Movement analogies are often employed by ecologists to describe how ecological dynamics relate to one another. For instance, two communities whose similarity increases in time may be said to converge. Here we argue that the movement analogies used by ecologists to compare ecological dynamics could be enriched with other notions such as “pursuit” or “parallel” movements, if accompanied by appropriate statistical testing. By building on the framework of Ecological Trajectory Analysis, we present here Relative Trajectory Movement Assessment (RTMA), a framework to detect and qualify relative movements in ecological dynamics defined as trajectories in multivariate space. Using synthetic trajectory data, we illustrate how RTMA can reveal a diverse range of relative movements beyond the convergence and divergence patterns already recognized in ecology. We exemplify the use of RTMA on real ecological datasets describing 1) old field successional dynamics in eastern North America and 2) temporal patterns in tree size structure of a New Zealand forest. RTMA provides ecologists with a new way of describing and comparing ecological dynamics that could be widely applied, from plot-scale dynamics to the effects of global change.

Abstract As succession proceeds, theory predicts increasingly asynchronous dynamics among species, thereby enhancing community temporal stability. However, recent studies often report decreased species asynchrony in older communities, and it remains unclear whether these successional changes in asynchrony reflect ecological processes or statistical mechanisms. Using a 60‐year vegetation time series from the Buell–Small Succession Study, we quantified temporal changes in species asynchrony during old‐field succession. We then decomposed species asynchrony into compensatory effects ( CPE ) and statistical‐averaging effects ( SAE ) to assess the relative importance of these components. We further examined how CPE and SAE are related to species richness and whether these relationships shift through time. We show that the long‐term decline in species asynchrony over succession was jointly explained by decreases in both CPE and SAE . SAE consistently accounted for a larger proportion of species asynchrony, but CPE declined more strongly over succession and therefore contributed more to the overall decline in species asynchrony. We further show that SAE , but not CPE , consistently increased with species richness at all stages, indicating that losses of diversity in later successional stages were associated with lower SAE . Consequently, both the direct decline in CPE and the indirect decline in SAE via decreased richness contributed to the observed decrease in species asynchrony over succession. Synthesis . Our results provide clear evidence that both the compensatory dynamics and statistical‐averaging mechanisms contribute to long‐term decreases in species asynchrony during succession, and that the stabilizing role of diversity is largely linked to statistical averaging. These insights refine classical views of successional dynamics and deepen our understanding of how biodiversity–stability relationships unfold over time.

Improved yields can occur in closely related cultivar mixtures. Despite increasing knowledge of the benefits of neighbour-relatedness in intraspecific interactions, little is known about chemically and microbially mediated kinship responses in cultivar mixtures. Using a series of field and controlled experiments that used two sets of rice cultivars of varying genetic relatedness, we demonstrated that increased yield in rice cultivar mixtures was mediated by a root signaling chemical and soil microbes in a relatedness-dependent manner. Focal rice cultivars could discriminate closely from distantly related cultivars responded by altering root behavior, biomass allocation, and flowering time, improving grain yield. Relatedness discrimination was accompanied by an alteration in root signaling (-)-loliolide and, subsequently, the soil microbial community. Furthermore, (-)-loliolide directly modified soil microbes that were related to flowering time and seed biomass. Therefore, neighbor relatedness shapes soil microbial communities, generating kinship effects in rice cultivar mixtures. In particular, root signaling (-)-loliolide levels and soil microbial responses generated improvement of grain yield in closely related rice cultivar mixtures. The findings not only yield critical insights into plant-neighbor and plant-soil interactions but also raise an intriguing possibility to increase crop production by manipulating kinship in cultivar mixtures.

Production of biofuels and bioproducts from lignocellulosic material is limited due to the complexity of the cell wall structure. This necessitates the use of physical, chemical, and/or physico-chemical pretreatment technologies, which adds significant capital, operational, and environmental costs. Biological pretreatment strategies have the potential to mitigate these expenses by harnessing the innate ability of specialized bacteria and fungi to deconstruct lignocellulose. White-rot fungi (e.g. Trametes versicolor) have been shown to be effective at biological pretreatment of lignocellulose, yet it was uncertain if these fungi are feedstock agnostic or are able to sense subtle changes in cell wall chemistry. The present study examined the transcriptome response by Trametes versicolor to transgenic hybrid poplar (Populus tremula × alba) lines with altered syringyl (S) and guaiacyl (G) lignin. Specifically, the transcriptional response of the fungus to wild-type wood was compared to that from the wood of six transgenic lines within three lignin phenotypes, LSX (low S with hydroxy-G), LSHG (low S with high G), and HS (high S), with 350 transcripts showing significant differences among the samples. The transcriptome of T. versicolor varied according to the lignin phenotype of the wood, with the LSX wood resulting in the most substantial changes in T. versicolor transcript abundance. Specifically, the LSX wood led to 50 upregulated and 48 downregulated transcripts from WT at the twofold or greater threshold. For example, transcripts for the lignin peroxidases LiP3 and LiP10 were downregulated (approximately 12X and 31X lower, respectively) by the fungus on LSX wood compared to wild-type wood. LSX wood also resulted in approximately 11X lower transcript numbers of endo-β-1,4-glucanase yet led to an increase in expression of certain hemicellulases, further highlighting the altered deconstruction strategy by the fungus on this wood type. Overall, the results of this study demonstrated that T. versicolor was able to respond to transgenic poplar wood with the same genetic background, which has important implications for biological pretreatment strategies involving feedstocks that are genetically modified or have considerable natural variations in cell wall chemistry.

Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small “many analyst” study found similar variability in ecology. We expanded the scope of this prior work by implementing a large-scale empirical exploration of the variation in effect sizes and model predictions generated by the analytical decisions of different researchers in ecology and evolutionary biology. We used two unpublished datasets, one from evolutionary ecology (blue tit, Cyanistes caeruleus, to compare sibling number and nestling growth) and one from conservation ecology (Eucalyptus, to compare grass cover and tree seedling recruitment). The project leaders recruited 174 analyst teams, comprising 246 analysts, to investigate the answers to prespecified research questions. Analyses conducted by these teams yielded 141 usable effects (compatible with our meta-analyses and with all necessary information provided) for the blue tit dataset, and 85 usable effects for the Eucalyptus dataset. We found substantial heterogeneity among results for both datasets, although the patterns of variation differed between them. For the blue tit analyses, the average effect was convincingly negative, with less growth for nestlings living with more siblings, but there was near continuous variation in effect size from large negative effects to effects near zero, and even effects crossing the traditional threshold of statistical significance in the opposite direction. In contrast, the average relationship between grass cover and Eucalyptus seedling number was only slightly negative and not convincingly different from zero, and most effects ranged from weakly negative to weakly positive, with about a third of effects crossing the traditional threshold of significance in one direction or the other. However, there were also several striking outliers in the Eucalyptus dataset, with effects far from zero. For both datasets, we found substantial variation in the variable selection and random effects structures among analyses, as well as in the ratings of the analytical methods by peer reviewers, but we found no strong relationship between any of these and deviation from the meta-analytic mean. In other words, analyses with results that were far from the mean were no more or less likely to have dissimilar variable sets, use random effects in their models, or receive poor peer reviews than those analyses that found results that were close to the mean. The existence of substantial variability among analysis outcomes raises important questions about how ecologists and evolutionary biologists should interpret published results, and how they should conduct analyses in the future.

The Lotka-Volterra competition model is the foundation of many ecological theories including competitive exclusion principle, limiting similarity and modern coexistence theory. However, competition between species is often modelled phenomenologically without explicitly considering the underlying mechanisms (e.g. resource competition with various resource supply forms and resource types). Deriving phenomenological models from the first principles and linking parameters in phenomenological models to the mechanisms of competition are critical to advance our understanding of population dynamics and community assembly.Here, we used time-scale separation to theoretically derive phenomenological competition models from mechanistic consumer-resource models with different resource supply forms (logistic and chemostatic) and resource types (substitutable and essential). We then compared the performance of the resulting phenomenological models with simulation experiments and observational plant dynamic data during 50 years of succession. We further explored how the resource supply ratio such as nutrient imbalance induced by human activities affected the critical parameters, including species' intrinsic growth rate and interaction strength in phenomenological models and consequently the population dynamics.We found that consumer population dynamics can be described by the Lotka-Volterra competition model when consumers are competing for substitutable or essential resources under logistic supply. In contrast, a novel reciprocal model was derived when consumers are competing for essential resources under chemostatic supply. Results from simulation experiments supported the model derivations. We also found that the reciprocal model outperformed the Lotka-Volterra model in explaining and predicting the population growth of 90 herbaceous plants during 50 years of succession. Moreover, the resource supply ratio affected species' intrinsic growth rates and competitive strengths differently under various resource supply forms and resource types and thus determined competitive outcomes.Synthesis. Our study provides an alternative model (reciprocal model) when organisms compete for essential resources under chemostatic supply and sets up a basis for the selection of phenomenological competition models through the lens of ecological processes and contributes to a more accurate prediction of population dynamics, especially those driven by human-induced nutrient imbalance. By linking phenomenological and mechanistic competition models, this study provides an alternative model (reciprocal model) when organisms compete for essential resources under chemostatic supply and sets up a basis for the selection of phenomenological competition models through the lens of ecological processes and contributes to a more accurate prediction of population dynamics, especially those driven by human-induced nutrient imbalance.image

The improvement of performance and yield in both cultivar and species mixtures has been well established. Despite the clear benefits of crop mixtures to agriculture, identifying the critical mechanisms behind performance increases are largely lacking. We experimentally demonstrated that the benefits of rice cultivar mixtures were linked to relatedness-mediated intraspecific neighbour recognition and discrimination under both field and controlled conditions. We then tested biochemical mechanisms of responses in incubation experiments involving the addition of root exudates and a root-secreted signal, (-)-loliolide, followed by transcriptome analysis. We found that closely related cultivar mixtures increased grain yields by modifying root behaviour and accelerating flowering over distantly related mixtures. Importantly, these responses were accompanied by altered concentration of signalling (-)-loliolide that affected rice transcriptome profiling, directly regulating root growth and flowering gene expression. These findings suggest that beneficial crop combinations may be generated a-priori by manipulating neighbour genetic relatedness in rice cultivar mixtures and that root-secreted (-)-loliolide functions as a key mediator of genetic relatedness interactions. The ability of relatedness discrimination to regulate rice flowering and yield raises an intriguing possibility to increase crop production.

What drives the composition of invaded communities and the local abundance of introduced species are key questions in ecology. Community-assembly theory provides a useful framework for addressing these questions. Specifically, the environmental filtering model of community assembly predicts that a species' presence and abundance in a community depend on the interaction between its functional traits and the local environmental filters. However, for introduced species, larger-scale dispersal and introduction-related filters may restrict their regional trait pool. Here, we tested this framework using long-term data from 50+ years of old-field vegetation succession. We asked whether native and introduced plant assemblages followed the same trait-based assembly rules. We also asked whether local functional dissimilarities between the two can be explained by regional species pool differences, a possibility that has rarely been addressed. We found strong similarities in the assembly processes of native and introduced plants. Average height and seed mass of both groups increased over time, consistent with previous studies of old-field succession. Moreover, the two showed similar trait-abundance relationships. While there were also some differences, particularly in their trait-incidence relationships, these differences appeared to be minor. Furthermore, we identified species pool constraints on introduced species and found that the exotic species pool was biased towards early successional traits. Lastly, we found that highly invasive exotic species were also likely to deviate from the expected trait-abundance relationship, suggesting a link between the two. These results imply that introduced species generally follow the same assembly rules as native species. They also indicate that species pool differences can result in local functional composition differences, even when the two groups follow the same assembly rules. Moreover, there may be a link between species invasiveness and deviation from assembly rules, which, if further confirmed, provides a potential method of identifying strong invaders. Synthesis: Using data from a long-term succession study, we showed several similarities, and some differences, in the assembly of native and introduced species assemblages. Our results provide a better understanding of the factors constraining and allowing invasion, and help in the identification of 'rule breaking' invaders. Using data from a long-term successional study, the authors found that introduced plant species generally followed the same trait-based assembly rules as native species, but were limited by lower species pool variation. However, highly invasive species were likely to deviate from the trait-abundance relationship shown by the rest of the community, suggesting a link between invasiveness and 'breaking' assembly rules.image

In many regions, the climate is changing faster during winter than during the other seasons, and a loss of snow cover combined with increased temperature variability can expose overwintering organisms to harmful conditions. Understanding how species respond to these changes during critical developmental times, such as seed germination, helps us assess the ecological implications of winter climate change. To address this concern, we measured the breaking of seed dormancy and cold tolerance of temperate grassland species in the lab and field. In the lab, we ran germination trials testing the tolerance of 17 species to an extreme cold event. In the field, we deployed seeds of two species within a snow manipulation experiment at three locations and measured germination success biweekly from seeds subjected to ambient and reduced snow cover from winter into spring. From lab trials, cold tolerance varied among species, with seed germination decreasing <10%-100% following extreme cold events. Cold tolerance was related to seed traits, specifically less round seeds, seeds that required cold stratification, and seeds that mature later in the season tended to be more impacted by extreme cold temperatures. This variation in seed cold tolerance may contribute to altered community composition with continued winter climate change. In the field, germination increased through late winter, coinciding with the accumulation of days where temperatures were favorable for cold stratification. Through spring, germination success decreased as warm temperatures accumulated. Collectively, species-specific seed cold tolerances and mortality rates may contribute to compositional changes in grasslands under continued winter climate change.

Grime's competitive, stress-tolerant, ruderal (CSR) theory predicts a shift in plant communities from ruderal to stress-tolerant strategies during secondary succession. However, this fundamental tenet lacks empirical validation using long-term continuous successional data. Utilizing a 60-year longitudinal data of old-field succession, we investigated the community-level dynamics of plant strategies over time. Our findings reveal that while plant communities generally transitioned from ruderal to stress-tolerant strategies during succession, initial abandonment conditions crucially shaped early successional strategies, leading to varied strategy trajectories across different fields. Furthermore, we found a notable divergence in the CSR strategies of alien and native species over succession. Initially, alien and native species exhibited similar ruderal strategies, but in later stages, alien species exhibited higher ruderal and lower stress tolerance compared to native species. Overall, our findings underscore the applicability of Grime's predictions regarding temporal shifts in CSR strategies depending on both initial community conditions and species origin.

Most oak savannas in the Midwestern United States have been lost to agriculture and habitat degradation. Because of their rarity and high plant and animal diversity, savannas are often a target for restoration, which frequently relies on the direct planting of oak seedlings to establish the necessary canopy. Returning fire to the system is critical to the herbaceous component, but with planted seedlings, managers risk damaging or killing trees if burning is introduced too soon. We studied the growth and physiological responses of three oak species ( Quercus alba , Quercus macrocarpa , and Quercus velutina ) to prescribed fire to determine impacts on planted trees. This study utilized two restored oak savanna units that were planted in 1995 and 1998, each with burned and unburned areas. We tracked trees ranging from 0.9 to 29.8 cm in diameter at breast height (DBH) to determine the size threshold above which top kill is unlikely and documented differences in leaf structure and extension growth between the burned and unburned areas. There was no mortality observed. Moreover, no trees larger than 4 cm DBH were top killed by the fire. Fire responses in leaf mass per unit area and chlorophyll content were small and inconsistent across species. However, all oak species grew more in burned areas than trees in adjacent unburned areas. Therefore, the addition of low‐intensity prescribed fire to an oak savanna planting may increase the growth rate of planted trees with minimal risk of mortality once trees have reached sufficient size.

PREMISE:Intraspecific variation may play a key role in shaping the relationships between plants and their interactions with soil microbial communities. The soil microbes of individual plants can generate intraspecific variation in the responsiveness of the plant offspring, yet have been much less studied. To address this need, we explored how the relatedness of seedlings from established clones of Solidago altissima altered the plant-soil interactions of the seedlings. METHODS:Seedlings of known parentage were generated from a series of 24 clones grown in a common garden. Seedlings from these crosses were inoculated with soils from maternal, paternal, or unrelated clones and their performance compared to sterilized control inocula. RESULTS:We found that soil inocula influenced by S. altissima clones had an overall negative effect on seedling biomass. Furthermore, seedlings inoculated with maternal or paternal soils tended to experience larger negative effects than seedlings inoculated with unrelated soils. However, there was much variation among individual crosses, with not all responding to relatedness. CONCLUSIONS:Our data argue that genetic relatedness to the plant from which the soil microbial inoculum was obtained may cause differential impacts on establishing seedlings, encouraging the regeneration of non-kin adjacent to established clones. Such intraspecific variation represents a potentially important source of heterogeneity in plant-soil microbe interactions with implications for maintaining population genetic diversity.

The study of plant-microbe interactions has become a foundational research focus of plant ecology. A recurring issue for this area is whether soil pooling introduces bias when quantifying the local soil microbial interactions experienced by plants. To address this issue, we exposed nine herbaceous species to field-collected soil inocula that were either pooled or kept separate in a greenhouse study with autoclaved controls. We determined whether pooling altered the strength, direction, or variance of plant-microbe impacts on plant growth and whether pooling changed which species were most responsive to soil microbes. Sample pooling, compared to individual samples, significantly altered the strength of plant-microbe interactions in four of nine herbaceous species, but the direction of the effect varied. Pooling reduced microbial inhibition of growth in two species, reversed the direction from negative to positive in another, and generated a positive interaction in the fourth. The patterns of microbial impacts on growth across species were strongly altered, leading to no correlation between results generated by pooled and unpooled soils. Contrary to expectations, variances were typically higher in pooled soils. These differences nearly disappeared in autoclaved soils, suggesting soil microbes as the driving factor. While neither universal nor predictable, sample pooling to generate experimental inocula altered the strength, direction, and variance of microbial impacts on plant growth in several species. This effect occurred often enough that researchers must carefully weigh whether pooled samples are appropriate in addressing their research questions.

Despite the growing number of dam removals, very few have been studied to understand their impacts on stream fish communities. An even smaller proportion of dam removal studies focus on the impacts of low-head dam removals, although they are the most common type of dam. Instead, the majority of removal studies focus on the impacts of larger dams. In this study, two previously impounded Illinois rivers were monitored to assess the impacts of low-head dam removal on the functional assemblage of stream fishes. Study sites were sampled each fall from 2012-2015 (pre-dam removal) and 2018-2020 (post-dam removal) in three habitat types: downstream of the dam, impounded areas, and runs of rivers. Fishes were aggregated into habitat and reproductive guilds, relating community changes to habitat, environmental metrics, and stream quality. Prior to removal, the slackwater guild was the most prevalent habitat guild throughout both rivers, while nest builders and benthic spawners were the most abundant reproductive guilds. During the two years following removal, habitat conditions and fish assemblages improved throughout both rivers, with improvements in QHEI, IBI, water temperature, and dissolved oxygen, as well as a shift to more evenly distributed representation of habitat and reproductive guilds. The improvements in environmental metrics and overall stream quality, particularly in the formerly impounded habitats, indicate diminished habitat homogeneity, and a shift towards natural habitat diversity. This habitat diversification likely led to the restoration of a range of potential niches, thereby increasing the array of guild types inhabiting these rivers, while simultaneously preventing single-guild dominance.

A widely assumed, but largely untested, tenet in ecology is that ecosystem stability tends to increase over succession. We rigorously test this idea using 60-year continuous data of old field succession across 480 plots nested within 10 fields. We found that ecosystem temporal stability increased over succession at the larger field scale (γ stability) but not at the local plot scale (α stability). Increased spatial asynchrony among plots within fields increased γ stability, while temporal increases in species stability and decreases in species asynchrony offset each other, resulting in no increase in α stability at the local scale. Furthermore, we found a notable positive diversity-stability relationship at the larger but not local scale, with the increased γ stability at the larger scale associated with increasing functional diversity later in succession. Our results emphasize the importance of spatial scale in assessing ecosystem stability over time and how it relates to biodiversity.

The production of defensive metabolites in plants can be induced by signaling chemicals released by neighboring plants. Induction is mainly known from volatile aboveground signals, with belowground signals and their underlying mechanisms largely unknown. We demonstrate that (-)-loliolide triggers defensive metabolite responses to competitors, herbivores, and pathogens in seven plant species. We further explore the transcriptional responses of defensive pathways to verify the signaling role of (-)-loliolide in wheat and rice models with well-known defensive metabolites and gene systems. In response to biotic and abiotic stressors, (-)-loliolide is produced and secreted by roots. This, in turn, induces the production of defensive compounds including phenolic acids, flavonoids, terpenoids, alkaloids, benzoxazinoids, and cyanogenic glycosides, regardless of plant species. (-)-Loliolide also triggers the expression of defense-related genes, accompanied by an increase in the concentration of jasmonic acid and hydrogen peroxide (H2O2). Transcriptome profiling and inhibitor incubation indicate that (-)-loliolide-induced defense responses are regulated through pathways mediated by jasmonic acid, H2O2, and Ca (2+). These findings argue that (-)-loliolide functions as a common belowground signal mediating chemical defense in plants. Such perception-dependent plant chemical defenses will yield critical insights into belowground signaling interactions.

Plants actively respond to their neighbors by altering root placement patterns. Neighbor-modulated root responses involve root detection and interactions mediated by root-secreted functional metabolites. However, chemically mediated root placement patterns and their underlying mechanisms remain elusive.We used an allelopathic wheat model system challenged with 60 target species to identify root placement responses in window rhizobox experiments. We then tested root responses and their biochemical mechanisms in incubation experiments involving the addition of activated carbon and functional metabolites with amyloplast staining and auxin localization in roots.Wheat and each target species demonstrated intrusive, avoidant or unresponsive root placement, resulting in a total of nine combined patterns. Root placement patterns were mediated by wheat allelochemicals and (-)-loliolide signaling of neighbor species. In particular, (-)-loliolide triggered wheat allelochemical production that altered root growth and placement, degraded starch grains in the root cap and induced uneven distribution of auxin in target species roots.Root placement patterns in wheat-neighbor interactions were perception dependent and species dependent. Signaling (-)-loliolide induced the production and release of wheat allelochemicals that modulated root placement patterns. Therefore, root placement patterns are generated by both signaling chemicals and allelochemicals in allelopathic plant-plant interactions.