Science Enabled by Specimen Data
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.
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.
Rodríguez-Merino, A. 2023. Identifying and Managing Areas under Threat in the Iberian Peninsula: An Invasion Risk Atlas for Non-Native Aquatic Plant Species as a Potential Tool. Plants 12: 3069. https://doi.org/10.3390/plants12173069
Predicting the likelihood that non-native species will be introduced into new areas remains one of conservation’s greatest challenges and, consequently, it is necessary to adopt adequate management measures to mitigate the effects of future biological invasions. At present, not much information is available on the areas in which non-native aquatic plant species could establish themselves in the Iberian Peninsula. Species distribution models were used to predict the potential invasion risk of (1) non-native aquatic plant species already established in the peninsula (32 species) and (2) those with the potential to invade the peninsula (40 species). The results revealed that the Iberian Peninsula contains a number of areas capable of hosting non-native aquatic plant species. Areas under anthropogenic pressure are at the greatest risk of invasion, and the variable most related to invasion risk is temperature. The results of this work were used to create the Invasion Risk Atlas for Alien Aquatic Plants in the Iberian Peninsula, a novel online resource that provides information about the potential distribution of non-native aquatic plant species. The atlas and this article are intended to serve as reference tools for the development of public policies, management regimes, and control strategies aimed at the prevention, mitigation, and eradication of non-native aquatic plant species.
Lima, V. P., R. A. Ferreira de Lima, F. Joner, L. D’Orangeville, N. Raes, I. Siddique, and H. ter Steege. 2023. Integrating climate change into agroforestry conservation: A case study on native plant species in the Brazilian Atlantic Forest. Journal of Applied Ecology. https://doi.org/10.1111/1365-2664.14464
Designing multispecies systems with suitable climatic affinity and identifying species' vulnerability under human‐driven climate change are current challenges to achieve successful adaptation of natural systems. To address this problem, we need to (1) identify groups of species with climatic similarity under climate scenarios and (2) identify areas with high conservation value under predicted climate change.To recognize species with similar climatic niche requirements that can be grouped for mixed cropping in Brazil, we employed ecological niche models (ENMs) and Spearman's ρ for overlap. We also used prioritization algorithms to map areas of high conservation value using two Shared Socioeconomic Pathways (SSP2‐4.5 and SSP5‐8.5) to assess mid‐term (2041–2060) and long‐term (2061–2080) climate change impacts.We identified 15 species groups with finer climatic affinities at different times depicted on hierarchical clustering dendrograms, which can be combined into agroecological agroforestry systems. Furthermore, we highlight the climatically suitable areas for these groups of species, thus providing an outlook of where different species will need to be planted over time to be conserved. In addition, we observed that climate change is predicted to modify the spatial association of these groups under different future climate scenarios, causing a mean negative change in species climatic similarity of 9.5% to 13.7% under SSP2‐4.5 scenario and 9.5% to 10.5% under SSP5‐8.5, for 2041–2060 and 2061–2080, respectively.Synthesis and applications. Our findings provide a framework for agroforestry conservation. The groups of species with finer climatic affinities identified and the climatically suitable areas can be combined into agroecological productive systems, and provide an outlook of where different species may be planted over time. In addition, the conservation priority zones displaying high climate stability for each species individually and all at once can be incorporated into Brazil's conservation plans by policymakers to prioritize specific sites. Lastly, we urge policymakers, conservation organizations and donors to promote interventions involving farmers and local communities, since the species' evaluated have proven to maintain landscapes with productive forest fragments and can be conserved in different Brazilian ecosystems.
Cousins-Westerberg, R., N. Dakin, L. Schat, G. Kadereit, and A. M. Humphreys. 2023. Evolution of cold tolerance in the highly stress-tolerant samphires and relatives (Salicornieae: Amaranthaceae). Botanical Journal of the Linnean Society. https://doi.org/10.1093/botlinnean/boad009
Low temperature constitutes one of the main barriers to plant distributions, confining many clades to their ancestrally tropical biome. However, recent evidence suggests that transitions from tropical to temperate biomes may be more frequent than previously thought. Here, we study the evolution of cold and frost tolerance in the globally distributed and highly stress-tolerant Salicornieae (Salicornioideae, Amaranthaceae s.l.). We first generate a phylogenetic tree comprising almost all known species (85-90%), using newly generated (n = 106) and published nuclear-ribosomal and plastid sequences. Next, we use geographical occurrence data to document in which clades and geographical regions cold-tolerant species occur and reconstruct how cold tolerance evolved. Finally, we test for correlated evolution between frost tolerance and the annual life form. We find that frost tolerance has evolved independently in up to four Northern Hemisphere lineages but that annuals are no more likely to evolve frost tolerance than perennials, indicating the presence of different strategies for adapting to cold environments. Our findings add to mounting evidence for multiple independent out-of-the-tropics transitions among close relatives of flowering plants and raise new questions about the ecological and physiological mechanism(s) of adaptation to low temperatures in Salicornieae.
Clemente, K. J. E., and M. S. Thomsen. 2023. High temperature frequently increases facilitation between aquatic foundation species: a global meta‐analysis of interaction experiments between angiosperms, seaweeds, and bivalves. Journal of Ecology. https://doi.org/10.1111/1365-2745.14101
Many studies have quantified ecological impacts of individual foundation species (FS). However, emerging data suggest that FS often co‐occur, potentially inhibiting or facilitating one another, thereby causing indirect, cascading effects on surrounding communities. Furthermore, global warming is accelerating, but little is known about how interactions between co‐occurring FS vary with temperature.Shallow aquatic sedimentary systems are often dominated by three types of FS: slower‐growing clonal angiosperms, faster‐growing solitary seaweeds, and shell‐forming filter‐ and deposit‐feeding bivalves. Here, we tested the impacts of one FS on another by analyzing manipulative interaction experiments from 148 papers with a global meta‐analysis.We calculated 1,942 (non‐independent) Hedges’ g effect sizes, from 11,652 extracted values over performance responses, such as abundances, growths or survival of FS, and their associated standard deviations and replication levels. Standard aggregation procedures generated 511 independent Hedges’ g that was classified into six types of reciprocal impacts between FS.We found that (i) seaweeds had consistent negative impacts on angiosperms across performance responses, organismal sizes, experimental approaches, and ecosystem types; (ii) angiosperms and bivalves generally had positive impacts on each other (e.g., positive effects of angiosperms on bivalves were consistent across organismal sizes and experimental approaches, but angiosperm effect on bivalve growth and bivalve effect on angiosperm abundance were not significant); (iii) bivalves positively affected seaweeds (particularly on growth responses); (iv) there were generally no net effects of seaweeds on bivalves (except for positive effect on growth) or angiosperms on seaweeds (except for positive effect on ‘other processes’); and (v) bivalve interactions with other FS were typically more positive at higher temperatures, but angiosperm‐seaweed interactions were not moderated by temperature.Synthesis: Despite variations in experimental and spatiotemporal conditions, the stronger positive interactions at higher temperatures suggest that facilitation, particularly involving bivalves, may become more important in a future warmer world. Importantly, addressing research gaps, such as the scarcity of FS interaction experiments from tropical and freshwater systems and for less studied species, as well as testing for density‐dependent effects, could better inform aquatic ecosystem conservation and restoration efforts and broaden our knowledge of FS interactions in the Anthropocene.
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.
Perez‐Navarro, M. A., O. Broennimann, M. A. Esteve, G. Bagaria, A. Guisan, and F. Lloret. 2022. Comparing climatic suitability and niche distances to explain populations responses to extreme climatic events. Ecography. https://doi.org/10.1111/ecog.06263
Habitat suitability calculated from species distribution models (SDMs) has been used to assess population performance, but empirical studies have provided weak or inconclusive support to this approach. Novel approaches measuring population distances to niche centroid and margin in environmental space have been recently proposed to explain population performance, particularly when populations experience exceptional environmental conditions that may place them outside of the species niche. Here, we use data of co‐occurring species' decay, gathered after an extreme drought event occurring in the southeast of the Iberian Peninsula which highly affected rich semiarid shrubland communities, to compare the relationship between population decay (mortality and remaining green canopy) and 1) distances between populations' location and species niche margin and centroid in the environmental space, and 2) climatic suitability estimated from frequently used SDMs (here MaxEnt) considering both the extreme climatic episode and the average reference climatic period before this. We found that both SDMs‐derived suitability and distances to species niche properly predict populations performance when considering the reference climatic period; but climatic suitability failed to predict performance considering the extreme climate period. In addition, while distance to niche margins accurately predict both mortality and remaining green canopy responses, centroid distances failed to explain mortality, suggesting that indexes containing information about the position to niche margin (inside or outside) are better to predict binary responses. We conclude that the location of populations in the environmental space is consistent with performance responses to extreme drought. Niche distances appear to be a more efficient approach than the use of climate suitability indices derived from more frequently used SDMs to explain population performance when dealing with environmental conditions that are located outside the species environmental niche. The use of this alternative metrics may be particularly useful when designing conservation measures to mitigate impacts of shifting environmental conditions.
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.
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.