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1. A quantitative approach to species coexistence based on the invasibility criterion has led to an appreciation of coexistence mechanisms in terms of stabilizing and equalizing components, but major challenges are the need to consider general multispecies settings, interactions beyond competition, and multiple scales of space and time. Moreover, two essential concepts, species-level average fitness and scaling factors, have not had clear definitions. 2. A general approach to defining average fitnesses and scaling factors is given, along with the origin of stabilizing mechanisms as deviations from a reference model where no coexistence is possible. Illustrations are general Lotka-Volterra models, models accounting specifically for resource use and natural enemies, and models with temporal fluctuations. 3. Community averages of stabilizing mechanisms reveal overall opportunities for coexistence, and define mechanisms more precisely through their formulae. Average fitnesses adjusted for the presence of coexistence mechanisms provide a better definition of equalizing mechanisms. While these ideas apply to the components of invasion rates, permanence theory and stochastic persistence theory show how invasion rates can be used to demonstrate species coexistence in complex settings. 4. Although species coexistence has often focused on competition, detailed models of the roles of natural enemies provide a new perspective on the opportunities for coexistence in nature. The concept of apparent competition recognizes the essential symmetry between density-dependence from resource depletion and from supporting natural enemies. Natural enemy partitioning is the natural analogue of resource partitioning and has an equivalent role in promoting coexistence. Rather than reinforcing each other, however, the strength of coexistence is often intermediate between that implied by resource partitioning alone and that implied by natural enemy partitioning alone, as elucidated by recent LotkaVolterra theory. 5. Synthesis. Although there are alternative approaches for understanding coexistence in multispecies settings, ideas based on stabilizing and equalizing mechanisms continue to provide new insights. Multiple species and multiple trophic levels are naturally challenging, but the new theories of permanence and stochastic persistence support the critical role of invasion rates in species coexistence, and thus support the understanding to be derived by partitioning invasion rates into average fitness differences and stabilizing components.

Locally, plant species richness supports many ecosystem functions. Yet, the mechanisms driving these often-positive biodiversity-ecosystem functioning relationships are not well understood. Spatial resource partitioning across vertical resource gradients is one of the main hypothesized causes for enhanced ecosystem functioning in more biodiverse grasslands. Spatial resource partitioning occurs if species differ in where they acquire resources and can happen both above- and belowground. However, studies investigating spatial resource partitioning in grasslands provide inconsistent evidence. We present the results of a meta-analysis of 21 data sets from experimental species-richness gradients in grasslands. We test the hypothesis that increasing spatial resource partitioning along vertical resource gradients enhances ecosystem functioning in diverse grassland plant communities above- and belowground. To test this hypothesis, we asked three questions. (1) Does species richness enhance biomass production or community resource uptake across sites? (2) Is there evidence of spatial resource partitioning as indicated by resource tracer uptake and biomass allocation above- and belowground? (3) Is evidence of spatial resource partitioning correlated with increased biomass production or community resource uptake? Although plant species richness enhanced community nitrogen and potassium uptake and biomass production above- and belowground, we found that plant communities did not meet our criteria for spatial resource partitioning, though they did invest in significantly more aboveground biomass in higher canopy layers in mixture relative to monoculture. Furthermore, the extent of spatial resource partitioning across studies was not positively correlated with either biomass production or community resource uptake. Our results suggest that spatial resource partitioning across vertical resource gradients alone does not offer a general explanation for enhanced ecosystem functioning in more diverse temperate grasslands.

• The optimal partitioning theory predicts that plants of a given species acclimate to different environments by allocating a larger proportion of biomass to the organs acquiring the most limiting resource. Are similar patterns found across species adapted to environments with contrasting levels of abiotic stress? • We tested the optimal partitioning theory by analysing how fractional biomass allocation to leaves, stems and roots differed between woody species with different tolerances of shade and drought in plants of different age and size (seedlings to mature trees) using a global dataset including 604 species. • No overarching biomass allocation patterns at different tolerance values across species were found. Biomass allocation varied among functional types as a result of phenological (deciduous vs evergreen broad-leaved species) and broad phylogenetical (angiosperms vs gymnosperms) differences. Furthermore, the direction of biomass allocation responses between tolerant and intolerant species was often opposite to that predicted by the optimal partitioning theory. • We conclude that plant functional type is the major determinant of biomass allocation in woody species. We propose that interactions between plant functional type, ontogeny and species-specific stress tolerance adaptations allow woody species with different shade and drought tolerances to display multiple biomass partitioning strategies.

Elucidating the variation of allocation pattern of ecosystem net primary productivity (NPP) and its underlying mechanisms is critically important for understanding the changes of aboveground and belowground ecosystem functions. Under optimal partitioning theory, plants should allocate more NPP to the organ that acquires the most limiting resource, and this expectation has been widely used to explain and predict NPP allocation under changing precipitation. However, confirmatory evidence for this theory has mostly come from observed spatial variation in the relationship between precipitation and NPP allocation across ecosystems, rather than directly from the influences of changing precipitation on NPP allocation within systems. We performed a 6-yr five-level precipitation manipulation experiment in a semiarid steppe to test whether changes in NPP allocation can be explained by the optimal partitioning theory, and how water requirement of plant community is maintained if NPP allocation is unaltered. The 30 precipitation levels (5 levels × 6 yr) were divided into dry, nominal, and wet precipitation ranges, relative to historical precipitation variation over the past six decades. We found that NPP in both aboveground (ANPP) and belowground (BNPP) increased nonlinearly as precipitation increased, while the allocation of NPP to BNPP (f BNPP) showed a concave quadratic relationship with precipitation. The declined f BNPP as precipitation increased in the dry range supported the optimal partitioning theory. However, in the nominal range, NPP allocation was not influenced by the changed precipitation; instead, BNPP was distributed more in the surface soil horizon (0–10 cm) as precipitation increased, and conversely more in the deeper soil layers (10–30 cm) as precipitation decreased. This response in root foraging appears to be a strategy to satisfy plant water requirements and partially explains the stable NPP allocation patterns. Overall, our results suggest that plants can adjust their vertical BNPP distribution in response to drought stress, and that only under extreme drought does the optimal partitioning theory strictly apply, highlighting the context dependency of the adaption and growth of plants under changing precipitation.

Ecological niche differences are necessary for stable species coexistence but are often difficult to discern. Models of dietary niche differentiation in large mammalian herbivores invoke the quality, quantity, and spatiotemporal distribution of plant tissues and growth forms but are agnostic toward food plant species identity. Empirical support for these models is variable, suggesting that additional mechanisms of resource partitioning may be important in sustaining large-herbivore diversity in African savannas. We used DNA metabarcoding to conduct a taxonomically explicit analysis of large-herbivore diets across southeastern Africa, analyzing ∼4,000 fecal samples of 30 species from 10 sites in seven countries over 6 y. We detected 893 food plant taxa from 124 families, but just two families—grasses and legumes—accounted for the majority of herbivore diets. Nonetheless, herbivore species almost invariably partitioned food plant taxa; diet composition differed significantly in 97% of pairwise comparisons between sympatric species, and dissimilarity was pronounced even between the strictest grazers (grass eaters), strictest browsers (nongrass eaters), and closest relatives at each site. Niche differentiation was weakest in an ecosystem recovering from catastrophic defaunation, indicating that food plant partitioning is driven by species interactions, and was stronger at low rainfall, as expected if interspecific competition is a predominant driver. Diets differed more between browsers than grazers, which predictably shaped community organization: Grazer-dominated trophic networks had higher nestedness and lower modularity. That dietary differentiation is structured along taxonomic lines complements prior work on how herbivores partition plant parts and patches and suggests that common mechanisms govern herbivore coexistence and community assembly in savannas.

Background Biomass allocation reflects functional tradeoffs among plant organs and thus represents life history strategies. However, little is known about the patterns and drivers of biomass allocation between reproductive and vegetative organs along large environmental gradients. Here, we examined how environmental gradients affect biomass and the allocation between reproductive and vegetative organs. We also tested whether the allocation patterns conform optimal or allometric partitioning theory. Methods We collected 22 Artemisia species along a large environmental gradient in China and measured reproductive (infructescences including seeds) and vegetative (leaves, stems and roots) mass for each plant. We then used standardized major axes regressions to quantify the relationships between reproductive and vegetative organs and linear mixed-effect models to examine the effect of environmental gradients (climate and soil) on biomass allocation patterns. Results We found significant negative correlations between total biomass of Artemisia and the first principal component of climate, an axis that was negatively correlated with temperature and precipitation. Overall, there were significant isometric relationships between reproductive and vegetative mass. In addition, the ratio of reproductive to vegetative mass increased with the second principal component of climate (representing climate variability), but decreased with the second principal component of soil (representing bulk density and available water capacity). These patterns were consistent at the individual and interspecific levels, but were mixed at the intraspecific level. Conclusions Our findings of the plastic responses of biomass allocation to environmental gradients support the optimal partitioning theory (OPT). The isometric relationships between reproductive and vegetative organs indicate that plant growth and reproduction are intricately linked. Furthermore, the plasticity of biomass ratios of reproductive to vegetative organs to climate variability and soil physical properties suggests that the flexible allocation between growth and reproduction is crucial for successful adaptation to diverse habitats.

• There are two theories about how allocation of metabolic products occurs. The allometric biomass partitioning theory (APT) suggests that all plants follow common allometric scaling rules. The optimal partitioning theory (OPT) predicts that plants allocate more biomass to the organ capturing the most limiting resource. • Whole-plant harvests of mature and juvenile tropical deciduous trees, evergreen trees, and lianas and model simulations were used to address the following knowledge gaps: (1) Do mature lianas comply with the APT scaling laws or do they invest less biomass in stems compared to trees? (2) Do juveniles follow the same allocation patterns as mature individuals? (3) Is either leaf phenology or life form a predictor of rooting depth? • It was found that: (1) mature lianas followed the same allometric scaling laws as trees; (2) juveniles and mature individuals do not follow the same allocation patterns; and (3) mature lianas had shallowest coarse roots and evergreen trees had the deepest. • It was demonstrated that: (1) mature lianas invested proportionally similar biomass to stems as trees and not less, as expected; (2) lianas were not deeper-rooted than trees as had been previously proposed; and (3) evergreen trees had the deepest roots, which is necessary to maintain canopy during simulated dry seasons.

Ultraconserved (UCEs) are popular markers for phylogenomic studies. They are relatively simple to collect from distantly-related organisms, and contain sufficient information to infer relationships at almost all taxonomic levels. Most studies of UCEs use partitioning to account for variation in rates and patterns of molecular evolution among sites, for example by estimating an independent model of molecular evolution for each UCE. However, rates and patterns of molecular evolution vary substantially within as well as between UCEs, suggesting that there may be opportunities to improve how UCEs are partitioned for phylogenetic inference. We propose and evaluate new partitioning methods for phylogenomic studies of UCEs: Sliding-Window Site Characteristics (SWSC), and UCE Site Position (UCESP). The first method uses site characteristics such as entropy, multinomial likelihood, and GC content to generate partitions that account for heterogeneity in rates and patterns of molecular evolution within each UCE. The second method groups together nucleotides that are found in similar physical locations within the UCEs. We examined the new methods with seven published data sets from a variety of taxa. We demonstrate the UCESP method generates partitions that are worse than other strategies used to partition UCE data sets (e.g., one partition per UCE). The SWSC method, particularly when based on site entropies, generates partitions that account for within-UCE heterogeneity and leads to large increases in the model fit. All of the methods, code, and data used in this study, are available from https://github.com/Tagliacollo/PartitionUCE. Simplified code for implementing the best method, the SWSC-EN, is available from https://github.com/Tagliacollo/PFinderUCE-SWSC-EN.

1. Below-ground resource partitioning is often proposed as the underlying mechanism for the positive relationship between plant species richness and productivity. For example, if species have different root distributions, a mixture of plant species may be able to use the available resources more completely than the individual species in a monoculture. However, there is little experimental evidence for differentiation in vertical root distributions among species and its contribution to biodiversity effects. 2. We determined species-specific root standing biomass over depth using molecular techniques (real-time qPCR) in a large grassland biodiversity experiment (one to eight plant species mixtures), in 2 years. Species-specific root biomass data were used to disentangle the effects of positive interactions between species (complementarity effects) and effects due to dominance of productive species (selection effects) on root biomass in mixtures. In a next step, these biodiversity effects were linked to the diversity of rooting depths and the averaged rooting depth of the community. 3. Root biomass increased with species richness. This was mainly due to positive interactions (the complementarity effect), which increased with species richness below-ground. In contrast, the selection effect decreased with species richness. Although there was considerable variation in vertical root distribution between species in monocultures, the diversity of rooting strategies did not explain the complementarity effect. Rather, the abudance of deep-rooting species in mixtures (i.e. high community-weighted mean) was significantly related to the complementarity effect. Comparing the \"predicted\" root distribution (based on monocultures) to the actual distribution in mixtures, we found that mixtures rooted deeper than expected, but this did not better explain the complementarity effect. 4. Synthesis. This study demonstrates that vertical root distributions of species provide only subtle evidence for resource partitioning. W e found no evidence that functional diversity in vertical rooting patterns was important for the complementarity effect, in contrast to our expectation that the enhancement of productivity was due to resource partitioning. Alternatively, we found significant but weak relationships between the complementarity effect and deep-rooting communities, based on the communityweighted mean root distribution. This suggests that factors other than below-ground resource partitioning alone may drive the biodiversity-productivity relationship.

Quantifying relative contributions of plant transpiration (T) and soil evaporation to evapotranspiration (ET) is crucial to better understand how vegetation influences and controls ET, the largest efflux of the terrestrial water balance. Here, we derive estimates of transpiration fraction (T/ET) using consistent isotope‐based ET partitioning methods for 13 sites spanning five ecosystem types of the continental US, capturing 56 snapshots of T/ET during the growing season. We found transpiration dominated the ET flux across all sites with a mean T/ET of 0.81 ± 0.08 (±standard error). Sites and dates with higher vegetation indices exhibited higher T/ET and transpiration rates, with the latter increasing 0.30 mm/day per unit Leaf Area Index and 2.9 mm/day per unit Normalized Difference Vegetation Index. Counter to expectations, antecedent precipitation had no effect on T/ET. Despite the breadth of ecosystems and conditions represented, evaporation exceeded transpiration only once, suggesting that evaporation rarely dominates ET in the growing season.