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Zhang, H., W. Guo, and W. Wang. 2023. The dimensionality reductions of environmental variables have a significant effect on the performance of species distribution models. Ecology and Evolution 13. https://doi.org/10.1002/ece3.10747

How to effectively obtain species‐related low‐dimensional data from massive environmental variables has become an urgent problem for species distribution models (SDMs). In this study, we will explore whether dimensionality reduction on environmental variables can improve the predictive performance of SDMs. We first used two linear (i.e., principal component analysis (PCA) and independent components analysis) and two nonlinear (i.e., kernel principal component analysis (KPCA) and uniform manifold approximation and projection) dimensionality reduction techniques (DRTs) to reduce the dimensionality of high‐dimensional environmental data. Then, we established five SDMs based on the environmental variables of dimensionality reduction for 23 real plant species and nine virtual species, and compared the predictive performance of those with the SDMs based on the selected environmental variables through Pearson's correlation coefficient (PCC). In addition, we studied the effects of DRTs, model complexity, and sample size on the predictive performance of SDMs. The predictive performance of SDMs under DRTs other than KPCA is better than using PCC. And the predictive performance of SDMs using linear DRTs is better than using nonlinear DRTs. In addition, using DRTs to deal with environmental variables has no less impact on the predictive performance of SDMs than model complexity and sample size. When the model complexity is at the complex level, PCA can improve the predictive performance of SDMs the most by 2.55% compared with PCC. At the middle level of sample size, the PCA improved the predictive performance of SDMs by 2.68% compared with the PCC. Our study demonstrates that DRTs have a significant effect on the predictive performance of SDMs. Specifically, linear DRTs, especially PCA, are more effective at improving model predictive performance under relatively complex model complexity or large sample sizes.

Huang, T., J. Chen, K. E. Hummer, L. A. Alice, W. Wang, Y. He, S. Yu, et al. 2023. Phylogeny of Rubus (Rosaceae): Integrating molecular and morphological evidence into an infrageneric revision. TAXON. https://doi.org/10.1002/tax.12885

Rubus (Rosaceae), one of the most complicated angiosperm genera, contains about 863 species, and is notorious for its taxonomic difficulty. The most recent (1910–1914) global taxonomic treatment of the genus was conducted by Focke, who defined 12 subgenera. Phylogenetic results over the past 25 years suggest that Focke's subdivisions of Rubus are not monophyletic, and large‐scale taxonomic revisions are necessary. Our objective was to provide a comprehensive phylogenetic analysis of the genus based on an integrative evidence approach. Morphological characters, obtained from our own investigation of living plants and examination of herbarium specimens are combined with chloroplast genomic data. Our dataset comprised 196 accessions representing 145 Rubus species (including cultivars and hybrids) and all of Focke's subgenera, including 60 endemic Chinese species. Maximum likelihood analyses inferred phylogenetic relationships. Our analyses concur with previous molecular studies, but with modifications. Our data strongly support the reclassification of several subgenera within Rubus. Our molecular analyses agree with others that only R. subg. Anoplobatus forms a monophyletic group. Other subgenera are para‐ or polyphyletic. We suggest a revised subgeneric framework to accommodate monophyletic groups. Character evolution is reconstructed, and diagnostic morphological characters for different clades are identified and discussed. Based on morphological and molecular evidence, we propose a new classification system with 10 subgenera: R. subg. Anoplobatus, R. subg. Batothamnus, R. subg. Chamaerubus, R. subg. Cylactis, R. subg. Dalibarda, R. subg. Idaeobatus, R. subg. Lineati, R. subg. Malachobatus, R. subg. Melanobatus, and R. subg. Rubus. The revised infrageneric nomenclature inferred from our analyses is provided along with synonymy and type citations. Our new taxonomic backbone is the first systematic and complete global revision of Rubus since Focke's treatment. It offers new insights into deep phylogenetic relationships of Rubus and has important theoretical and practical significance for the development and utilization of these important agronomic crops.

Wilson Brown, M. K., and E. B. Josephs. 2023. Evaluating niche changes during invasion with seasonal models in Capsella bursa‐pastoris. American Journal of Botany. https://doi.org/10.1002/ajb2.16140

Premise Researchers often use ecological niche models to predict where species might establish and persist under future or novel climate conditions. However, these predictive methods assume species have stable niches across time and space. Furthermore, ignoring the time of occurrence data can obscure important information about species reproduction and ultimately fitness. Here, we assess compare ecological niche models generated from full-year averages to seasonal models Methods In this study, we generate full-year and monthly ecological niche models for Capsella bursa-pastoris in Europe and North America to see if we can detect changes in the seasonal niche of the species after long-distance dispersal. Key Results We find full-year ecological niche models have low transferability across continents and there are continental differences in the climate conditions that influence the distribution of C. bursa-pastoris. Monthly models have greater predictive accuracy than full-year models in cooler seasons, but no monthly models are able to predict North American summer occurrences very well. Conclusions The relative predictive ability of European monthly models compared to North American monthly models suggests a change in the seasonal timing between the native range to the non-native range. These results highlight the utility of ecological niche models at finer temporal scales in predicting species distributions and unmasking subtle patterns of evolution.

Marcussen, T., H. E. Ballard, J. Danihelka, A. R. Flores, M. V. Nicola, and J. M. Watson. 2022. A Revised Phylogenetic Classification for Viola (Violaceae). Plants 11: 2224. https://doi.org/10.3390/plants11172224

The genus Viola (Violaceae) is among the 40–50 largest genera among angiosperms, yet its taxonomy has not been revised for nearly a century. In the most recent revision, by Wilhelm Becker in 1925, the then-known 400 species were distributed among 14 sections and numerous unranked groups. Here, we provide an updated, comprehensive classification of the genus, based on data from phylogeny, morphology, chromosome counts, and ploidy, and based on modern principles of monophyly. The revision is presented as an annotated global checklist of accepted species of Viola, an updated multigene phylogenetic network and an ITS phylogeny with denser taxon sampling, a brief summary of the taxonomic changes from Becker’s classification and their justification, a morphological binary key to the accepted subgenera, sections and subsections, and an account of each infrageneric subdivision with justifications for delimitation and rank including a description, a list of apomorphies, molecular phylogenies where possible or relevant, a distribution map, and a list of included species. We distribute the 664 species accepted by us into 2 subgenera, 31 sections, and 20 subsections. We erect one new subgenus of Viola (subg. Neoandinium, a replacement name for the illegitimate subg. Andinium), six new sections (sect. Abyssinium, sect. Himalayum, sect. Melvio, sect. Nematocaulon, sect. Spathulidium, sect. Xanthidium), and seven new subsections (subsect. Australasiaticae, subsect. Bulbosae, subsect. Clausenianae, subsect. Cleistogamae, subsect. Dispares, subsect. Formosanae, subsect. Pseudorupestres). Evolution within the genus is discussed in light of biogeography, the fossil record, morphology, and particular traits. Viola is among very few temperate and widespread genera that originated in South America. The biggest identified knowledge gaps for Viola concern the South American taxa, for which basic knowledge from phylogeny, chromosome counts, and fossil data is virtually absent. Viola has also never been subject to comprehensive anatomical study. Studies into seed anatomy and morphology are required to understand the fossil record of the genus.

Canavan, S., Z. T. Brym, G. Brundu, K. Dehnen-Schmutz, D. Lieurance, T. Petri, W. H. Wadlington, et al. 2022. Cannabis de-domestication and invasion risk. Biological Conservation 274: 109709. https://doi.org/10.1016/j.biocon.2022.109709

Cultivated plants provide food, fiber, and energy but they can escape, de-domesticate, colonize agroecosystems as weeds, and disrupt natural ecosystems as invasive species. Escape and invasion depend on traits of the species, type and rate of domestication, and cultivation context. Understanding this “de-domestication invasion process” is critical for managing conservation efforts to reduce unintended consequences of cultivated species in novel areas. Cannabis (Cannabis sativa L.) is an ideal case study to explore this process because it was one of the earliest plants to co-evolve with humans, has a crop to weed history, and has been introduced and cultivated globally. Moreover, recent liberalization of cannabis cultivation and use policies have raised concerns about invasion risk. Here, we synthesize knowledge on cannabis breeding, cultivation, and processing relevant to invasion risk and outline research and management priorities to help overcome the research deficit on the invasion ecology of the species. Understanding the transition of cannabis through the de-domestication-invasion process will inform policy and minimize agricultural and environmental risks associated with cultivation of domesticated species.

Lu, L.-L., B.-H. Jiao, F. Qin, G. Xie, K.-Q. Lu, J.-F. Li, B. Sun, et al. 2022. Artemisia pollen dataset for exploring the potential ecological indicators in deep time. Earth System Science Data 14: 3961–3995. https://doi.org/10.5194/essd-14-3961-2022

Abstract. Artemisia, along with Chenopodiaceae, is the dominant component growing in the desert and dry grassland of the Northern Hemisphere. Artemisia pollen with its high productivity, wide distribution, and easy identification is usually regarded as an eco-indicator for assessing aridity and distinguishing grassland from desert vegetation in terms of the pollen relative abundance ratio of Chenopodiaceae/Artemisia (C/A). Nevertheless, divergent opinions on the degree of aridity evaluated by Artemisia pollen have been circulating in the palynological community for a long time. To solve the confusion, we first selected 36 species from nine clades and three outgroups of Artemisia based on the phylogenetic framework, which attempts to cover the maximum range of pollen morphological variation. Then, sampling, experiments, photography, and measurements were taken using standard methods. Here, we present pollen datasets containing 4018 original pollen photographs, 9360 pollen morphological trait measurements, information on 30 858 source plant occurrences, and corresponding environmental factors. Hierarchical cluster analysis on pollen morphological traits was carried out to subdivide Artemisia pollen into three types. When plotting the three pollen types of Artemisia onto the global terrestrial biomes, different pollen types of Artemisia were found to have different habitat ranges. These findings change the traditional concept of Artemisia being restricted to arid and semi-arid environments. The data framework that we designed is open and expandable for new pollen data of Artemisia worldwide. In the future, linking pollen morphology with habitat via these pollen datasets will create additional knowledge that will increase the resolution of the ecological environment in the geological past. The Artemisia pollen datasets are freely available at Zenodo (https://doi.org/10.5281/zenodo.6900308; Lu et al., 2022).

Sanczuk, P., E. De Lombaerde, S. Haesen, K. Van Meerbeek, M. Luoto, B. Van der Veken, E. Van Beek, et al. 2022. Competition mediates understorey species range shifts under climate change. Journal of Ecology 110: 1813–1825. https://doi.org/10.1111/1365-2745.13907

Biological communities are reshuffling owing to species range shifts in response to climate change. This process inherently leads to novel assemblages of interacting species. Yet, how climatic change and local dynamics in biotic interactions jointly affect range shifts is still poorly understood.We combine a unique long‐term transplant competition‐exclusion experiment with species distribution models (SDMs) to test the effects of biotic interactions on understorey species range shifts under climate change in European temperate forests. Using a time‐series of 18 years of individual‐level demographic data of four common understorey plant species transplanted beyond their cold range edge to plots with and without interspecific competition, we built integral projection models (IPMs) and analysed the effects of competition on five key vital rates and population growth. We assessed the results of the transplant experiment in the context of the modelled species’ current and future potential distributions.We find that species’ population performances in the transplant experiment decreased with lower predicted habitat suitability from the SDMs. The population performance at the transplant sites was mediated by biotic interactions with the local plant community: for two species with intermediate levels of predicted habitat suitability at the transplant sites, competition effects could explicitly differentiate between net population growth (λ > 1) or shrinkage (λ < 1).Synthesis: Our findings contest the long‐standing idea that at cold range edges, mainly abiotic factors structure species’ distributions. We conclude that biotic interactions, through acting on local population dynamics, may impact species distributions at the continental scale. Hence, predicting climate‐change impacts on biodiversity redistributions ultimately requires us to also integrate dynamics in biotic interactions.

Sarker, U., Y.-P. Lin, S. Oba, Y. Yoshioka, and K. Hoshikawa. 2022. Prospects and potentials of underutilized leafy Amaranths as vegetable use for health-promotion. Plant Physiology and Biochemistry 182: 104–123. https://doi.org/10.1016/j.plaphy.2022.04.011

Climate change causes environmental variation worldwide, which is one of the most serious threats to global food security. In addition, more than 2 billion people in the world are reported to suffer from serious malnutrition, referred to as ‘hidden hunger.’ Dependence on only a few crops could lead to the loss of genetic diversity and high fragility of crop breeding in systems adapting to global scale climate change. The exploitation of underutilized species and genetic resources, referred to as orphan crops, could be a useful approach for resolving the issue of adaptability to environmental alteration, biodiversity preservation, and improvement of nutrient quality and quantity to ensure food security. Moreover, the use of these alternative crops will help to increase the human health benefits and the income of farmers in developing countries. In this review, we highlight the potential of orphan crops, especially amaranths, for use as vegetables and health-promoting nutritional components. This review highlights promising diversified sources of amaranth germplasms, their tolerance to abiotic stresses, and their nutritional, phytochemical, and antioxidant values for vegetable purposes. Betalains (betacyanins and betaxanthins), unique antioxidant components in amaranth vegetables, are also highlighted regarding their chemodiversity across amaranth germplasms and their stability and degradation. In addition, we discuss the physiological functions, antioxidant, antilipidemic, anticancer, and antimicrobial activities, as well as the biosynthesis pathway, molecular, biochemical, genetics, and genomic mechanisms of betalains in detail.

Charitonidou, M., K. Kougioumoutzis, M. C. Karypidou, and J. M. Halley. 2022. ‘Fly to a Safer North’: Distributional Shifts of the Orchid Ophrys insectifera L. Due to Climate Change. Biology 11: 497. https://doi.org/10.3390/biology11040497

Numerous orchid species around the world have already been affected by the ongoing climate change, displaying phenological alterations and considerable changes to their distributions. The fly orchid (Ophrys insectifera L.) is a well-known and distinctive Ophrys species in Europe, with a broad distribution across the continent. This study explores the effects of climate change on the range of O. insectifera, using a species distribution models (SDMs) framework that encompasses different climatic models and scenarios for the near- and long-term future. The species’ environmentally suitable area is projected to shift northwards (as expected) but downhill (contrary to usual expectations) in the future. In addition, an overall range contraction is predicted under all investigated combinations of climatic models and scenarios. While this is moderate overall, it includes some regions of severe loss and other areas with major gains. Specifically, O. insectifera is projected to experience major area loss in its southern reaches (the Balkans, Italy and Spain), while it will expand its northern limits to North Europe, with the UK, Scandinavia, and the Baltic countries exhibiting the largest gains.View Full-Text

Filartiga, A. L., A. Klimeš, J. Altman, M. P. Nobis, A. Crivellaro, F. Schweingruber, and J. Doležal. 2022. Comparative anatomy of leaf petioles in temperate trees and shrubs: the role of plant size, environment and phylogeny. Annals of Botany 129: 567–582. https://doi.org/10.1093/aob/mcac014

Background and Aims Petioles are important plant organs connecting stems with leaf blades and affecting light-harvesting ability of the leaf as well as transport of water, nutrients and biochemical signals. Despite the high diversity in petiole size, shape and anatomy, little information is availabl…