reveal that whole-genome duplication associated with greater diversity of genomic structural variation and their possible function in adaptation.

Bürger, M., and J. Chory. 2024. A potential role of heat‐moisture couplings in the range expansion of Striga asiatica. Ecology and Evolution 14. https://doi.org/10.1002/ece3.11332

Parasitic weeds in the genera Orobanche, Phelipanche (broomrapes) and Striga (witchweeds) have a devastating impact on food security across much of Africa, Asia and the Mediterranean Basin. Yet, how climatic factors might affect the range expansion of these weeds in the context of global environmental change remains unexplored. We examined satellite‐based environmental variables such as surface temperature, root zone soil moisture, and elevation, in relation to parasitic weed distribution and environmental conditions over time, in combination with observational data from the Global Biodiversity Information Facility (GBIF). Our analysis reveals contrasting environmental and altitude preferences in the genera Striga and Orobanche. Asiatic witchweed (Striga asiatica), which infests corn, rice, sorghum, and sugar cane crops, appears to be expanding its range in high elevation habitats. It also shows a significant association with heat‐moisture coupling events, the frequency of which is rising in such environments. These results point to geographical shifts in distribution and abundance in parasitic weeds due to climate change.

Raggi, L., C. Zucchini, E. Sayde, D. Gigante, and V. Negri. 2024. Priority areas for the establishment of genetic reserves to actively protect key crop wild relative species in Italy. Global Ecology and Conservation 50: e02836. https://doi.org/10.1016/j.gecco.2024.e02836

Crop Wild Relatives (CWR) are wild plant taxa genetically close to a crop. Being a precious source of genetic variability and of traits for crop improvement, CWR have a high socio-economic value and are identified among the main plant genetic resources. Alarming enough, the inter- and intraspecific diversity, as well as their habitat diversity, is under threat of irremediable loss. Italy is the second richest country in Europe in terms of plant species number; applying the taxon group concept 5712 have been recently identified as CWR. The aims of the present research are to identify the best sites for: i) the institution of genetic reserves to actively protect CWR species of the key crop genera as Allium, Brassica and Triticum and ii) performing new collection missions to reach adequate ex situ conservation of target species. Georeferenced data were retrieved from different online databases. CAPFITOGEN tools were initially used to develop an ecogeographic land characterisation map (ELC) of Italy. Geographical distribution data were assembled for 379 populations of 18 CWR taxa. Results of the complementarity analysis showed that 10 protected areas provide coverage of the 46.4% of the target conservation units and include 66.7% of the priority CWR taxa investigated. Alarming enough, only 7.4% of the 379 populations are currently conserved ex situ; among the 18 ecogeographic land characterisation categories only 3 are covered by ex situ conservation. This is the first study where most suitable protected areas for the institution of genetic reserves are proposed for Italy for the protection of multiple CWR taxa of key genera; this is relevant also considering the global value of many of the related crop such as different wheat species, cabbages, rape, garlic and onion. Being already dedicated to habitat and species conservation, the identified sites are optimal candidates for the institution of genetic reserves. Results will hopefully also guide new collecting missions that are urgently needed to strength ex situ conservation of such precious genetic resources.