Skewness in bee and flower phenological distributions.

Phenological distributions are characterized by their central tendency, breadth, and shape, and all three determine the extent to which interacting species overlap in time. Pollination mutualisms rely on temporal co-occurrence of pollinators and their floral resources, and although much work has been done to characterize the shapes of flower phenological distributions, similar studies that include pollinators are lacking. Here, we provide the first broad assessment of skewness, a component of distribution shape, for a bee community. We compare skewness in bees to that in flowers, relate bee and flower skewness to other properties of their phenology, and quantify the potential consequences of differences in skewness between bees and flowers. Both bee and flower phenologies tend to be right-skewed, with a more exaggerated asymmetry in bees. Early-season species tend to be the most skewed, and this relationship is also stronger in bees than in flowers. Based on a simulation experiment, differences in bee and flower skewness could account for up to 14% of pairwise overlap differences. Given the potential for interaction loss, we argue that difference in skewness of interacting species is an underappreciated property of phenological change.

INHABIT: A web-based decision support tool for invasive plant species habitat visualization and assessment across the contiguous United States.

Narrowing the communication and knowledge gap between producers and users of scientific data is a longstanding problem in ecological conservation and land management. Decision support tools (DSTs), including websites or interactive web applications, provide platforms that can help bridge this gap. DSTs can most effectively disseminate and translate research results when producers and users collaboratively and iteratively design content and features. One data resource seldom incorporated into DSTs are species distribution models (SDMs), which can produce spatial predictions of habitat suitability. Outputs from SDMs can inform management decisions, but their complexity and inaccessibility can limit their use by resource managers or policy makers. To overcome these limitations, we present the Invasive Species Habitat Tool (INHABIT), a novel, web-based DST built with R Shiny to display spatial predictions and tabular summaries of habitat suitability from SDMs for invasive plants across the contiguous United States. INHABIT provides actionable science to support the prevention and management of invasive species. Two case studies demonstrate the important role of end user feedback in confirming INHABIT's credibility, utility, and relevance.

The legacy of the extinct Neotropical megafauna on plants and biomes.

Large mammal herbivores are important drivers of plant evolution and vegetation patterns, but the extent to which plant trait and ecosystem geography currently reflect the historical distribution of extinct megafauna is unknown. We address this question for South and Central America (Neotropical biogeographic realm) by compiling data on plant defence traits, climate, soil, and fire, as well as on the historical distribution of extinct megafauna and extant mammal herbivores. We show that historical mammal herbivory, especially by extinct megafauna, and soil fertility explain substantial variability in wood density, leaf size, spines and latex. We also identified three distinct regions (''antiherbiomes''), differing in plant defences, environmental conditions, and megafauna history. These patterns largely matched those observed in African ecosystems, where abundant megafauna still roams, and suggest that some ecoregions experienced savanna-to-forest shifts following megafauna extinctions. Here, we show that extinct megafauna left a significant imprint on current ecosystem biogeography.

Global patterns of potential future plant diversity hidden in soil seed banks.

Soil seed banks represent a critical but hidden stock for potential future plant diversity on Earth. Here we compiled and analyzed a global dataset consisting of 15,698 records of species diversity and density for soil seed banks in natural plant communities worldwide to quantify their environmental determinants and global patterns. Random forest models showed that absolute latitude was an important predictor for diversity of soil seed banks. Further, climate and soil were the major determinants of seed bank diversity, while net primary productivity and soil characteristics were the main predictors of seed bank density. Moreover, global mapping revealed clear spatial patterns for soil seed banks worldwide; for instance, low densities may render currently species-rich low latitude biomes (such as tropical rain-forests) less resilient to major disturbances. Our assessment provides quantitative evidence of how environmental conditions shape the distribution of soil seed banks, which enables a more accurate prediction of the resilience and vulnerabilities of plant communities and biomes under global changes.

Using climatic variables alone overestimate climate change impacts on predicting distribution of an endemic species.

Plant species distribution is constrained by both dynamic and static environmental variables. However, relative contribution of dynamic and static variables in determining species distributions is not clear and has far reaching implications for range change dynamics in a changing world. Prunus eburnea (Spach) Aitch. & Hemsl. is an endemic and medicinal plant species of Iran. It has rendered itself as ecologically important for its functions and services and is currently in need of habitat conservation measures requiring investigation of future potential distribution range. We conducted sampling of 500 points that cover most of Iran plateau and recorded the P. eburnea presence and absence during the period 2015-2017. In this study, we evaluated impacts of using only climatic variables versus combined with topographic and edaphic variables on accuracy criteria and predictive ability of current and future habitat suitability of this species under climate change (CCSM4, RCP 2.6 in 2070) by generalized linear model and generalized boosted model. Models' performances were evaluated using area under the curve, sensitivity, specificity and the true skill statistic. Then, we evaluated here, driving environmental variables determining the distribution of P. eburnea by using principal component analysis and partitioning methods. Our results indicated that prediction with high accuracy of the spatial distribution of P. eburnea requires both climate information, as dynamic primary factors, but also detailed information on soil and topography variables, as static factors. The results emphasized that environmental variable grouping influenced the modelling prediction ability strongly and the use of only climate variables would exaggerate the predicted distribution range under climate change. Results supported using both dynamic and static variables improved accuracy of the modeling and provided more realistic prediction of species distribution under influence of climate change.

Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis.

BACKGROUND: Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees. RESULTS: We identify 55 novel quantitative trait loci (QTLs) that are associated with phenotypic variation. The largest number of QTLs is associated with the budburst stage, followed by diameter at breast height, wood quality, and frost damage. Two QTLs with the largest effect have a pleiotropic effect for budburst stage, frost damage, and diameter and are associated with MAP3K genes. Genotype data called from exome capture, recently developed SNP array and gene expression data indirectly support this discovery. CONCLUSION: Several important QTLs associated with growth and frost damage have been verified in several southern and northern progeny plantations, indicating that these loci can be used in QTL-assisted genomic selection. Our study also demonstrates that existing heterogeneous phenotypic data from breeding programs, collected over several decades, is an important source for GWAS and that such integration into GWAS should be a major area of inquiry in the future.

Decalepis salicifolia (Bedd. ex Hook. f.) Venter: A steno-endemic and critically endangered medicinal and aromatic plant from Western Ghats, India.

Decalepis salicifolia (Bedd. ex Hook. f.) Venter is a potential medicinal and highly aromatic plant species confined to the southernmost part of the Western Ghats of India. The plant is well known for its traditional uses among the various tribal communities of south India. The tubers of the plant possess characteristic vanillin-like aroma due to the presence of the compound 2-hydroxy-4-methoxybenzaldehyde. The tubers are used to substitute Hemidesmus indicus in various herbal formulations. The plants in the wild are continuously uprooted for their roots, leading to the irreversible destruction of the whole plant. The resulting tremendous loss of populations in the wild led to the species being declared as critically endangered by IUCN. Our group is working on the various aspects of this species including population status, distribution mapping, prospection, and conservation management. In the present review, we have brought out the available information till date on D. salicifolia, including taxonomy, ethno-medicinal uses, phytochemistry, pharmacology, population status, and conservation efforts along with research gap and lacunae to provide direction for further research into this less explored medicinal and aromatic plant.

Optimization study on spatial distribution of rice based on a virtual plant approach.

How to increase crop yield is the most important issue in agricultural production. Many studies have been devoted to optimizing spatial distribution of crops, to improve light interception and increase photosynthetic assimilation. However, finding an optimal solution based on field experiments is almost impossible since the large number of combinations of factors that are related, and the cost in terms of finances and time are prohibitive. A new optimization strategy was proposed in this study, integrating a Functional-Structural Model of rice with a workflow based on a Mixed Particle Swarm Optimization (MPSO) algorithm. The 3D modelling platform GroIMP was used to implement the model and optimization workflow. MPSO is a new Particle Swarm Optimization-based algorithm with multistage disturbances, which has improved abilities to get rid of local optima and to explore solution space. Spacing between plants was used as optimization target in the first example. An optimal plant spacing was obtained within the model framework of current environmental settings together with the functional and structural modules. Simulation results indicate that the optimized plant spacing could increase rice yield, and that the optimization results remain stable.

Short-term impact of sediment addition on plants and invertebrates in a southern California salt marsh.

The implementation and monitoring of management strategies is integral to protect coastal marshes from increased inundation and submergence under sea-level rise. Sediment addition is one such strategy in which sediment is added to marshes to raise relative elevations, decrease tidal inundation, and enhance ecosystem processes. This study looked at the plant and invertebrate community responses over 12 months following a sediment addition project on a salt marsh located in an urbanized estuary in southern California, USA. This salt marsh is experiencing local subsidence, is sediment-limited from landscape modifications, has resident protected species, and is at-risk of submergence from sea-level rise. Abiotic measurements, invertebrate cores, and plant parameters were analyzed before and after sediment application in a before-after-control-impact (BACI) design. Immediately following the sediment application, plant cover and invertebrate abundance decreased significantly, with smothering of existing vegetation communities without regrowth, presumably creating resulting harsh abiotic conditions. At six months after the sediment application treatment, Salicornia bigelovii minimally colonized the sediment application area, and Spartina foliosa spread vegetatively from the edges of the marsh; however, at 12 months following sediment application overall plant recovery was still minimal. Community composition of infaunal invertebrates shifted from a dominance of marsh-associated groups like oligochaetes and polychaetes to more terrestrial and more mobile dispersers like insect larvae. In contrast to other studies, such as those with high organic deposition, that showed vegetation and invertebrate community recovery within one year of sediment application, our results indicated a much slower recovery following a sediment addition of 32 cm which resulted in a supratidal elevation with an average of 1.62 m (NAVD88) at our sampling locations. Our results indicate that the site did not recover after one year and that recovery may take longer which illustrates the importance of long-term monitoring to fully understand restoration trajectories and inform adaptive management. Testing and monitoring sea-level rise adaptation strategies like sediment addition for salt marshes is important to prevent the loss of important coastal ecosystems.

Bryophytes are predicted to lag behind future climate change despite their high dispersal capacities.

The extent to which species can balance out the loss of suitable habitats due to climate warming by shifting their ranges is an area of controversy. Here, we assess whether highly efficient wind-dispersed organisms like bryophytes can keep-up with projected shifts in their areas of suitable climate. Using a hybrid statistical-mechanistic approach accounting for spatial and temporal variations in both climatic and wind conditions, we simulate future migrations across Europe for 40 bryophyte species until 2050. The median ratios between predicted range loss vs expansion by 2050 across species and climate change scenarios range from 1.6 to 3.3 when only shifts in climatic suitability were considered, but increase to 34.7-96.8 when species dispersal abilities are added to our models. This highlights the importance of accounting for dispersal restrictions when projecting future distribution ranges and suggests that even highly dispersive organisms like bryophytes are not equipped to fully track the rates of ongoing climate change in the course of the next decades.

Species richness both impedes and promotes alien plant invasions in the Brazilian Cerrado.

Worldwide, alien plant invasions have been intensively studied in the past decades, but mechanisms controlling the invasibility of native communities are not fully understood yet. The stochastic niche hypothesis predicts that species-rich plant communities are less prone to alien plant invasions than species-poor communities, which is supported by some but not all field studies, with some very species-rich communities such as the Brazilian Cerrado becoming heavily invaded. However, species-rich communities potentially contain a greater variety of facilitative interactions in resource exploitation than species-poor communities, from which invasive plants might benefit. This alternative hypothetical mechanism might explain why nutrient-poor, species-rich ecosystems are prone to invasion. Here we show that a high species richness both impedes and promotes invasive plants in the Brazilian Cerrado, using structural equation modelling and data from 38 field sites. We found support for the stochastic niche hypothesis through an observed direct negative influence of species richness on abundance of alien invasive species, but an indirect positive effect of species richness on invasive alien plants through soil phosphatase activity that enhances P availability was also found. These field observations were supported with results from a mesocosm experiment. Root phosphatase activity of plants increased with species richness in the mesocosms, which was associated with greater community P and N uptake. The most prominent alien grass species of the region, Melinis minutiflora, benefited most from the higher N and P availability in the species mixtures. Hence, this study provides a novel explanation of why species-richness may sometimes promote rather than impede invasion, and highlights the need to perform facilitation experiments in multi-species communities.

"Puffing" in Sarcoscypha austriaca: Back to Ziegenspeck.

Many discomycetes show the phenomenon of "puffing": the quasi-simultaneous discharge of large numbers of ascospores, rendering them visible to the unaided eye as a whiff of smoke above the fruitbody. Obviously, some kind of synchronization mechanism must be present to make all asci involved burst at about the same time. This mechanism has generally been understood to be of a mechanical nature. For a (small, dung-inhabiting) Ascobolus species, puffing was shown to involve a discharge wave propagating radially outward from a random origin at a speed of about 1.5 cm/s. Using high-speed imaging, we have found no evidence for such a wave in puffing by the (much larger, wood-inhabiting) apothecia of Sarcoscypha austriaca. Rather, extended (but limited) areas seem to become active essentially simultaneously, and within these areas a few percent of the asci discharge their spores randomly. In these large fruitbodies, puffing is found to be preceded by a small but distinct deformation of the apothecium, the geometry of which is such that it increases the lateral compressive stress in the hymenium. The observations suggest that this increase in stress is instrumental in causing many asci to burst quasi-simultaneously in the affected area, a hypothesis essentially already proposed by H. Ziegenspeck, about a century ago.

Statistical Comparison of Trait-Dependent Biogeographical Models Indicates That Podocarpaceae Dispersal Is Influenced by Both Seed Cone Traits and Geographical Distance.

The ability of lineages to disperse long distances over evolutionary timescales may be influenced by the gain or loss of traits adapted to enhance local, ecological dispersal. For example, some species in the southern conifer family Podocarpaceae have fleshy cones that encourage bird dispersal, but it is unknown how this trait has influenced the clade's historical biogeography, or its importance compared with other predictors of dispersal such as the geographic distance between regions. We answer these questions quantitatively by using a dated phylogeny of 197 species of southern conifers (Podocarpaceae and their sister family Araucariaceae) to statistically compare standard, trait-independent biogeography models with new BioGeoBEARS models where an evolving trait can influence dispersal probability, and trait history, biogeographical history, and model parameters are jointly inferred. We validate the method with simulation-inference experiments. Comparing all models, those that include trait-dependent dispersal accrue 87.5% of the corrected Akaike Information Criterion (AICc) model weight. Averaged across all models, lineages with nonfleshy cones had a dispersal probability multiplier of 0.49 compared with lineages with fleshy cones. Distance is included as a predictor of dispersal in all credible models (100% model weight). However, models with changing geography earned only 22.0% of the model weight, and models submerging New Caledonia/New Zealand earned only 0.01%. The importance of traits and distance suggests that long-distance dispersal over macroevolutionary timespans should not be thought of as a highly unpredictable chance event. Instead, long-distance dispersal can be modeled, allowing statistical model comparison to quantify support for different hypotheses.

Invasion intensity influences scale-dependent effects of an exotic species on native plant diversity.

Invasive plant species reduce the diversity of natives by altering habitats or disturbance regimes, but it is less clear whether they do so via competitive exclusion. Here, we show that invader abundance alters scale-dependent competitive effects of invasion on native plant richness. Large-seeded exotic annual Erodium cicutarium invaded a site that manipulated rodent granivores. The invader became dominant on all plots but attained its highest abundance on plots that removed rodents. Invasion reduced plant abundance but not evenness; site-wide richness did not change over time on control plots but declined significantly on rodent removal plots. Species-area relationships within plots changed differently with invasion intensity: slopes increased and y-intercepts decreased on control plots relative to rodent removal plots. Changes in species-area slopes and y-intercepts following invasion suggest that common rather than rare species were most strongly impacted at small spatial scales on control plots, while common and rare species were both negatively impacted at all spatial scales on rodent removal plots. Small-seeded species declined in abundance following invasion more so than large-seeded species, indicative of competitive interactions mediated by seed size. These results reveal variation in scale-dependent competitive effects of invasion on native richness associated with invasion intensity.

High heat tolerance in plants from the Andean highlands: Implications for paramos in a warmer world.

Tropical plant species are expected to have high heat tolerance reflecting phenotypic adjustments to warm regions or their evolutionary adaptation history. However, tropical highland specialists adapted to the colder temperatures found in the highlands, where short and prostrated vegetation decouples plants from ambient conditions, could exhibit different upper thermal limits than those of their lowland counterparts. Here we evaluated leaf heat tolerance of 21 tropical alpine paramo species to determine: 1) whether species with restricted distribution (i.e., highland specialists) have lower heat tolerance and are more vulnerable to warming than species with widespread distribution; 2) whether different growth forms have different heat tolerance; and 3) whether species height (i.e., microhabitat) influences its heat tolerance. We quantified heat tolerance by evaluating T50, which is the temperature that causes a reduction in 50% of initial Fv/Fm values and reflects an irreversible damage to the photosynthetic apparatus. Additionally, we estimated the thermal safety margins as the difference between T50 and the maximum leaf temperature registered for the species. All species presented high T50 values ranging between 45.4°C and 53.9°C, similar to those found for tropical lowland species. Heat tolerance was not correlated with species distributions or plant height, but showed a strong relationship with growth form, with rosettes having the highest heat tolerance. Thermal safety margins ranged from 12.1 to 31.0°C. High heat tolerance and broad thermal safety margins suggest low vulnerability of paramo species to warming as long as plants are capable of regulating the leaf temperature within this threshold. Whether paramo plants would be able to regulate leaf temperature if drought episodes become more frequent and transpirational cooling is compromised is the next question that needs to be answered.

Climatic niche characteristics of native and invasive Lilium lancifolium.

One of the topics currently under discussion in biological invasions is whether the species' climatic niche has been conserved or, alternatively, has diverged during invasions. Here, we explore niche dynamic processes using the complex invasion history model of Lilium lancifolium, which is the first tested case of a native species (Korea) with two hypothesized spatial (regional and intercontinental) and temporal arrivals: (1) as an archaeophyte in East Asia (before AD 1500); and (2) as a neophyte in Europe, North America, Australia, and New Zealand (after AD 1500). Following a niche examination through both environmental and geographical spaces, the species in the archaeophyte range has apparently filled the ancestral native niche and, rather, would have increased it considerably. The species as a neophyte shows a closer climatic match with the archaeophyte range than with the native one. This pattern of niche similarity suggests that the neophyte range was probably colonized by a subset of archaeophyte propagules adapted to local climate that promoted the species' establishment. Overall, niche conservatism is proposed at each colonization step, from native to archaeophyte, and from archaeophyte to neophyte ranges. We detected signals of an advanced invasion stage within the archaeophyte range and traces of an early introduction stage in neophyte ranges.

Distribution and relative age of endemism across islands worldwide.

Islands have remarkable levels of endemism and contribute greatly to global biodiversity. Establishing the age of island endemics is important to gain insights into the processes that have shaped the biodiversity patterns of island biota. We investigated the relative age of monocots across islands worldwide, using different measures of phylogenetic endemism tested against null models. We compiled a species occurrence dataset across 4,306 islands, and identified 142 sites with neo-, paleo-, mixed and super-endemism. These sites were distributed across the world, although they tended to be more common at low latitudes. The most frequent types of endemism were mixed and super-endemism, which suggests that present-day island biodiversity has frequently been shaped by processes that took place at different points in times. We also identified the environmental factors that contributed most to different types of endemism; we found that latitude, habitat availability and climate stability had a significant impact on the persistence of ancient taxa and on recent diversification events. The islands identified here are irreplaceable both for the uniqueness and the evolutionary history of their flora, and because they are a source of "option values" and evolutionary potential. Therefore, our findings will help guide biodiversity conservation on a global scale.

Grazing enhances species diversity in grassland communities.

In grassland studies, an intermediate level of grazing often results in the highest species diversity. Although a few hypotheses have been proposed to explain this unimodal response of species diversity to grazing intensity, no convincing explanation has been provided. Here, we build a lattice model of a grassland community comprising multiple species with various levels of grazing. We analyze the relationship between grazing and plant diversity in grasslands under variable intensities of grazing pressure. The highest species diversity is observed at an intermediate grazing intensity. Grazers suppress domination by the most superior species in birth rate, resulting in the coexistence of inferior species. This unimodal grazing effect disappears with the introduction of a small amount of nongrazing natural mortality. Unimodal patterns of species diversity may be limited to the case where grazers are the principal source of natural mortality.

A Lévy expansion strategy optimizes early dune building by beach grasses.

Lifeforms ranging from bacteria to humans employ specialized random movement patterns. Although effective as optimization strategies in many scientific fields, random walk application in biology has remained focused on search optimization by mobile organisms. Here, we report on the discovery that heavy-tailed random walks underlie the ability of clonally expanding plants to self-organize and dictate the formation of biogeomorphic landscapes. Using cross-Atlantic surveys, we show that congeneric beach grasses adopt distinct heavy-tailed clonal expansion strategies. Next, we demonstrate with a spatially explicit model and a field experiment that the Lévy-type strategy of the species building the highest dunes worldwide generates a clonal network with a patchy shoot organization that optimizes sand trapping efficiency. Our findings demonstrate Lévy-like movement in plants, and emphasize the role of species-specific expansion strategies in landscape formation. This mechanistic understanding paves the way for tailor-made planting designs to successfully construct and restore biogeomorphic landscapes and their services.

Natural and human-impacted diversity of bryophytes along an elevational gradient on an oceanic island (La Palma, Canarias).

Bryophytes have been proposed as ideal indicators of ecosystem change, because they are important components of forest integrity, and considerable research indicates that some groups are sensitive to the changes associated with specific human disturbances. Bryophyte richness and abundance have been found to vary predictably along elevational gradients, but the role of human impacts on these distribution patterns remains unclear. The aim of this study is to explore the impact of human disturbance on the elevational patterns of bryophyte diversity, along an elevational gradient. Along the gradient we collected three datasets in the following sites: preserved (P), forest track roadsides (R) and disturbed by agriculture/silviculture practices (D). Two survey plots of 100 m2 were established at every 200 m elevational step for each sites P, R, D, and in each plot bryophytes were sampled in a stratified manner. At each plot we recorded all species on available substrates and estimated their percentage cover. Our results showed that species number did not differ among studied sites, but that species diversity pattern differs among the three gradient types and species life strategy composition along the elevational gradient showed a clear response to the disturbance of mature communities. We conclude that human impact has strongly changed the elevational pattern of diversity, and that these changes vary depending on the ecological and taxonomical group considered.