Science Enabled by Specimen Data
MOLINO, S., G. SANTOS, R. VÃZQUEZ, R. MEDINA, and J. M. G. Y. GALÃN. 2024. Monograph of the genera Struthiopteris Scop. and Spicantopsis Nakai (Blechnaceae, Polypodiopsida). Phytotaxa 677: 1â48. https://doi.org/10.11646/phytotaxa.677.1.1
The Blechnaceae fern family, comprising approximately 250 species, exhibits a subcosmopolitan distribution but showcases notable diversity in South America and the Austropacific region. Recent taxonomic revisions expanded the generic treatment within the family, Resulting, among other things, in the resurrection of the genus Spicantopsis. This genus, segregated from Struthiopteris, now encompasses three species endemic to East Asia. Struthiopteris, on the other hand, has three species distributed in Japan, Europe, North of Africa, and western North America. Molecular evidence, coupled with morphoanatomical traits, supported this taxonomic distinction. Despite subsequent studies on palynological and morphoanatomical characteristics, a comprehensive global monograph of Struthiopteris and Spicantopsis is lacking. This paper aims to fill this gap by synthesizing available information, providing identification keys, full descriptions, taxonomic notes, and some necessary type designation for all species within both genera. The study, based on the examination of 1,649 herbarium specimens and digital materials, underscores the importance of anatomical and morphological characters in fern taxonomy. Mapping distribution data further enhances understanding of the geographic ranges of these ferns. This comprehensive synthesis contributes to the ongoing elucidation of fern diversity and taxonomy.
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.
H. S. Min, H. Shinwoo, and K. K. Soo. 2024. Ensemble Projection of Climate Suitability for Alfalfa (Medicago Sativa L.) in Hamkyongbukdo. Journal of The Korean Society of Grassland and Forage Science 44: 71–82. https://doi.org/10.5333/kgfs.2024.44.2.71
It would be advantageous to grow legume forage crops in order to increase the productivity and sustainability of sloped croplands in Hamkyongbukdo. In particular, the identification of potential cultivation areas for alfalfa in the given region could aid decision-making on policies and management related to forage crop production in the future. This study aimed to analyze the climate suitability of alfalfa in Hamkyongbukdo under current and future climate conditions using the Fuzzy Union model. The climate suitability predicted by the Fuzzy Union model was compared with the actual alfalfa cultivation area in the northern United States. Climate data obtained from 11 global climate models were used as input data for calculation of climate suitability in the study region to examine the uncertainty of projections under future climate conditions. The area where the climate suitability index was greater than a threshold value (22.6) explained about 44% of the variation in actual alfalfa cultivation areas by state in the northern United States. The climatic suitability of alfalfa was projected to decrease in most areas of Hamkyongbukdo under future climate scenarios. The climatic suitability in Onseong and Gyeongwon County was analyzed to be over 88 in the current climate conditions. However, it was projected to decrease by about 66% in the given areas by the 2090s. Our study illustrated that the impact of climate change on suitable cultivation areas was highly variable when different climate data were used as inputs to the Fuzzy Union model. Still, the ensemble of the climate suitability projections for alfalfa was projected to decrease considerably due to summer depression in Hamkyongbukdo. It would be advantageous to predict suitable cultivation areas by adding soil conditions or to predict the climate suitability of other leguminous crops such as hairy vetch, which merits further studies.
Reichgelt, T. 2024. Linking the macroclimatic niche of native lithophytic ferns and their prevalence in urban environments. American Journal of Botany 111. https://doi.org/10.1002/ajb2.16364
Premise Vertical surfaces in urban environments represent a potential expansion of niche space for lithophytic fern species. There are, however, few records of differential success rates of fern species in urban environments.MethodsThe occurrence rates of 16 lithophytic fern species native to the northeastern USA in 14 biomes, including four urban environments differentiated by percentage of impervious surfaces, were evaluated. In addition, the natural macroclimatic ranges of these species were analyzed to test whether significant differences existed in climatic tolerance between species that occur in urban environments and species that do not.ResultsThree species appear to preferentially occur in urban environments, two species may facultatively occur in urban environments, and the remaining 11 species preferentially occur in nondeveloped rural environments. The natural range of fern species that occur in urban environments had higher summer temperatures than the range of species that do not, whereas other macroclimatic variables, notably winter temperatures and precipitation, were less important or insignificant.ConclusionsVertical surfaces in urban environments may represent novel niche space for some native lithophytic fern species in northeastern USA. However, success in this environment depends, in part, on tolerance of the urban heat island effect, especially heating of impervious surfaces in summer.
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.
Fedorov, N., A. Muldashev, O. Mikhaylenko, S. Zhigunova, E. Baisheva, P. Shirokikh, I. Bikbaev, and V. Martynenko. 2024. Forecast the Habitat Sustainability of Schoenus ferrugineus L. (Cyperaceae) in the Southern Urals under Climate Change. Plants 13: 1563. https://doi.org/10.3390/plants13111563
An analysis of the current potential range of the Pleistocene relict plant species Schoenus ferrugineus and modeling of changes in its future range under moderate (RCP4.5) and strong (RCP8.5) climate change in the middle and second half of the 21st century were carried out. The MaxEnt program was used for modeling. Climate variables from CHELSA Bioclim, the global digital soil mapping system SoilGrids, and a digital elevation model were used as predictors. Modeling has shown that climate change will lead to a significant reduction in the suitability of S. ferrugineus habitat conditions by the mid-21st century. The predicted changes in the distribution of habitats of S. ferrugineus, a diagnostic species of calcareous mires and an indicator of their ecological state, indicate a possible strong transformation of wetland complexes in the Southern Urals region even under moderate climate change. A reduction in the distribution of S. ferrugineus at the eastern limit of its range will also be facilitated by more frequent extreme droughts. To maintain the distribution of S. ferrugineus on the eastern border of its range, a number of measures are proposed to mitigate the negative consequences of climate change, contributing to the preservation of the hydrological regime of calcareous mires.
Anon. 2023. Ecological Niche Modelling of an Industrially Important Mushroom - Ganoderma lucidum (Leys.) Karsten: A Machine Learning Global Appraisal. Journal of Scientific & Industrial Research 82. https://doi.org/10.56042/jsir.v82i12.1973
Species Distribution Modelling (SDM) involves utilizing observations of a given species and its surrounding environment to produce a sound approximation of the species' potential distribution. The intricate relationships between organisms and their surroundings, coupled with the profusion of data, have captured the attention of ecologists and statisticians alike. Consequently, they have directed their efforts towards exploring the potential of machine learning techniques. Our study employs an ensemble machine learning approach to simulate the global ecological niche modelling of Ganoderma lucidum fungus. This involves the utilization of various environmental predictors and the averaging of multiple algorithms to achieve a comprehensive analysis. 563 spatially thinned presence points of G. lucidum were projected with three bio-climatic time frames, namely current, 2050, and 2070, and four Representative Concentration Pathways (RCPs), namely 2.6, 4.5, 6.0, and 8.5, as well as non-climatic variables (surface soil features, land use, rooting depth and water storage capacity at rooting zone). We observed excellent model qualities as the Area Under the receiver operating Curve (AUC) approached 0.90. Random Forest was identified as the best individual algorithm, while the Maxent entropy was identified as the least effective for Ecological Niche Modelling (ENM) of G. lucidum. Globally, under the current bio-climatic and non-bioclimatic projection, optimum habitat for this fungus covers 12510876.3 km2 area while, maximum area (13248546.9 Sq. km.) under this habitat class with future projections was recorded with RCP of 8.5 in 2070. The primary determinants of its current global distribution were ecosystem rooting depth, water storage capacity, and precipitation seasonality. While, with two future bioclimatic time frames and RCPs, Isothermality was identified as the most influential predictor. Based on our assessment, it has been determined that this particular fungus is exhibiting a persistent pattern of proliferation across the regions of Europe, America, and certain areas of India. The present investigation sought to underscore the importance of discerning the native habitats of this species, taking into account both current and anticipated climatic shifts. This knowledge is essential for effectively coordinating the artificial cultivation and natural harvesting of G. lucidum, which is necessary to meet the ever-increasing industrial demands.