Quantifying dispersal between two colonies of northern elephant seals across 17 birth cohorts

Dispersal drives extinction-recolonization dynamics of metapopulations and is necessary for endangered species to recolonize former ranges. Yet few studies quantify dispersal and even fewer examine consistency of dispersal over many years. The northern elephant seal (Mirounga angustirostris) provides an example of the importance of dispersal. It quickly recolonized its full range after near extirpation by 19th century hunting, and though dispersal was observed it was not quantified. Here we enumerate lifetime dispersal events among females marked as pups at two colonies during 1994-2010, then correct for detection biases to estimate bidirectional dispersal rates. An average of 16% of females born at the Piedras Blancas colony dispersed northward 200 km to breed at Año Nuevo, while 8.0% of those born at Año Nuevo dispersed southward to Piedras Blancas. The northward rate fluctuated considerably but was higher than southward in 15 of 17 cohorts. The population at Piedras Blancas expanded 15-fold during the study, while Año Nuevo's declined slightly, but the expectation that seals would emigrate away from high density colonies was not supported. During the 1990s, dispersal was higher away from the small colony toward the large. Moreover, cohorts born later at Piedras Blancas, when the colony had grown, dispersed no more than early cohorts. Consistently high natal dispersal in northern elephant seals means the population must be considered a single large unit in terms of response to environmental change. High dispersal was fortuitous to the past recovery of the species, and continued dispersal means elephant seals will likely expand their range further.

Breakdown of the growth-mortality trade-off along a soil phosphorus gradient in a diverse tropical forest

An ecological paradigm predicts that plant species adapted to low resource availability grow slower and live longer than those adapted to high resource availability when growing together. We tested this by using hierarchical Bayesian analysis to quantify variations in growth and mortality of ca 40 000 individual trees from greater than 400 species in response to limiting resources in the tropical forests of Panama. In contrast to theoretical expectations of the growth-mortality paradigm, we find that tropical tree species restricted to low-phosphorus soils simultaneously achieve faster growth rates and lower mortality rates than species restricted to high-phosphorus soils. This result demonstrates that adaptation to phosphorus limitation in diverse plant communities modifies the growth-mortality trade-off, with important implications for understanding long-term ecosystem dynamics.

Physiological tipping points in the relationship between foraging success and lifetime fitness of a long-lived mammal

Although anthropogenic change is often gradual, the impacts on animal populations may be precipitous if physiological processes create tipping points between energy gain, reproduction or survival. We use 25 years of behavioural, diet and demographic data from elephant seals to characterise their relationships with lifetime fitness. Survival and reproduction increased with mass gain during long foraging trips preceding the pupping seasons, and there was a threshold where individuals that gained an additional 4.8% of their body mass (26 kg, from 206 to 232 kg) increased lifetime reproductive success three-fold (from 1.8 to 4.9 pups). This was due to a two-fold increase in pupping probability (30% to 76%) and a 7% increase in reproductive lifespan (6.0 to 6.4 years). The sharp threshold between mass gain and reproduction may explain reproductive failure observed in many species and demonstrates how small, gradual reductions in prey from anthropogenic disturbance could have profound implications for animal populations.

RecruitNet: A global database of plant recruitment networks

Plant recruitment interactions (i.e., what recruits under what) shape the composition, diversity, and structure of plant communities. Despite the huge body of knowledge on the mechanisms underlying recruitment interactions among species, we still know little about the structure of the recruitment networks emerging in ecological communities. Modeling and analyzing the community-level structure of plant recruitment interactions as a complex network can provide relevant information on ecological and evolutionary processes acting both at the species and ecosystem levels. We report a data set containing 143 plant recruitment networks in 23 countries across five continents, including temperate and tropical ecosystems. Each network identifies the species under which another species recruits. All networks report the number of recruits (i.e., individuals) per species. The data set includes >850,000 recruiting individuals involved in 118,411 paired interactions among 3318 vascular plant species across the globe. The cover of canopy species and open ground is also provided. Three sampling protocols were used: (1) The Recruitment Network (RN) protocol (106 networks) focuses on interactions among established plants ("canopy species") and plants in their early stages of recruitment ("recruit species"). A series of plots was delimited within a locality, and all the individuals recruiting and their canopy species were identified; (2) The paired Canopy-Open (pCO) protocol (26 networks) consists in locating a potential canopy plant and identifying recruiting individuals under the canopy and in a nearby open space of the same area; (3) The Georeferenced plot (GP) protocol (11 networks) consists in using information from georeferenced individual plants in large plots to infer canopy-recruit interactions. Some networks incorporate data for both herbs and woody species, whereas others focus exclusively on woody species. The location of each study site, geographical coordinates, country, locality, responsible author, sampling dates, sampling method, and life habits of both canopy and recruit species are provided. This database will allow researchers to test ecological, biogeographical, and evolutionary hypotheses related to plant recruitment interactions. There are no copyright restrictions on the data set; please cite this data paper when using these data in publications.

Estimating population size when individuals are asynchronous: A model illustrated with northern elephant seal breeding colonies

Our aim was to develop a method for estimating the number of animals using a single site in an asynchronous species, meaning that not all animals are present at once so that no one count captures the entire population. This is a common problem in seasonal breeders, and in northern elephant seals, we have a model for quantifying asynchrony at the Año Nuevo colony. Here we test the model at several additional colonies having many years of observations and demonstrate how it can account for animals not present on any one day. This leads to correction factors that yield total population from any single count throughout a season. At seven colonies in California for which we had many years of counts of northern elephant seals, we found that female arrival date varied < 2 days between years within sites and by < 5 days between sites. As a result, the correction factor for any one day was consistent, and at each colony, multiplying a female count between 26 and 30 Jan by 1.15 yielded an estimate of total population size that minimized error. This provides a method for estimating the female population size at colonies not yet studied. Our method can produce population estimates with minimal expenditure of time and resources and will be applicable to many seasonal species with asynchronous breeding phenology, particularly colonial birds and other pinnipeds. In elephant seals, it will facilitate monitoring the population over its entire range.

Density-dependent effects on reproductive output in a capital breeding carnivore, the northern elephant seal (Mirounga angustirostris)

All organisms face resource limitations that will ultimately restrict population growth, but the controlling mechanisms vary across ecosystems, taxa, and reproductive strategies. Using four decades of data, we examine how variation in the environment and population density affect reproductive outcomes in a capital-breeding carnivore, the northern elephant seal (Mirounga angustirostris). This species provides a unique opportunity to examine the relative importance of resource acquisition and density-dependence on breeding success. Capital breeders accrue resources over large temporal and spatial scales for use during an abbreviated reproductive period. This strategy may have evolved, in part, to confer resilience to short-term environmental variability. We observed density-dependent effects on weaning mass, and maternal age (experience) was more important than oceanographic conditions or maternal mass in determining offspring weaning mass. Together these findings show that the mechanisms controlling reproductive output are conserved across terrestrial and marine systems and vary with population dynamics, an important consideration when assessing the effect of extrinsic changes, such as climate change, on a population.

Species packing and the latitudinal gradient in beta-diversity

The decline in species richness at higher latitudes is among the most fundamental patterns in ecology. Whether changes in species composition across space (beta-diversity) contribute to this gradient of overall species richness (gamma-diversity) remains hotly debated. Previous studies that failed to resolve the issue suffered from a well-known tendency for small samples in areas with high gamma-diversity to have inflated measures of beta-diversity. Here, we provide a novel analytical test, using beta-diversity metrics that correct the gamma-diversity and sampling biases, to compare beta-diversity and species packing across a latitudinal gradient in tree species richness of 21 large forest plots along a large environmental gradient in East Asia. We demonstrate that after accounting for topography and correcting the gamma-diversity bias, tropical forests still have higher beta-diversity than temperate analogues. This suggests that beta-diversity contributes to the latitudinal species richness gradient as a component of gamma-diversity. Moreover, both niche specialization and niche marginality (a measure of niche spacing along an environmental gradient) also increase towards the equator, after controlling for the effect of topographical heterogeneity. This supports the joint importance of tighter species packing and larger niche space in tropical forests while also demonstrating the importance of local processes in controlling beta-diversity.

Demographic trade-offs predict tropical forest dynamics

Understanding tropical forest dynamics and planning for their sustainable management require efficient, yet accurate, predictions of the joint dynamics of hundreds of tree species. With increasing information on tropical tree life histories, our predictive understanding is no longer limited by species data but by the ability of existing models to make use of it. Using a demographic forest model, we show that the basal area and compositional changes during forest succession in a neotropical forest can be accurately predicted by representing tropical tree diversity (hundreds of species) with only five functional groups spanning two essential trade-offs-the growth-survival and stature-recruitment trade-offs. This data-driven modeling framework substantially improves our ability to predict consequences of anthropogenic impacts on tropical forests.

Testing for changes in biomass dynamics in large-scale forest datasets

Tropical forest responses to climate and atmospheric change are critical to the future of the global carbon budget. Recent studies have reported increases in estimated above-ground biomass (EAGB) stocks, productivity, and mortality in old-growth tropical forests. These increases could reflect a shift in forest functioning due to global change and/or long-lasting recovery from past disturbance. We introduce a novel approach to disentangle the relative contributions of these mechanisms by decomposing changes in whole-plot biomass fluxes into contributions from changes in the distribution of gap-successional stages and changes in fluxes for a given stage. Using 30 years of forest dynamic data at Barro Colorado Island, Panama, we investigated temporal variation in EAGB fluxes as a function of initial EAGB (EAGB_i ) in 10 × 10 m quadrats. Productivity and mortality fluxes both increased strongly with initial quadrat EAGB. The distribution of EAGB (and thus EAGB_i ) across quadrats hardly varied over 30 years (and seven censuses). EAGB fluxes as a function of EAGB_i varied largely and significantly among census intervals, with notably higher productivity in 1985-1990 associated with recovery from the 1982-1983 El Niño event. Variation in whole-plot fluxes among census intervals was explained overwhelmingly by variation in fluxes as a function of EAGB_i , with essentially no contribution from changes in EAGB_i distributions. The high observed temporal variation in productivity and mortality suggests that this forest is very sensitive to climate variability. There was no consistent long-term trend in productivity, mortality, or biomass in this forest over 30 years, although the temporal variability in productivity and mortality was so strong that it could well mask a substantial trend. Accurate prediction of future tropical forest carbon budgets will require accounting for disturbance-recovery dynamics and understanding temporal variability in productivity and mortality.

Performance of tropical forest seedlings under shade and drought: an interspecific trade-off in demographic responses

Seedlings in moist tropical forests must cope with deep shade and seasonal drought. However, the interspecific relationship between seedling performance in shade and drought remains unsettled. We quantified spatiotemporal variation in shade and drought in the seasonal moist tropical forest on Barro Colorado Island (BCI), Panama, and estimated responses of naturally regenerating seedlings as the slope of the relationship between performance and shade or drought intensity. Our performance metrics were relative height growth and first-year survival. We investigated the relationship between shade and drought responses for up to 63 species. There was an interspecific trade-off in species responses to shade versus species responses to dry season intensity; species that performed worse in the shade did not suffer during severe dry seasons and vice versa. This trade-off emerged in part from the absence of species that performed particularly well or poorly in both drought and shade. If drought stress in tropical forests increases with climate change and as solar radiation is higher during droughts, the trade-off may reinforce a shift towards species that resist drought but perform poorly in the shade by releasing them from deep shade.

Pervasive decreases in living vegetation carbon turnover time across forest climate zones

Forests play a major role in the global carbon cycle. Previous studies on the capacity of forests to sequester atmospheric CO2 have mostly focused on carbon uptake, but the roles of carbon turnover time and its spatiotemporal changes remain poorly understood. Here, we used long-term inventory data (1955 to 2018) from 695 mature forest plots to quantify temporal trends in living vegetation carbon turnover time across tropical, temperate, and cold climate zones, and compared plot data to 8 Earth system models (ESMs). Long-term plots consistently showed decreases in living vegetation carbon turnover time, likely driven by increased tree mortality across all major climate zones. Changes in living vegetation carbon turnover time were negatively correlated with CO2 enrichment in both forest plot data and ESM simulations. However, plot-based correlations between living vegetation carbon turnover time and climate drivers such as precipitation and temperature diverged from those of ESM simulations. Our analyses suggest that forest carbon sinks are likely to be constrained by a decrease in living vegetation carbon turnover time, and accurate projections of forest carbon sink dynamics will require an improved representation of tree mortality processes and their sensitivity to climate in ESMs.

Lifetime reproductive success of northern elephant seals (Mirounga angustirostris)

Lifetime reproductive success of individuals in a natural population provides an estimate of Darwinian fitness. We calculated lifetime reproductive success in a colony of female northern elephant seals (Mirounga angustirostris (Gill, 1866)) by monitoring annual breeding throughout life of 7735 female weanlings marked individually at Año Nuevo, California, USA, from 1963 to 2005. Great variation in lifetime reproductive success was evident in three aspects of life history: (1) 75% of the females died before reaching breeding age and produced no pups; (2) nearly half of the survivors bred for only a few years before dying, and young females had low weaning success; (3) less than 1% of the females in the sample were exceptionally successful producing up to 20 pups in life. Many females that bred early, while still growing, had decreased lifespan, low weaning success, and lower lifetime reproductive success than females that postponed first breeding. Exceptional reproductive success was associated with giving birth annually, living long (up to age 23), and weaning large pups that were more likely to survive and breed. We conclude that there is strong selection for increased lifespan and multiparous supermoms that contribute significantly to pup production in the next generation.

Seed-to-seedling transitions exhibit distance-dependent mortality but no strong spacing effects in a Neotropical forest

Patterns of seed dispersal and seed mortality influence the spatial structure of plant communities and the local coexistence of competing species. Most seeds are dispersed in proximity to the parent tree, where mortality is also expected to be the highest, because of competition with siblings or the attraction of natural enemies. Whereas distance-dependent mortality in the seed-to-seedling transition was often observed in tropical forests, few studies have attempted to estimate the shape of the survival-distance curves, which determines whether the peak of seedling establishment occurs away from the parent tree (Janzen-Connell pattern) or if the peak attenuates but remains at the parent location (Hubbell pattern). In this study, we inferred the probability density of seed dispersal and two stages of seedling establishment (new recruits, and seedlings 20 cm or taller) with distance for 24 tree species present in the 50-ha Forest Dynamics Plot of Barro Colorado Island, Panama. Using data from seed traps, seedling survey quadrats, and tree-census records spanning the 1988-2014 period, we fit hierarchical Bayesian models including parameters for tree fecundity, the shape of the dispersal kernel, and overdispersion of seed or seedling counts. We combined predictions from multiple dispersal kernels to obtain more robust inferences. We find that Hubbell patterns are the most common and Janzen-Connell patterns are very rare among those species; that distance-dependent mortality may be stronger in the seed stage, in the early recruit stage, or comparable in both; and that species with larger seeds experience less overall mortality and less distance-dependent mortality. Finally, we describe how this modeling approach could be extended at a community scale to include less abundant species.

Temporal population variability in local forest communities has mixed effects on tree species richness across a latitudinal gradient

Among the local processes that determine species diversity in ecological communities, fluctuation-dependent mechanisms that are mediated by temporal variability in the abundances of species populations have received significant attention. Higher temporal variability in the abundances of species populations can increase the strength of temporal niche partitioning but can also increase the risk of species extinctions, such that the net effect on species coexistence is not clear. We quantified this temporal population variability for tree species in 21 large forest plots and found much greater variability for higher latitude plots with fewer tree species. A fitted mechanistic model showed that among the forest plots, the net effect of temporal population variability on tree species coexistence was usually negative, but sometimes positive or negligible. Therefore, our results suggest that temporal variability in the abundances of species populations has no clear negative or positive contribution to the latitudinal gradient in tree species richness.

The Forest Observation System, building a global reference dataset for remote sensing of forest biomass

Forest biomass is an essential indicator for monitoring the Earth's ecosystems and climate. It is a critical input to greenhouse gas accounting, estimation of carbon losses and forest degradation, assessment of renewable energy potential, and for developing climate change mitigation policies such as REDD+, among others. Wall-to-wall mapping of aboveground biomass (AGB) is now possible with satellite remote sensing (RS). However, RS methods require extant, up-to-date, reliable, representative and comparable in situ data for calibration and validation. Here, we present the Forest Observation System (FOS) initiative, an international cooperation to establish and maintain a global in situ forest biomass database. AGB and canopy height estimates with their associated uncertainties are derived at a 0.25 ha scale from field measurements made in permanent research plots across the world's forests. All plot estimates are geolocated and have a size that allows for direct comparison with many RS measurements. The FOS offers the potential to improve the accuracy of RS-based biomass products while developing new synergies between the RS and ground-based ecosystem research communities.

Biodiversity recovery of Neotropical secondary forests

Old-growth tropical forests harbor an immense diversity of tree species but are rapidly being cleared, while secondary forests that regrow on abandoned agricultural lands increase in extent. We assess how tree species richness and composition recover during secondary succession across gradients in environmental conditions and anthropogenic disturbance in an unprecedented multisite analysis for the Neotropics. Secondary forests recover remarkably fast in species richness but slowly in species composition. Secondary forests take a median time of five decades to recover the species richness of old-growth forest (80% recovery after 20 years) based on rarefaction analysis. Full recovery of species composition takes centuries (only 34% recovery after 20 years). A dual strategy that maintains both old-growth forests and species-rich secondary forests is therefore crucial for biodiversity conservation in human-modified tropical landscapes.

Direct and indirect effects of climate on richness drive the latitudinal diversity gradient in forest trees

Climate is widely recognised as an important determinant of the latitudinal diversity gradient. However, most existing studies make no distinction between direct and indirect effects of climate, which substantially hinders our understanding of how climate constrains biodiversity globally. Using data from 35 large forest plots, we test hypothesised relationships amongst climate, topography, forest structural attributes (stem abundance, tree size variation and stand basal area) and tree species richness to better understand drivers of latitudinal tree diversity patterns. Climate influences tree richness both directly, with more species in warm, moist, aseasonal climates and indirectly, with more species at higher stem abundance. These results imply direct limitation of species diversity by climatic stress and more rapid (co-)evolution and narrower niche partitioning in warm climates. They also support the idea that increased numbers of individuals associated with high primary productivity are partitioned to support a greater number of species.

Effects of biotic interactions on tropical tree performance depend on abiotic conditions

Predicting biotic responses to environmental change requires understanding the joint effects of abiotic conditions and biotic interactions on community dynamics. One major challenge is to separate the potentially confounding effects of abiotic environmental variation and local biotic interactions on individual performance. The stress gradient hypothesis (SGH) addresses this issue directly by predicting that the effects of biotic interactions on performance become more positive as the abiotic environment becomes more stressful. It is unclear, however, how the predictions of the SGH apply to plants of differing functional strategies in diverse communities. We asked (1) how the effect of crowding on performance (growth and survival) of trees varies across a precipitation gradient, and (2) how functional strategies (as measured by two key traits: wood density and leaf mass per area, LMA) mediate average demographic rates and responses to crowding across the gradient. We built trait-based neighborhood models of growth and survival across a regional precipitation gradient where increasing precipitation is associated with reduced abiotic stress. In total, our dataset comprised ~170,000 individual trees belonging to 252 species. The effect of crowding on tree performance varied across the gradient; crowding negatively affected growth across plots and positively affected survival in the wettest plot. Functional traits mediated average demographic rates across the gradient, but we did not find clear evidence that the strength of these responses depends on species' traits. Our study lends support to the SGH and demonstrates how a trait-based perspective can advance these concepts by linking the diversity of species interactions with functional variation across abiotic gradients.

Contrasting outcomes of species- and community-level analyses of the temporal consistency of functional composition

Multiple anthropogenic drivers affect every natural community, and there is broad interest in using functional traits to understand and predict the consequences for future biodiversity. There is, however, no consensus regarding the choice of analytical methods. We contrast species- and community-level analyses of change in the functional composition for four traits related to drought tolerance using three decades of repeat censuses of trees in the 50-ha Forest Dynamics Plot on Barro Colorado Island, Panama. Community trait distributions shifted significantly through time, which may indicate a shift toward more drought tolerant species. However, at the species level, changes in abundance were unrelated to trait values. To reconcile these seemingly contrasting results, we evaluated species-specific contributions to the directional shifts observed at the community level. Abundance changes of just one to six of 312 species were responsible for the community-level shifts observed for each trait. Our results demonstrate that directional changes in community-level functional composition can result from idiosyncratic change in a few species rather than widespread community-wide changes associated with functional traits. Future analyses of directional change in natural communities should combine community-, species-, and possibly individual-level analyses to uncover relationships with function that can improve understanding and enable prediction.

Community-level species' correlated distribution can be scale-independent and related to the evenness of abundance

The spatial distribution of species is not random; instead, individuals tend to gather, resulting in a non-random pattern. Previous studies used the independent negative binomial distribution (NBD) to model the distributional aggregation of a single species, in which the independence of the distribution of individuals of a species in different quadrats had been assumed. This way of analyzing aggregation will result in the scale-dependent estimation of the aggregation or shape parameter. However, because non-random (and therefore non-independent) distribution of individuals of a species in a finite area can be caused by either correlated or clumped distribution of individuals of a species between neighboring sites, an alternative model would assume that the distribution of individuals of a species over different sampling areas is multinomial. Here, we showed that, by assuming that regional species abundance followed a NBD while using a multinomial distribution to assign individuals of species in different non-overlapped sampling quadrats that are from a partition of the entire region (quantifying positive correlation or synchrony), the estimation of the shape parameter in this probabilistic model, which is the negative multinomial distribution (NMD), was scale-invariant (i.e., the estimated shape parameter is identical across different partitions of the study region). Accordingly, the estimation of the shape parameter was related to regional species distribution alone. This implied that, the shape parameter at the community level, using the NMD model, reflected the evenness of interspecific abundance. As a comparison, if the distribution of individuals of a single species followed independent NBDs as studied previously, the shape parameter would measure the evenness of intraspecific abundance (quantifying single-species' distributional aggregation). Moreover, our study highlighted the necessity for adjusting the model for the effects of unsampled species when studying community-level distributional patterns. Collectively, as long as a target area is partitioned into non-overlapping quadrats (no matter how their sizes vary), the proposed NMD model in this study, along with the independent NBDs model, can be jointly formulated as a framework to reconcile the scale-dependent debate on the shape parameter, unifying the relationship between inter- or intraspecific abundance and distributional patterns.

Resolving the paradox of clumped seed dispersal: positive density and distance dependence in a bat-dispersed species

One of the hypothesized benefits of seed dispersal is to escape density- and distance-responsive, host-specific, natural enemies near maternal plants where conspecific seed and seedling densities are high. Such high conspecific neighbor densities typically result in lower offspring growth and survival (i.e., negative density-dependent effects), yet many dispersal modes result in clumped seed distributions. New World leaf-nosed bats transport fruits to their feeding roosts and deposit seeds, thereby creating high-density seed/seedling patches beneath feeding roosts in heterospecific trees away from maternal trees, which seemingly nullifies a key benefit of seed dispersal. Such dispersal may still be adaptive if negative density-dependent effects are reduced under feeding roosts or if the benefit of being dispersed away from maternal trees outweighs negative effects of conspecific seed/seedling density below roosts. We mapped the entire post-germination population of a bat-dispersed tree species Calophyllum longifolium (Calophyllaceae) in a 50-ha plot on Barro Colorado Island, Panama in each of three successive years. We tested two hypotheses: (1) distance-dependent effects are stronger than density-dependent effects on seedling performance because seedlings far from conspecific adults are more likely to escape natural enemies even when at high densities and (2) negative density-dependent effects will be reduced far from vs. near conspecific adults. Density and distance were naturally decoupled, as expected. However, in contrast to our expectation, we found positive density effects on seedling survival and density-dependent effects did not differ with distance from conspecific adults. Both density and distance had positive effects on seedling survival when considered together, while only year had a significant effect on seedling growth. Thus, both being dispersed under bat feeding roosts and escaping the vicinity of conspecific adults were beneficial for C. longifolium seedling survival, supporting the directed dispersal and escape hypotheses, respectively. Despite resulting in high densities of conspecific seedlings, favorable habitat under bat feeding roosts and lack of negative density-dependent effects appear to provide evolutionary advantages in C. longifolium.

Spatial scale changes the relationship between beta diversity, species richness and latitude

The relationship between β-diversity and latitude still remains to be a core question in ecology because of the lack of consensus between studies. One hypothesis for the lack of consensus between studies is that spatial scale changes the relationship between latitude and β-diversity. Here, we test this hypothesis using tree data from 15 large-scale forest plots (greater than or equal to 15 ha, diameter at breast height ≥ 1 cm) across a latitudinal gradient (3-30^o) in the Asia-Pacific region. We found that the observed β-diversity decreased with increasing latitude when sampling local tree communities at small spatial scale (grain size ≤0.1 ha), but the observed β-diversity did not change with latitude when sampling at large spatial scales (greater than or equal to 0.25 ha). Differences in latitudinal β-diversity gradients across spatial scales were caused by pooled species richness (γ-diversity), which influenced observed β-diversity values at small spatial scales, but not at large spatial scales. Therefore, spatial scale changes the relationship between β-diversity, γ-diversity and latitude, and improving sample representativeness avoids the γ-dependence of β-diversity.

Role of tree size in moist tropical forest carbon cycling and water deficit responses

Drought disproportionately affects larger trees in tropical forests, but implications for forest composition and carbon (C) cycling in relation to dry season intensity remain poorly understood. In order to characterize how C cycling is shaped by tree size and drought adaptations and how these patterns relate to spatial and temporal variation in water deficit, we analyze data from three forest dynamics plots spanning a moisture gradient in Panama that have experienced El Niño droughts. At all sites, aboveground C cycle contributions peaked below 50-cm stem diameter, with stems ≥ 50 cm accounting for on average 59% of live aboveground biomass, 45% of woody productivity and 49% of woody mortality. The dominance of drought-avoidance strategies increased interactively with stem diameter and dry season intensity. Although size-related C cycle contributions did not vary systematically across the moisture gradient under nondrought conditions, woody mortality of larger trees was disproportionately elevated under El Niño drought stress. Thus, large (> 50 cm) stems, which strongly mediate but do not necessarily dominate C cycling, have drought adaptations that compensate for their more challenging hydraulic environment, particularly in drier climates. However, these adaptations do not fully buffer the effects of severe drought, and increased large tree mortality dominates ecosystem-level drought responses.

Variation in hydroclimate sustains tropical forest biomass and promotes functional diversity

The fate of tropical forests under climate change is unclear as a result, in part, of the uncertainty in projected changes in precipitation and in the ability of vegetation models to capture the effects of drought-induced mortality on aboveground biomass (AGB). We evaluated the ability of a terrestrial biosphere model with demography and hydrodynamics (Ecosystem Demography, ED2-hydro) to simulate AGB and mortality of four tropical tree plant functional types (PFTs) that operate along light- and water-use axes. Model predictions were compared with observations of canopy trees at Barro Colorado Island (BCI), Panama. We then assessed the implications of eight hypothetical precipitation scenarios, including increased annual precipitation, reduced inter-annual variation, El Niño-related droughts and drier wet or dry seasons, on AGB and functional diversity of the model forest. When forced with observed meteorology, ED2-hydro predictions capture multiple BCI benchmarks. ED2-hydro predicts that AGB will be sustained under lower rainfall via shifts in the functional composition of the forest, except under the drier dry-season scenario. These results support the hypothesis that inter-annual variation in mean and seasonal precipitation promotes the coexistence of functionally diverse PFTs because of the relative differences in mortality rates. If the hydroclimate becomes chronically drier or wetter, functional evenness related to drought tolerance may decline.

BioTIME: A database of biodiversity time series for the Anthropocene

MOTIVATION

The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.

MAIN TYPES OF VARIABLES INCLUDED

The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.

SPATIAL LOCATION AND GRAIN

BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).

TIME PERIOD AND GRAIN

BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.

MAJOR TAXA AND LEVEL OF MEASUREMENT

BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.

SOFTWARE FORMAT

.csv and .SQL.

Abiotic niche partitioning and negative density dependence drive tree seedling survival in a tropical forest

In tropical tree communities, processes occurring during early life stages play a critical role in shaping forest composition and diversity through differences in species' performance. Predicting the future of tropical forests depends on a solid understanding of the drivers of seedling survival. At the same time, factors determining spatial and temporal patterns of seedling survival can play a large role in permitting species coexistence in diverse communities. Using long-term data on the survival of more than 45 000 seedlings of 238 species in a Neotropical forest, we assessed the relative importance of key abiotic and biotic neighbourhood variables thought to influence individual seedling survival and tested whether species vary significantly in their responses to these variables, consistent with niche differences. At the community level, seedling survival was significantly correlated with plant size, topographic habitat, neighbourhood densities of conspecific seedlings, conspecific and heterospecific trees and annual variation in water availability, in descending order of effect size. Additionally, we found significant variation among species in their sensitivity to light and water availability, as well as in their survival within different topographic habitats, indicating the potential for niche differentiation among species that could allow for species coexistence.

Publisher Correction: Pervasive phosphorus limitation of tree species but not communities in tropical forests

In this Letter, the y axis of the right-hand panel of Fig. 2a was mislabelled 'Phosphomonoesterase' instead of 'Phosphodiesterase'. This error has been corrected online.

Species-area relationships and biodiversity loss in fragmented landscapes

To estimate species loss from habitat destruction, ecologists typically use species-area relationships, but this approach neglects the spatial pattern of habitat fragmentation. Here, we provide new, easily applied, analytical methods that place upper and lower bounds on immediate species loss at any spatial scale and for any spatial pattern of habitat loss. Our formulas are expressed in terms of what we name the 'Preston function', which describes triphasic species-area relationships for contiguous regions. We apply our method to case studies of deforestation and tropical tree species loss at three different scales: a 50 ha forest plot in Panama, the tropical city-state of Singapore and the Brazilian Amazon. Our results show that immediate species loss is somewhat insensitive to fragmentation pattern at small scales but highly sensitive at larger scales: predicted species loss in the Amazon varies by a factor of 16 across different spatial structures of habitat loss.

Pervasive phosphorus limitation of tree species but not communities in tropical forests

Phosphorus availability is widely assumed to limit primary productivity in tropical forests, but support for this paradigm is equivocal. Although biogeochemical theory predicts that phosphorus limitation should be prevalent on old, strongly weathered soils, experimental manipulations have failed to detect a consistent response to phosphorus addition in species-rich lowland tropical forests. Here we show, by quantifying the growth of 541 tropical tree species across a steep natural phosphorus gradient in Panama, that phosphorus limitation is widespread at the level of individual species and strengthens markedly below a threshold of two parts per million exchangeable soil phosphate. However, this pervasive species-specific phosphorus limitation does not translate into a community-wide response, because some species grow rapidly on infertile soils despite extremely low phosphorus availability. These results redefine our understanding of nutrient limitation in diverse plant communities and have important implications for attempts to predict the response of tropical forests to environmental change.

Plant diversity increases with the strength of negative density dependence at the global scale

Theory predicts that higher biodiversity in the tropics is maintained by specialized interactions among plants and their natural enemies that result in conspecific negative density dependence (CNDD). By using more than 3000 species and nearly 2.4 million trees across 24 forest plots worldwide, we show that global patterns in tree species diversity reflect not only stronger CNDD at tropical versus temperate latitudes but also a latitudinal shift in the relationship between CNDD and species abundance. CNDD was stronger for rare species at tropical versus temperate latitudes, potentially causing the persistence of greater numbers of rare species in the tropics. Our study reveals fundamental differences in the nature of local-scale biotic interactions that contribute to the maintenance of species diversity across temperate and tropical communities.

THE EVOLUTION OF TRANSPOSABLE ELEMENTS: CONDITIONS FOR ESTABLISHMENT IN BACTERIAL POPULATIONS

Previous theoretical studies have shown that bacterial transposons can become established in populations by infectious transfer, even if they reduce the fitness of their host cells. Conditions for the persistence of "parasitic" transposons are, however, restrictive: i) transposition must be replicative, rather than conservative; ii) the rate of transposition must be greater than the loss in host fitness caused by the transposon; and iii) cells must exchange plasmids at rates greater than the fitness cost of the transposon. I sought to test the validity of the model underlying this theory by performing experiments with laboratory populations of the bacterium Escherichia coli, the conjugative plasmid R100, and the transposons Tn3 and Tn5. A plasmid-borne transposon was introduced at low frequency into a population of bacteria carrying the same plasmid without the transposon in a habitat where the transposon offered no benefit to its host. The fate of the invading transposon was followed by tracking the various bacterial populations appearing in the cultures. Using independent estimates of the parameters of the model, predicted population changes were generated with numerical solutions of the model, and these were compared to experimental results. Plasmids transferred into new hosts as predicted by the model, and the resulting transconjugant populations either maintained a steady low density or rose slowly in abundance. Transposition appeared to play no role in population changes. Abundance of all cell types fit theoretical predictions of a system with no transposition, despite evidence that transposition was taking place. This is exactly what the model predicted. It thus appears unlikely that deleterious or neutral transposons have much impact on the genetics of bacterial populations. This is consistent with the hypothesis that most bacterial transposons are not parasitic DNA, but rather invade and persist in populations by providing a fitness advantage to cells carrying them.

No evidence that boron influences tree species distributions in lowland tropical forests of Panama

It was recently proposed that boron might be the most important nutrient structuring tree species distributions in tropical forests. Here we combine observational and experimental studies to test this hypothesis for lowland tropical forests of Panama. Plant-available boron is uniformly low in tropical forest soils of Panama and is not significantly associated with any of the > 500 species in a regional network of forest dynamics plots. Experimental manipulation of boron supply to seedlings of three tropical tree species revealed no evidence of boron deficiency or toxicity at concentrations likely to occur in tropical forest soils. Foliar boron did not correlate with soil boron along a local scale gradient of boron availability. Fifteen years of boron addition to a tropical forest increased plant-available boron by 70% but did not significantly change tree productivity or boron concentrations in live leaves, wood or leaf litter. The annual input of boron in rainfall accounts for a considerable proportion of the boron in annual litterfall and is similar to the pool of plant-available boron in the soil, and is therefore sufficient to preclude boron deficiency. We conclude that boron does not influence tree species distributions in Panama and presumably elsewhere in the lowland tropics.

Extracting Environmental Benefits from a New Canal in Nicaragua: Lessons from Panama

Biologists have raised objections to a new canal in Nicaragua, but in this Essay I argue that dire predictions of environmental catastrophe are exaggerated. I present an alternative view based on my research experience in Panama, where Canal operations foster forest conservation. Currently in Nicaragua, the rate of forest loss is so rapid that the canal cannot make it worse. Rather, I contend, adoption of international standards in canal construction could lead to net environmental and social benefits for the country.

Distribución, mortalidad y asociación con plantas, de nidos de <i>Paraponera clavata</i> (Hymenoptera: Formicidae) en la isla de Barro Colorado, Panamá

Se estudióla distribución, mortalidad, reclutarrúento y asociación con plantas, de 308 nidos de la hOnIÚga neotropical Paraponera clavata en una parcela de cincuenta hectáreas de bosque viejo en la isla de Barró Colorado entre septiembre de 1993 y febrero de 1995. Los nidos estaban distribuidos uniformemente a través de toda la parcela; y se asociaban de manera significativa con el· tipo de hábitat, existían más nidos de los esperados en las planicies altas y en la sección de bosque más joven de la parcela. La densidad promedio era de 6.2 nidos por hectárea. Los nidos con un mayor número de vecinos entre O y 20 m de distancia, tenían una mayor prob¡¡bilidad de morir, si se comparaban con aquéllos que se encontraban separados por distancias mayores. La mortalidad era entre 13.36 y 69.64% dependiendo del intervalo de censo, y el reclutamiento fue del 22.63 y 31.72%. Los nidos se encontraron en las bases de 84 especies de plantas, en 34 familias con cuatro categorías de forma de vida: 76 especies eran árboles, 5 especies eran arbustos, 2 especies eran palmas y l era liana. Ocho especies de plantas se asociaban positivamente con los nidos de la honIÚga. Plantas medianas entre 8 y 63.9 cm de DAP eran las más utilizadas. Arboles y arbustos pequeños presentan muy poca asociación con los nidos. La hOnIÚga no se asocia con árboles que tienen nectarios extratlorales. El 53% de los nidos tenían a Phrynus gervaisii (Amblypygi: Phrynidae) habitando en el interior. Estos nidos presentaron menores tasas de mortalidad en comparación con el resto.

Temporal variability of forest communities: empirical estimates of population change in 4000 tree species

Long-term surveys of entire communities of species are needed to measure fluctuations in natural populations and elucidate the mechanisms driving population dynamics and community assembly. We analysed changes in abundance of over 4000 tree species in 12 forests across the world over periods of 6-28 years. Abundance fluctuations in all forests are large and consistent with population dynamics models in which temporal environmental variance plays a central role. At some sites we identify clear environmental drivers, such as fire and drought, that could underlie these patterns, but at other sites there is a need for further research to identify drivers. In addition, cross-site comparisons showed that abundance fluctuations were smaller at species-rich sites, consistent with the idea that stable environmental conditions promote higher diversity. Much community ecology theory emphasises demographic variance and niche stabilisation; we encourage the development of theory in which temporal environmental variance plays a central role.

Response of demographic rates of tropical trees to light availability: can position-based competition indices replace information from canopy census data?

For trees in tropical forests, competition for light is thought to be a central process that offers opportunities for niche differentiation through light gradient partitioning. In previous studies, a canopy index based on three-dimensional canopy census data has been shown to be a good predictor of species-specific demographic rates across the entire tree community on Barro Colorado Island, Panama, and has allowed quantifying between-species variation in light response. However, almost all other forest census plots lack data on the canopy structure. Hence, this study aims at assessing whether position-based neighborhood competition indices can replace information from canopy census data and produce similar estimates of the interspecific variation of light responses. We used inventory data from the census plot at Barro Colorado Island and calculated neighborhood competition indices with varying relative effects of the size and distance of neighboring trees. Among these indices, we selected the one that was most strongly correlated with the canopy index. We then compared outcomes of hierarchical Bayesian models for species-specific recruitment and growth rates including either the canopy index or the selected neighborhood competition index as predictor. Mean posterior estimates of light response parameters were highly correlated between models (r>0.85) and indicated that most species regenerate and grow better in higher light. Both light estimation approaches consistently found that the interspecific variation of light response was larger for recruitment than for growth rates. However, the classification of species into different groups of light response, e.g. weaker than linear (decelerating) vs. stronger than linear (accelerating) differed between approaches. These results imply that while the classification into light response groups might be biased when using neighborhood competition indices, they may be useful for determining species rankings and between-species variation of light response and therefore enable large comparative studies between different forest census plots.

Geographical range and local abundance of tree species in China

Most studies on the geographical distribution of species have utilized a few well-known taxa in Europe and North America, with little research in China and its wide range of climate and forest types. We assembled large datasets to quantify the geographic ranges of tree species in China and to test several biogeographic hypotheses: 1) whether locally abundant species tend to be geographically widespread; 2) whether species are more abundant towards their range-centers; and 3) how abundances are correlated between sites. Local abundances of 651 species were derived from four tree plots of 20–25 ha where all individuals ≥1 cm in stem diameter were mapped and identified taxonomically. Range sizes of these species across China were then estimated from over 460,000 geo-referenced records; a Bayesian approach was used, allowing careful measures of error of each range estimate. The log-transformed range sizes had a bell-shaped distribution with a median of 703,000 km², and >90% of 651 species had ranges >10⁵ km². There was no relationship between local abundance and range size, and no evidence for species being more abundant towards their range-centers. Finally, species’ abundances were positively correlated between sites. The widespread nature of most tree species in China suggests few are vulnerable to global extinction, and there is no indication of the double-peril that would result if rare species also had narrow ranges.

Functional traits explain light and size response of growth rates in tropical tree species

Relationships between functional traits and average or potential demographic rates have provided insight into the functional constraints and trade-offs underlying life-history strategies of tropical tree species. We have extended this framework by decomposing growth rates of -130 000 trees of 171 Neotropical tree species into intrinsic growth and the response of growth to light and size. We related these growth characteristics to multiple functional traits (wood density, adult stature, seed mass, leaf traits) in a hierarchical Bayesian model that accounted for measurement error and intraspecific variability of functional traits. Wood density was the most important trait determining all three growth characteristics. Intrinsic growth rates were additionally strongly related to adult stature, while all traits contributed to light response. Our analysis yielded a predictive model that allows estimation of growth characteristics for rare species on the basis of a few easily measurable morphological traits.

Species distributions in response to individual soil nutrients and seasonal drought across a community of tropical trees

Tropical forest vegetation is shaped by climate and by soil, but understanding how the distributions of individual tree species respond to specific resources has been hindered by high diversity and consequent rarity. To study species over an entire community, we surveyed trees and measured soil chemistry across climatic and geological gradients in central Panama and then used a unique hierarchical model of species occurrence as a function of rainfall and soil chemistry to circumvent analytical difficulties posed by rare species. The results are a quantitative assessment of the responses of 550 tree species to eight environmental factors, providing a measure of the importance of each factor across the entire tree community. Dry-season intensity and soil phosphorus were the strongest predictors, each affecting the distribution of more than half of the species. Although we anticipated clear-cut responses to dry-season intensity, the finding that many species have pronounced associations with either high or low phosphorus reveals a previously unquantified role for this nutrient in limiting tropical tree distributions. The results provide the data necessary for understanding distributional limits of tree species and predicting future changes in forest composition.