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The plastid genome of the deep-shade plant Selaginella erythropus, which has highly unusual chloroplasts, was characterized using Illumina pair-end sequencing. This plastome is 140,151 bp in length...

PREMISE Unique among vascular plants, some species of Selaginella have single giant chloroplasts in their epidermal or upper mesophyll cells (monoplastidy, M), varying in structure between species. Structural variants include several forms of bizonoplast with unique dimorphic ultrastructure. Better understanding of these structural variants, their prevalence, environmental correlates and phylogenetic association, has the potential to shed new light on chloroplast biology unavailable from any other plant group. METHODS The chloroplast ultrastructure of 76 Selaginella species was studied with various microscopic techniques. Environmental data for selected species and subgeneric relationships were compared against chloroplast traits. RESULTS We delineated five chloroplast categories: ME (monoplastidy in a dorsal epidermal cell), MM (monoplastidy in a mesophyll cell), OL (oligoplastidy), Mu (multiplastidy, present in the most basal species), and RC (reduced or vestigial chloroplasts). Of 44 ME species, 11 have bizonoplasts, cup-shaped (concave upper zone) or bilobed (basal hinge, a new discovery), with upper zones of parallel thylakoid membranes varying subtly between species. Monoplastidy, found in 49 species, is strongly shade associated. Bizonoplasts are only known in deep-shade species (

In nature, foliar variegation has varied origins, and can be ascribed to two major mechanisms: pigment-related variegation and structural variegation caused by the optical properties of leaf structure. However, understanding of these mechanisms is still lacking, and structural mechanisms are often misinterpreted. In this study, six variegated plants native to Taiwan and two ornamental plants, with novel and unusual foliar variegation patterns, are studied to reveal their mechanisms of variegation. Two newly understood variegation patterns, the silvery white leaf surface of Begonia aptera and the varnish on basal leaflets of Oxalis corymbosa, are reported here. White to light green patches on leaf surfaces characterize the foliar variegation in the other six study species, Nervilia nipponica, O. acetosella subsp. griffithii var. formosana, Paphiopedilum concolor, Selaginella picta, Smilax bracteata subsp. verruculosa and Valeriana hsuii. All six Taiwan native plants exhibit structural variegation, five of which have air space type variegation. Surprisingly the silvery white leaf surface of B. aptera results from numerous sand-like white spots caused by intercellular space. The varnish on leaves of O. corymbosa is the epidermis type of variegation comprised of two newly identified subtypes, larger epidermal cells and thicker outer cell walls. The two ornamental plants have variegation caused by pigments: the chloroplast type from fewer chloroplasts in P. concolor and the chlorophyll type, from absence of chloroplasts in S. picta. This study extends understanding of the mechanisms of natural foliar variegation, illustrating the diversity of mechanisms by which plants may change the appearance of their leaves.

We analyze a general theory for coexistence and extinction of ecological communities that are influenced by stochastic temporal environmental fluctuations. The results apply to discrete time (stochastic difference equations), continuous time (stochastic differential equations), compact and non-compact state spaces and degenerate or non-degenerate noise. In addition, we can also include in the dynamics auxiliary variables that model environmental fluctuations, population structure, eco-environmental feedbacks or other internal or external factors. We are able to significantly generalize the recent discrete time results by Benaim and Schreiber (Journal of Mathematical Biology '19) to non-compact state spaces, and we provide stronger persistence and extinction results. The continuous time results by Hening and Nguyen (Annals of Applied Probability '18) are strengthened to include degenerate noise and auxiliary variables. Using the general theory, we work out several examples. In discrete time, we classify the dynamics when there are one or two species, and look at the Ricker model, Log-normally distributed offspring models, lottery models, discrete Lotka-Volterra models as well as models of perennial and annual organisms. For the continuous time setting we explore models with a resource variable, stochastic replicator models, and three dimensional Lotka-Volterra models., 65 pages, 3 figures

Ecological character displacement is a prominent hypothesis for the maintenance of ecological differences between species that are critical to stable coexistence. Models of character displacement often ascribe interspecific competitive interactions to a single character, but multiple characters contribute to competition, and their effects on selection can be nonadditive. Focusing on one character, we ask if other characters that affect competition alter evolutionary outcomes for the focal character. We address this question using the variable environment seed bank model for two species with two traits. The focal trait is the temporal pattern of germination, which is evolutionary labile. The other trait is the temporal pattern of plant growth, which is assumed fixed. We ask whether evolutionary divergence of germination patterns between species depends on species differences in plant growth. Patterns of growth can affect selection on germination patterns in two ways. First, cues present at germination can provide information about future growth. Second, germination and growth jointly determine the biomass of plants, which determines demand for resources. Germination and growth contribute to the selection gradient in distinct components, one density-independent and the other density-dependent. Importantly, the relative strengths of the components are key. When the density-dependent component is stronger, displacement in germination patterns between species is larger. Stronger cues at germination strengthen the density-independent component by increasing the benefits of germinating in years of favorable growth. But cues also affect the density-dependent component by boosting a species’ biomass, and hence its competitive effect, in good years. Consequently, cues weaken character displacement when growth patterns are similar for two competitors, but favor displacement when growth patterns are species-specific. Understanding how these selection components change between contexts can help understand the origin and maintenance of species differences in germination patterns in temporally fluctuating environments.

In most places on Earth, many similar species are found coexisting. This key observation is often explained in terms of ecological differences in how species interact with their shared environment, that is, in terms of their niche differences. Niche differences can to lead to stable coexistence in contrast to the ecological drift predicted by the neutral theory of community ecology. Coexistence becomes stabilized as density feedback within species is strengthened relative to density feedback between species. Coexistence is reflective of two distinct niche comparisons, niche overlap, and species relative average fitness. In general, low niche overlap (dissimilarity in use of the environment) and similar average fitnesses (similar average performance) favor coexistence. For a unified theory of species coexistence, it is shown how the Lotka–Volterra competition model can reflect and quantify several types of niche comparison, including comparisons of resource use, susceptibility to natural enemies, and temporal variation in activity.

Stream systems are characterized by a hierarchical dendritic branching pattern, which is thought to have important consequences for stream community structure. However, branching is associa...

Fluctuating environmental conditions have consequences for the evolution of life histories because they cause fitness variance. This variance can favor risk-spreading strategies, often known as bet-hedging strategies, in which growth or reproduction is spread over time or space, with some costs, but greater certainty of success. An important example is seed dormancy in annual plants, in which some fraction of seed remains dormant at any given germination opportunity with the potential of germinating later when environmental conditions may differ. Previous theory shows that environmental variation is critical for the evolution of dormancy. However, these studies have focused on temporal variation in reproduction, ignoring the strong observed effects of environmental variation on the germination fraction, a major contributor to fitness variance. We ask what effects germination fluctuations have on selection for dormancy by adding germination fluctuations to existing density-independent (d.i.) and density-dependent (d.d.) models of annual plant dynamics, extending previous analyses by including temporally fluctuating germination. Specifically, we ask how germination variance affects selection on the temporal average germination fraction, here used to define dormancy. When present alone, or when independently varying with other fitness components, germination fluctuations do not affect selection for dormancy in the d.i. model, despite generating fitness variance because this variance contribution is not reduced by higher dormancy. Germination fluctuations have strong effects in the d.d. model, favoring dormancy when present either alone or coupled with variation affecting plant growth. This is because germination variation causes seedling density to vary, which causes variable reproduction through variable intraspecific competition. Dormancy is advantaged under variable reproduction because it creates a more convex relationship between population growth and reproduction leading to benefits from nonlinear averaging. Predictive germination, a positive statistical association between germination and growth, weakens selection for dormancy under strong competition and strengthens it when competition is weak. Our results suggest that variable germination is a potential explanation for high levels of dormancy observed in nature, with implications for life-history theory for fluctuating environments.

The presence of foliar variegation challenges perceptions of leaf form and functioning. But variegation is often incorrectly identified and misinterpreted. The striking variegation found in juvenile Blastus cochinchinensis (Melastomataceae) provides an instructive case study of mechanisms and their ecophysiological implications. Variegated (white and green areas, vw and vg) and non-variegated leaves (normal green leaves, ng) of seedlings of Blastus were compared structurally with microtechniques, and characterized for chlorophyll content and fluorescence. More limited study of Sonerila heterostemon (Melastomataceae) and Kaempferia pulchra (Zingiberaceae) tested the generality of the findings. Variegation in Blastus combines five mechanisms: epidermal, air space, upper mesophyll, chloroplast and crystal, the latter two being new mechanisms. All mesophyll cells (vw, vg, ng) have functional chloroplasts with dense thylakoids. The vw areas are distinguished by flatter adaxial epidermal cells and central trichomes containing crystals, the presence of air spaces between the adaxial epidermis and a colorless spongy-like upper mesophyll containing smaller and fewer chloroplasts. The vw area is further distinguished by having the largest spongy-tissue chloroplasts and fewer stomata. Both leaf types have similar total chlorophyll content and similar F v/F m (maximum quantum yield of PSII), but vg has significantly higher F v/F m than ng. Variegation in Sonerila and Kaempferia is also caused by combined mechanisms, including the crystal type in Kaempferia. This finding of combined mechanisms in three different species suggests that combined mechanisms may occur more commonly in nature than current understanding. The combined mechanisms in Blastus variegated leaves represent intricate structural modifications that may compensate for and minimize photosynthetic loss, and reflect changing plant needs.

The maintenance of species diversity occurs at the regional scale but depends on interacting processes at the full range of lower scales. Although there is a long history of study of regional diversity as an emergent property, analyses of fully multiscale dynamics are rare. Here, we use scale transition theory for a quantitative analysis of multiscale diversity maintenance with continuous scales of dispersal and environmental variation in space and time. We develop our analysis with a model of a linear habitat, applicable to streams or coastlines, to provide a theoretical foundation for the long-standing interest in environmental variation and dispersal, including downstream drift. We find that the strength of regional coexistence is strongest when local densities and local environmental conditions are strongly correlated. Increasing dispersal and shortening environmental correlations weaken the strength of coexistence regionally and shift the dominant coexistence mechanism from fitness-density covariance to the spatial storage effect, while increasing local diversity. Analysis of the physical and biological determinants of these mechanisms improves understanding of traditional concepts of environmental filters, mass effects, and species sorting. Our results highlight the limitations of the binary distinction between local communities and a species pool and emphasize species coexistence as a problem of multiple scales in space and time.

Hutchinson's famous hypothesis for the "paradox of the plankton" has been widely accepted, but critical aspects have remained unchallenged. Hutchinson argued that environmental fluctuations would promote coexistence when the timescale for environmental change is comparable to the timescale for competitive exclusion. Using a consumer-resource model, we do find that timescales of processes are important. However, it is not the time to exclusion that must be compared with the time for environmental change but the time for resource depletion. Fast resource depletion, when resource consumption is favored for different species at different times, strongly promotes coexistence. The time for exclusion is independent of the rate of resource depletion. Therefore, the widely believed predictions of Hutchinson are misleading. Fast resource depletion, as determined by environmental conditions, ensures strong coupling of environmental processes and competition, which leads to enhancement over time of intraspecific competition relative to interspecific competition as environmental shifts favor different species at different times. This critical coupling is measured by the covariance between environment and competition. Changes in this quantity as densities change determine the stability of coexistence and provide the key to rigorous analysis, both theoretically and empirically, of coexistence in a variable environment. These ideas apply broadly to diversity maintenance in variable environments whether the issue is species diversity or genetic diversity and competition or apparent competition.

Selaginellaceae (Lycopodiophyta), an early divergent group of vascular plants, are a species-rich and taxonomically challenging family. Here we study silica bodies on the leaves of a prominently studied Selaginella, S. erythropus, with various methods of microscopy and energy disperse X-ray analysis (EDX) to characterize their properties in mature and emerging leaves. To detect silica bodies, a light microscope or a fluorescence microscope can be used to reveal colorless silica body protrusions in the epidermal cell walls. Silica bodies show as light spots with scanning electron microscopy (SEM). However, the recent tabletop SEM featured with low accelerating voltage and backscattered electron detectors provides a better contrast than standard SEM. EDX shows that these protrusions on leaf surfaces are silica bodies and that trichome apices and some stomata also have silica deposits. Atomic force microscopy provides three-dimensional images and quantitative measurements, but with an upper limit on silica body size. Under transmission electron microscopy silica bodies are characterized as compact electron-dense particles, gradually thinning and mingling with the cell wall. These analyses recognized two major forms of silica bodies, conical (small and large subforms) and sinuate-carinate. Distinct forms are found on different types of epidermal cells. Patterns on a leaf surface differ between the four types of leaf surface, dorsal and ventral surfaces of dorsal and ventral leaves, and may have taxonomic value. The silicification process on a young leaf begins from the central part. Large conical silica bodies appear first, along leaf margins and trichomes. Then, small conical silica bodies develop. Sinuate-carinate forms arise from the merger of large conical forms. A full understanding of the functional significance of silica bodies in Selaginella has yet to be developed, but we hope this report can help researchers detect silica bodies, and inspire more studies.

The study of the role of environmental variation in community dynamics has traditionally assumed that the environment is a stationary stochastic process or a periodic deterministic process. However, the physical environment in nature is nonstationary. Moreover, anthropogenically driven climate change provides a new challenge emphasizing a persistent but frequently ignored problem: how to make predictions about the dynamics of communities when the nonstationarity of the physical environment is recognized. Recent work is providing a path to conclusions with none of the traditional assumptions of environmental stationarity or periodicity. Traditional assumptions about convergence of long-term averages of functions of environmental states can be replaced by assumptions about temporal sums, allowing convergence and persistence of population processes to be demonstrated in general nonstationary environments. These tools are further developed and illustrated here with some simple models of nonstationary community dynamics, including the Beverton-Holt model, the threshold exponential and the lottery model.

Iridoplasts (modified plastids in adaxial epidermal cells) reported from Begonia were originally hypothesized to cause iridescence, which was broadly accepted for decades. However, several species of Begonia with iridoplasts are not iridescent causing confusion. Here chloroplast ultrastructure was observed in 40 taxa of Begoniaceae to explore the phenomenon of iridescence. However, 22 Begonias and Hillebrandia were found to have iridoplasts, but only nine display visually iridescent blue to blue-green leaves. Unexpectedly, a new type of plastid, a 'minichloroplast,' was found in the abaxial epidermal cells of all taxa, but was present in adaxial epidermal cells only if iridoplasts were absent. Comparative ultrastructural study of iridoplasts and a shading experiment of selected taxa show that a taxon with iridoplasts does not inevitably have visual iridescence, but iridescence is greatly affected by the spacing between thylakoid lamellae (stoma spacing). Thus, we propose instead the name 'lamelloplast' for plastids filled entirely with regular lamellae to avoid prejudging their function. To evaluate photosynthetic performance, chlorophyll fluorescence (F v /F m ) was measured separately from the chloroplasts in the adaxial epidermis and lower leaf tissues by using leaf dermal peels. Lamelloplasts and minichloroplasts have much lower photosynthetic efficiency than mesophyll chloroplasts. Nevertheless, photosynthetic proteins (psbA protein of PSII, RuBisCo and ATPase) were detected in both plastids as well as mesophyll chloroplasts in an immunogold labeling. Spectrometry revealed additional blue to blue-green peaks in visually iridescent leaves. Micro-spectrometry detected a blue peak from single blue spots in adaxial epidermal cells confirming that the color is derived from lamelloplasts. Presence of lamelloplasts or minichloroplasts is species specific and exclusive. High prevalence of lamelloplasts in Begoniaceae, including the basal clade Hillebrandia, highlights a unique evolutionary development. These new findings clarify the association between iridescence and lamelloplasts, and with implications for new directions in the study of plastid morphogenesis.

Resin ducts provide important characters for classifying the Pinaceae. Here we study Pinus massoniana and P. taiwanensis and show that the generally-used term marginal (=external) resin duct, applied to ducts in needle leaves, needs to be further differentiated into marginal (strongly attaching to the dermal tissue, and lacking the complete ring structure formed by the sheath cells) and submarginal ducts (adjacent to hypodermal cells, with a complete ring structure formed by the sheath cells). On this basis P. massoniana and P. taiwanensis, which are nearly indistinguishable based on external morphology, are clearly differentiated. Their similar morphology has led to a long standing debate on where P. massoniana occurs in Taiwan. Based on this new classification of resin ducts, we examined old herbarium specimens previously identified as P. massoniana, surveyed current hard pines in Taiwan, and checked historical documents. Needle leaves of these two taxa were studied and compared with the material of P. massoniana from mainland China as a reference. Pinus massoniana shows almost exclusively marginal resin ducts, with extremely rare changes along the length of the duct to submarginal positions. In contrast, P. taiwanensis shows a mixture of medial, submarginal, septal, and rarely endonal ducts, with occasional changes of the duct between various types. Re-identification of specimens showed that only 5 specimens are possible native P. massoniana collected from northern Taiwan and the others are all P. taiwanensis. The hard pine of Junjianyan is unexpectedly found to be the only currently known P. massoniana in Taiwan, which is likely a relic of historical afforestation. The hard pine from Huoyansan and the Coastal Range, which is widely accepted as P. massoniana, is not this species. In addition to the taxonomic value of the new definition applied to these two studied taxa, we expect that this approach can generally be applied distinguishing the respective characters in the genus Pinus and in other conifers.

a b s t r a c t Temporal environmental variation is a leading hypothesis for the coexistence of desert annual plants. Environmental variation is hypothesized to cause species-specific patterns of variation in germination, which then generates the storage effect coexistence mechanism. However, it has never been shown how sufficient species differences in germination patterns for multispecies coexistence can arise from a shared fluctuating environment. Here we show that nonlinear germination responses to a single fluctuating physical environmental factor can lead to sufficient differences between species in germination pattern for the storage effect to yield coexistence of multiple species. We derive these nonlinear germination responses from experimental data on the effects of varying soil moisture duration. Although these nonlinearities lead to strong species asymmetries in germination patterns, the relative nonlinearity coexistence mechanism is minor compared with the storage effect. However, these asymmetries mean that the storage effect can be negative for some species, which then only persist in the face of interspecific competition through average fitness advantages. This work shows how a low dimensional physical environment can nevertheless stabilize multispecies coexistence when the species have different nonlinear responses to common conditions, as supported by our experimental data.

Colleters are multicellular secretory structures found on various organs in flowering plants. Colleters on the adaxial sides of stipules have been hypothesized to play a role in protecting the developing shoot. Rhizophoraceae is a stipulate family with a broad distribution from mangrove to montane environments, which makes the family well suited for the examination of this hypothesis, but the colleters of Rhizophoraceae are not well known. We compared species from all three tribes of Rhizophoraceae, including five inland genera and all four mangrove genera. In all species, several to hundreds of colleters, sessile or stalked, arranged in rows aggregated in genus-specific shapes, are found at the adaxial bases of open and closed stipules. Pellacalyx uniquely has additional colleters at the stipule margins. Colleters are all of the standard type, comprising a central axis of core parenchyma with large vacuoles and tannins, and an outer palisade-like epidermis with organelles involved in secretory activity. An exception is Pellacalyx axillaris, in which colleters appear as extremely small epidermal protrusions. Kandelia obovata has a tracheary element in some colleters. Pellacalyx uniquely has an unusual fleshy outgrowth on the adaxial stipule base. We propose an evolutionary sequence in which Macarisia has plesiomorphic stipule and colleter traits and the mangrove Kandelia obovata with colleter vascular traces is most derived. Colleter and stipule structures are largely concordant with habitat and phylogeny, and show taxonomic value. The strong alignment of colleter and stipule patterns with habitat is suggestive that colleters have a protective function, although some components of these patterns may be phylogenetically determined. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172, 449–464.

It is well established theoretically that competing species may coexist by having different responses to variation over time in the physical environment. Whereas previous theory has focused mostly on year-to-year environmental variation, we investigate how within-year variation can be the basis of species coexistence. We ask also the important but often neglected question of whether the species differences that allow coexistence are compatible with evolutionary processes. We seek the simplest circumstances that permit coexistence based on within-year environmental variation, and then evaluate the robustness of coexistence in the face of evolutionary forces. Our focus is on coexistence of annual plant species living in arid regions. We first consider environmental variation of a very simple structure where a single pulse of rain occurs, and different species have different patterns of growth activity following the rain pulse. We show that coexistence of two species is possible based on the storage effect coexistence mechanism in this simplest of varying environments. We find an exact expression for the magnitude of the storage effect that allows the functioning of the coexistence mechanism to be analyzed. However, in these simplest of circumstances, coexistence in our models is not evolutionarily stable. Increasing the complexity of the environment to two rain pulses leads to evolutionarily stable species coexistence, and a route to diversity via evolutionary branching. This demonstration of the compatibility of a coexistence mechanism with evolutionary processes is an important step in assessing the likely importance of a mechanism in nature.

Seed dispersal by caching rodents is a context‐dependent mutualism in many systems. Plants benefit when seed remaining in shallow caches germinates before being eaten, often gaining protection from beetles and a favorable microsite in the process. Caching in highly unfavorable microsites, conversely, could undermine the dispersal benefit for the plant. Plant invasions could disrupt dispersal benefits of seed caching by attracting rodents to the protection of a dense invasive canopy which inhibits the establishment of native seedlings beneath it. To determine whether rodents disproportionately cache seed under the dense canopy of an invasive grass in southeastern Arizona, we used nontoxic fluorescent powder and ultraviolet light to locate caches of seed offered to rodents in the field. We fitted a general habitat‐use model, which showed that disproportionate use of plant cover by caching rodents (principally Chaetodipus spp.) increased with moonlight. Across all moon phases, when rodents cached under plants, they cached under the invasive grass disproportionately to its relative cover. A greenhouse experiment showed that proximity to the invasive grass reduced the growth and survival of seedlings of a common native tree (Parkinsonia microphylla) whose seeds are dispersed by caching rodents. Biased dispersal of native seed to the base of an invasive grass could magnify the competitive effect of this grass on native plants, further reducing their recruitment and magnifying the effect of the invasion.

Optimal foraging is one of the major predictive theories of predator foraging behavior. However, how an optimally foraging predator affects the coexistence of competing prey is not well understood either in a constant or variable environment, especially for multiple prey species. We study the impact of optimal foraging on prey coexistence using an annual plant model, with and without annual variation in seed germination. Seed predators are modeled using Charnov’s model of adaptive diet choice. Our results reveal that multiple prey species can coexist because of this type of predator, and that their effect is not greatly modified by environmental variation. However, in diverse communities, the requirements for coexistence by optimal foraging alone are very restrictive. Optimally foraging predators can have a strong equalizing effect on their prey by creating a competition–predation trade-off. Thus, their main role in promoting diversity may be to reduce species-average fitness differences, making it easier for other mechanisms, such as the storage effect, to allow multiple species to coexist. Like previous models, our model showed that when germination rates vary, the storage effect from competition promotes coexistence. Our results also show that optimally foraging predators can generate a negative storage effect from predation, undermining coexistence, but that this effect will be minor whenever predators commonly differentiate their prey.

Ceriops (Rhizophoraceae) is a genus comprised of five species of mangroves distributed in tropical and subtropical coastal regions. In this study, sequences from nuclear ribosomal ITS and the plastid trnL intron are used to construct molecular phylogenies of this genus revealing two species complexes, the C. tagal complex (C. tagal and C. australis), and the C. decandra complex (C. decandra, C. pseudodecandra and C. zippeliana), each forming a distinct clade. All five species, including the newly designated species C. pseudodecandra, are well supported. However, natural hybridization and historical introgression between Ceriops species are also demonstrated. The ITS sequences of Ceriops species, in contrast to their plastid trnL intron sequences, show a great amount of homoplasy during evolution. Historical introgression originating from natural hybridization was demonstrated based on the additivity of ITS sequences from putative parents. Of the five Ceriops species, C. pseu- dodecandra is a relatively isolated species. C. decandra and C. zippeliana show mutual introgression in most populations. According to both the nuclear ITS sequences and the plastid trnL intron, an intermediate form from Darwin is likelya natural hybrid, with C. tagal and C. australis respectively the maternal and paternal parents.

Scale transition theory is an approach to understanding population and community dynamics in the presence of spatial or temporal variation in environmental factors or population densities. It focuses on changes in the equations for population dynamics as the scale enlarges. These changes are explained in terms of interactions between nonlinearities and variation on lower scales, and they predict the emergence of new properties on larger scales that are not predicted by lower scale dynamics in the absence of variation on those lower scales. These phenomena can be understood in terms of statistical inequalities arising from the process of nonlinear averaging, which translates the rules for dynamics from lower to higher scales. Nonlinearities in population dynamics are expressions of the fundamental biology of the interactions between individual organisms. Variation that interacts with these nonlinearities also involves biology fundamentally in several different ways. First, there are the aspects of biology that are sensitive to variation in space or time. These determine which aspects of a nonlinear dynamical equation are affected by variation, and whether different individuals or different species are sensitive to different extents or to different aspects of variation. Second is the nature of the variation, for example, whether it is variation in the physical environment or variation in population densities. From the interplay between variation and nonlinearities in population dynamics, scale transition theory builds a theory of changes in dynamics with changes in scale. In this article, the focus is on spatial variation, and the theory is illustrated with examples relevant to the dynamics of insect communities. In these communities, one commonly occurring nonlinear relationship is a negative exponential relationship between survival of an organism and the densities of natural enemies or competitors. This negative exponential has a biological origin in terms of independent actions of many individuals. The subsequent effects of spatial variation can be represented naturally in terms of Laplace transforms and related statistical transforms to obtain both analytical solutions and an extra level of understanding. This process allows us to analyze the meaning and effects of aggregation of insects in space. Scale transition theory more generally, however, does not aim to have fully analytical solutions but partial analytical solutions applicable for circumstances too complex for full analytical solution. These partial solutions are intended to provide a framework for understanding of numerical solutions, simulations and field studies where key quantities can be estimated from empirical data.

Dispersal is a major and critical process in population biology that has been particularly challenging to study. Animals can have major roles in seed dispersal even in species that do not appear specifically adapted to animal-aided dispersal. This can occur by two processes: direct movement of diaspores by animals and modification of landscape characteristics by animals in ways that greatly influence dispersal. We exploited the production of large, persistent dispersal structures (seed heads, henceforth) by Erodiophyllum elderi (Asteraceae), a daisy from arid Australia, to further understand secondary dispersal. Seed head dispersal on and off animal tracks in eight E. elderi patches was monitored for 9.5 months by periodically recording the location of marked seed heads. Sites were located inside a reserve that excludes sheep but not kangaroos, and in a nearby area with both kangaroos and sheep. The distance moved and likelihood of seed head movement was higher in areas with sheep, and especially along animal tracks. There was clear evidence that seed heads were channeled down animal tracks during large rainfall events. Seed head dispersal away from patches occurred to a limited extent via their physical contact with sheep and potentially via wind dispersal. Thus, the advantages of this study system allowed us to demonstrate the two postulated effects of herbivores on dispersal via direct movement of seed heads, and two distinct indirect effects through landscape modification by herbivores from the creation of animal tracks and the denudation of vegetation.

†Background and Aims Foliar variegation is recognized as arising from two major mechanisms: leaf structure and pigment-related variegation. Begonia has species with a variety of natural foliar variegation patterns, providing diverse examples of this phenomenon. The aims of this work are to elucidate the mechanisms underlying different foliar variegation patterns in Begonia and to determine their physiological consequences. †Methods Six species and one cultivar of Begonia were investigated. Light and electron microscopy revealed the leaf structure and ultrastructure of chloroplasts in green and light areas of variegated leaves. Maximum quantum yields of photosystem II were measured by chlorophyll fluorescence. Comparison with a cultivar of Ficus revealed key features distinguishing variegation mechanisms. †Key Results Intercellular space above the chlorenchyma is the mechanism of variegation in these Begonia. This intercellular space can be located (a) below the adaxial epidermis or (b) below the adaxial water storage tissue (the first report for any taxa), creating light areas on a leaf. In addition, chlorenchyma cell shape and chloroplast distribution within chlorenchyma cells differ between light and green areas. Chloroplasts from both areas showed dense stacking of grana and stromathylakoid membranes. The maximum quantum yield did not differ significantly between these areas, suggesting minimal loss of function with variegation. However, the absence of chloroplasts in light areas of leaves in the Ficus cultivar led to an extremely low quantum yield. †Conclusions Variegation in these Begonia is structural, where light areas are created by internal reflection between air spaces and cells in a leaf. Two forms of air space structural variegation occur, distinguished by the location of the air spaces. Both forms may have a common origin in development where dermal tissue becomes loosely connected to mesophyll. Photosynthetic functioning is retained in light areas, and these areas do not include primary veins, potentially limiting the costs of variegation.

We modify the commonly used invasibility concept for coexistence of species to the stronger concept of uniform invasibility. For two-species discrete-time competition and predator-prey models, we use this concept to find broad easily checked sufficient conditions for the rigorous concept of permanent coexistence. With these results, permanent coexistence becomes a tractable concept for many discrete-time population models. To understand how these conditions apply to nonpoint attractors, we generalize the concept of relative nonlinearity and use it to show how population fluctuations affect the long-term low-density growth rate ("the invasion rate") of a species when it is invading the system consisting of the other species ("the resident") at a single-species attractor. The concept of relative nonlinearity defines circumstances when this invasion rate is increased or decreased by resident population fluctuations arising from a nonpoint attractor. The presence and sign of relative nonlinearity is easily checked in models of interacting species. When relative nonlinearity is zero or positive, fluctuations cannot decrease the invasion rate. It follows that permanence is then determined by invasibility of the resident's fixed points. However, when relative nonlinearity is negative, invasibility, and hence permanent coexistence, can be undermined by resident population fluctuations. These results are illustrated with specific two-species competition and predator-prey models of generic forms.

How biological diversity is generated and maintained is a fundamental question in ecology. Ecologists have delineated many mechanisms that can, in principle, favor species coexistence and hence maintain biodiversity. Most such coexistence mechanisms require or imply tradeoffs between different aspects of species performance. However, it remains unknown whether simple functional tradeoffs underlie coexistence mechanisms in diverse natural systems. We show that functional tradeoffs explain species differences in long-term population dynamics that are associated with recovery from low density (and hence coexistence) for a community of winter annual plants in the Sonoran Desert. We develop a new general framework for quantifying the magnitude of coexistence via the storage effect and use this framework to assess the strength of the storage effect in the winter annual community. We then combine a 25-year record of vital rates with morphological and physiological measurements to identify functional differences between species in the growth and reproductive phase of the life cycle that promote storage-effect coexistence. Separation of species along a tradeoff between growth capacity and low-resource tolerance corresponds to differences in demographic responses to environmental variation across years. Growing season precipitation is one critical environmental variable underlying the demographic decoupling of species. These results demonstrate how partially decoupled population dynamics that promote local biodiversity are associated with physiological differences in resource uptake and allocation between species. These results for a relatively simple system demonstrate how long-term community dynamics relate to functional biology, a linkage scientists have long sought for more complex systems.

We investigate the effects of disturbance on species coexistence using a general mathematical model. The model can be applied to a variety of communities, and we show how it applies in particular to communities of shrubs in Mediterranean heathlands. Our analysis demonstrates that when species have distinct fire response strategies, disturbance allows for stable species coexistence. Furthermore, we show how the size of the coexistence region depends on fire frequency and dispersal ability. The stabilizing mechanism is classified as the spatial storage effect, which is identified by the covariance between environmental and competitive responses. This is the first time that disturbance, defined as a fluctuating mortality factor, has been definitively shown to promote coexistence via the storage effect. Moreover, we show that the biological driver is a trade-off between resistance and resilience to disturbance. The resistance-resilience trade-off is a biological mechanism of coexistence under patchy disturbance. However, the resistance-resilience trade-off has not previously featured in mathematical models of species coexistence. Although the storage effect depends on fluctuations in life-history parameters presumed to result from environmental variation, rarely are life-history parameters explicitly linked to environmental phenomena. Here the link is clear and concrete, allowing better definition of the intended application.

We investigate the effect of seed predation on the coexistence of competing annual plants. We demonstrate a role for predation that is opposite to the conventional wisdom that predation promotes coexistence by reducing the intensity of competition. In the common situation where competitive coexistence involves intraspecific competition exceeding interspecific competition, predation can undermine coexistence by reducing the overall magnitude of competition, replacing competition with "apparent competition" in a way that does not lead to differential intraspecific and interspecific effects. We demonstrate this outcome in the case where coexistence occurs by "the storage effect" in a variable environment. The storage effect arises when the environment interacts with competition to create opportunities for species to increase from low density. Critical to the storage effect is positive covariance between the response of population growth to the environment and its response to competition, when a species is at high density. This outcome prevents species at high density from taking advantage of favorable environmental conditions. A species at low density has lower covariance and can take advantage of favorable environmental conditions, giving it an advantage over a high-density species, fostering its recovery from low density. Hence, species coexistence is promoted. Here we find that density-dependent predation lowers population densities, and so weakens competition, replacing competition with apparent competition, which does not covary with the environment. As a consequence, covariance between environment and competition is weakened, reducing the advantage to a species at low density. The species still strongly interact through the combination of competition and apparent competition, but the reduced low-density advantage reduces their ability to coexist. Although this result is demonstrated specifically for the storage effect with a focus on annual plant communities, the principles involved are general ones.

Understanding how interactions between species contributes to the maintenance of species diversity is a fundamental question in ecology. New theoretical results presented by Peter Chesson and Jessica Kuang highlight the mutually interdependent roles of predation and competition in governing coexistence. They find that each mechanism can promote diversity through diverse relationships with the particular species, or limit diversity through narrow relationships that pit certain species against each other. Each mechanism can also undercut the effects of the other, or work together promoting diversity, depending on the circumstances. Competition and predation are the most heavily investigated species interactions in ecology, dominating studies of species diversity maintenance. However, these two interactions are most commonly viewed highly asymmetrically. Competition for resources is seen as the primary interaction limiting diversity, with predation modifying what competition does1, although theoretical models have long supported diverse views1,2,3,4,5. Here we show, using a comprehensive three-trophic-level model, that competition and predation should be viewed symmetrically: these two interactions are equally able to either limit or promote diversity. Diversity maintenance requires within-species density feedback loops to be stronger than between-species feedback loops. We quantify the contributions of predation and competition to these loops in a simple, interpretable form, showing their equivalent potential to strengthen or weaken diversity maintenance. Moreover, we show that competition and predation can undermine each other, with the tendency of the stronger interaction to promote or limit diversity prevailing. The past failure to appreciate the symmetrical effects and interactions of competition and predation has unduly restricted diversity maintenance studies. A multitrophic perspective should be adopted to examine a greater variety of possible effects of predation than generally considered in the past. Conservation and management strategies need to be much more concerned with the implications of changes in the strengths of trophic interactions.

We studied the germination of seeds of Carrichtera annua L. from a single cohort, stored in the field for up to 18 months, when retrieved at different times and subject to different combinations of temperature and water availability. Germination was affected by season of retrieval, and temperature and water availability in a complex interactive way. Germination rates were lowest when seeds were retrieved during summer or spring, but seeds germinated readily when retrieved during autumn and winter, if exposed to temperatures simulating autumn or winter conditions, and provided water equivalent to at least 50% field capacity. High temperatures and low water availability reduced germination substantially. The results indicate that this species has a combination of cyclic dormancy and germination requirements that minimizes the risk of germination during periods when the risk of prereproductive mortality is high. Given the short life of the seeds of this species, these mechanisms may be essential for the persistence of the species in the highly unpredictable arid lands of southern Australia.

We investigate the interacting effects of predation and competition on species coexistence in a model of seasonally recruiting species in a constant environment. For these species, life-history parameters, such as maximum productivity and survival, have important roles in fluctuation-dependent species coexistence in that they introduce nonlinearities into population growth rates and cause endogenous population fluctuations, which can activate the coexistence mechanism termed "relative nonlinearity." Under this mechanism, different species must differ in the nonlinearities of their growth rates and must make different contributions to fluctuations in competition and predation. Both of these features can result from life-history trade-offs associated with seasonal recruitment. Coexistence by relative nonlinearity can occur with or without predation. However, predation can undermine coexistence. It does this by reducing variance contrasts between species. However, when competition is not sufficient to cause endogenous population fluctuations, predation can enable fluctuation-dependent coexistence by destabilizing the equilibrium. This model also reproduces the classic finding that coexistence can occur with selective predation provided that it causes a trade-off between competition and predation. Our model is formulated for competition between annual plant species subject to seed predation, but it also applies to perennial communities where competition and predation limit recruitment to the adult population.

Recent theory supports the long-held proposition that coexistence is promoted by species-specific responses to a spatially varying environment. The underlying coexistence mechanism, the spatial storage effect, can be quantified by the covariance between response to the environment and competition. Here, "competition" is generalized to encompass similar processes such as facilitation and apparent competition. In the present study, we use a model field system of desert annual plants to demonstrate this method and to provide insight into the dynamics of the field system. Specifically, we use neighborhood competition experiments to quantify the spatial storage effect and compare it to the separate (but not mutually exclusive) process of neighborhood-scale resource partitioning. As our basic experimental design has been used frequently in community ecology, these methods can be applied to many existing data sets, as well as future field studies.

The overarching issue for understanding biodiversity maintenance is how fitness advantages accrue to a species as it becomes rare, as this is the defining feature of stable coexistence mechanisms. Without these fitness advantages, average fitness differences between species will lead to exclusion. However, empirical evidence is lacking, especially for forests, due to the difficulty of manipulating density on a large-enough scale. Here we took advantage of naturally occurring contrasts in abundance between sites of a subtropical tree species, Ormosia glaberrima, to demonstrate how low-density fitness advantages accrue by the Janzen–Connell mechanism. The results showed that soil pathogens suppressed seedling recruitment of O. glaberrima when it is abundant but had little effect on the seedlings when it is at low density due to the lack of pathogens. The difference in seedling survival between abundant and low-density sites demonstrates strong dependence of pathogenic effect on the abundance of host species., Fitness advantages conferred on species living at low density is thought to be one mechanism by which stable biodiversity is maintained. Here, Liu et al. show that recruitment of seedlings in high-density populations of a subtropical tree is suppressed by soil pathogens, with little effect at low-density.

The Janzen-Connell hypothesis states that tree diversity in tropical forests is maintained by specialist predators that are distance- or density-responsive (i.e. predators that reduce seed or seedling survival near adults of their hosts). Many empirical studies have investigated whether predators are distance-responsive; however, few studies have examined whether distance-responsiveness matters for how predators maintain tree diversity. Using a site-occupancy model, we show analytically that distance-responsive predators are actually less able to maintain diversity than specialist predators that are not distance-responsive. Generally, specialist predators maintain diversity because they become rare when their host's densities are low, reducing predation risk. However, if predators are distance-responsive, and most seeds cannot disperse away from these predators, then seed predation rates will remain high, even if predator density is low across the landscape. Consequently, a reduction in a host's population density may not lead to a significant reduction in seed and seedling predation. We show that habitat partitioning can cause recruitment to be highest near conspecific adults, even in the presence of distance-responsive predators, without any change in the effect that the predators have on coexistence (a result contrary to predictions of the Janzen-Connell hypothesis). Rather, specialist predators and habitat partitioning have additive effects on species coexistence in our model, i.e., neither mechanism alters the effect of the other one.

Applying the recent developments of scale transition theory, we demonstrate a systematic approach to the problem of scaling up local scale interactions to regional scale dynamics with field data. Dynamics on larger spatial scales differ from the predictions of local dynamics alone because of an interaction between nonlinearity in population dynamics at the local scale and spatial variation in density and environmental factors over the regional population. Our systematic approach to scaling up involves the following five steps. First, define a model for dynamics on the local spatial scale. Second, apply scale transition theory to identify key interactions between nonlinearity and spatial variation that translate local dynamics to the regional scale. Third, measure local-scale model parameters to determine nonlinearities at local scales. Fourth, measure spatial variation. Finally, combine nonlinearity and variation measures to obtain the scale transition. Using field data for the dynamics of grazers and periphyton in a freshwater stream, we show that scale transition terms greatly reduce the growth and equilibrium density of the periphyton population at the stream scale compared to rock scale populations, confirming the importance of spatial mechanisms to stream-scale dynamics.