Science Enabled by Specimen Data

Campbell, L. C. E., E. T. Kiers, and G. Chomicki. 2022. The evolution of plant cultivation by ants. Trends in Plant Science. https://doi.org/10.1016/j.tplants.2022.09.005

Outside humans, true agriculture was previously thought to be restricted to social insects farming fungus. However, obligate farming of plants by ants was recently discovered in Fiji, prompting a re-examination of plant cultivation by ants. Here, we generate a database of plant cultivation by ants, identify three main types, and show that these interactions evolved primarily for shelter rather than food. We find that plant cultivation evolved at least 65 times independently for crops (~200 plant species), and 15 times in farmer lineages (~37 ant taxa) in the Neotropics and Asia/Australasia. Because of their high evolutionary replication, and variation in partner dependence, these systems are powerful models to unveil the steps in the evolution and ecology of insect agriculture.

Heo, N., D. J. Leopold, M. V. Lomolino, S. Yun, and D. D. Fernando. 2022. Global and regional drivers of abundance patterns in the hart’s tongue fern complex (Aspleniaceae). Annals of Botany. https://doi.org/10.1093/aob/mcac129

Abstract Background and Aims The hart’s tongue fern (HTF) complex is a monophyletic group composed of five geographically segregated members with divergent abundance patterns across its broad geographic range. We postulated hierarchical systems of environmental controls in which climatic and land-use change drive abundance patterns at the global scale, while various ecological conditions function as finer-scale determinants that further increase geographic disparities at regional to local scales. Methods After quantifying the abundance patterns of the HTF complex, we estimated their correlations with global climate and land-use dynamics. Regional determinants were assessed using boosted regression tree models with 18 potential ecological variables. Moreover, we investigated long-term population trends in the U.S. to understand the interplay of climate change and anthropogenic activities on a temporal scale. Key Results Latitudinal climate shifts drove latitudinal abundance gradients, and regionally different levels of land-use change resulted in global geographic disparities in population abundance. At a regional scale, population isolation, which accounts for rescue effects, played an important role, particularly in Europe and East Asia where several hotspots occurred. Furthermore, the variables most strongly influencing abundance patterns greatly differed by region: precipitation seasonality in Europe, spatial heterogeneity of temperature and precipitation in East Asia, and magnitudes of past climate change, temperature seasonality, and edaphic conditions in North America. In the U.S., protected populations showed increasing trends compared to unprotected populations at the same latitude, highlighting the critical role of habitat protection in conservation measures. Conclusions Geographic disparities in the abundance patterns of HTF complex were determined by hierarchical systems of environmental controls, wherein climatic and land-use dynamics act globally but are modulated by various regional and local determinants operating at increasingly finer scales. We highlighted that fern conservation must be tailored to particular geographic contexts and environmental conditions by incorporating a better understanding of the dynamics acting at different spatiotemporal scales.

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).

Führding‐Potschkat, P., H. Kreft, and S. M. Ickert‐Bond. 2022. Influence of different data cleaning solutions of point‐occurrence records on downstream macroecological diversity models. Ecology and Evolution 12. https://doi.org/10.1002/ece3.9168

Digital point‐occurrence records from the Global Biodiversity Information Facility (GBIF) and other data providers enable a wide range of research in macroecology and biogeography. However, data errors may hamper immediate use. Manual data cleaning is time‐consuming and often unfeasible, given that the databases may contain thousands or millions of records. Automated data cleaning pipelines are therefore of high importance. Taking North American Ephedra as a model, we examined how different data cleaning pipelines (using, e.g., the GBIF web application, and four different R packages) affect downstream species distribution models (SDMs). We also assessed how data differed from expert data. From 13,889 North American Ephedra observations in GBIF, the pipelines removed 31.7% to 62.7% false positives, invalid coordinates, and duplicates, leading to datasets between 9484 (GBIF application) and 5196 records (manual‐guided filtering). The expert data consisted of 704 records, comparable to data from field studies. Although differences in the absolute numbers of records were relatively large, species richness models based on stacked SDMs (S‐SDM) from pipeline and expert data were strongly correlated (mean Pearson's r across the pipelines: .9986, vs. the expert data: .9173). Our results suggest that all R package‐based pipelines reliably identified invalid coordinates. In contrast, the GBIF‐filtered data still contained both spatial and taxonomic errors. Major drawbacks emerge from the fact that no pipeline fully discovered misidentified specimens without the assistance of taxonomic expert knowledge. We conclude that application‐filtered GBIF data will still need additional review to achieve higher spatial data quality. Achieving high‐quality taxonomic data will require extra effort, probably by thoroughly analyzing the data for misidentified taxa, supported by experts.

Tazikeh, S., S. Zendehboudi, S. Ghafoori, A. Lohi, and N. Mahinpey. 2022. Algal bioenergy production and utilization: Technologies, challenges, and prospects. Journal of Environmental Chemical Engineering 10: 107863. https://doi.org/10.1016/j.jece.2022.107863

Increasing demand for energy and also escalating environmental pollution show that industries cannot rely on fossil fuels, and it is necessary to adopt an alternative. In recent decades, algal bioenergy has emerged as a renewable energy source in different industries. However, algal bioenergy production is costly and faces different challenges and unknown aspects that need to be addressed. Experimental and theoretical research works have revealed that the efficiency of algal bioenergy production is influenced by several factors, including algae species, temperature, light, CO2, cultivation method, and available nutrients. Algal bioenergy production on commercial scales in cost-effective ways is the main aim of industries to compete with fossil fuels. Hence, it is vital to have a comprehensive knowledge of the previous findings and attain a suitable pathway for future studies/activities. In the present review paper, the potential of microalgae bioenergy production, influential parameters, previous experimental and theoretical studies, and different methods for microalgae biofuel production from cultivation stage to utilization are reviewed. Moreover, this work discusses the engineering activities and economic analysis of microalgae cultivation to utilization, and also useful suggestions are made for future research works. The outcomes of the present work confirm that innovative engineering methods can overcome scale-up challenging, increase the rate of production, and decrease the cost of algae bioenergy production. Hence, there is no long way to produce cost-effective algae bioenergy on commercial scales.

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.

Campbell, C., G. Granath, and H. Rydin. 2021. Climatic drivers of Sphagnum species distributions. Frontiers of Biogeography 13. https://doi.org/10.21425/f5fbg51146

Peatmosses(genus Sphagnum) dominate most Northern mires and show distinct distributional limits in Europe despite having efficient dispersal and few dispersal barriers. This pattern indicates that Sphagnum species distributions are strongly linked to climate. Sphagnumdominated mires have been the la…

Xue, T., S. R. Gadagkar, T. P. Albright, X. Yang, J. Li, C. Xia, J. Wu, and S. Yu. 2021. Prioritizing conservation of biodiversity in an alpine region: Distribution pattern and conservation status of seed plants in the Qinghai-Tibetan Plateau. Global Ecology and Conservation 32: e01885. https://doi.org/10.1016/j.gecco.2021.e01885

The Qinghai-Tibetan Plateau (QTP) harbors abundant and diverse plant life owing to its high habitat heterogeneity. However, the distribution pattern of biodiversity hotspots and their conservation status remain unclear. Based on 148,283 high-resolution occurrence coordinates of 13,450 seed plants, w…

de Jesús Hernández-Hernández, M., J. A. Cruz, and C. Castañeda-Posadas. 2020. Paleoclimatic and vegetation reconstruction of the miocene southern Mexico using fossil flowers. Journal of South American Earth Sciences 104: 102827. https://doi.org/10.1016/j.jsames.2020.102827

Concern about the course of the current environmental problems has raised interest in investigating the different scenarios that have taken place in our planet throughout time. To that end, different methodologies have been employed in order to determine the different variables that compose the envi…

Xue, L., L. Jia, G. Nam, Y. Huang, S. Zhang, Y. Wang, Z. Zhou, and Y. Chen. 2020. Involucre fossils of Carpinus, a northern temperate element, from the Miocene of China and the evolution of its species diversity in East Asia. Plant Diversity 42: 155–167. https://doi.org/10.1016/j.pld.2020.01.001

East Asia has long been recognized as a major center for temperate woody plants diversity. Although several theories have been proposed to explain how the diversity of these temperate elements accumulated in the region, the specific process remains unclear. Here we describe six species of Carpinus, …