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Populations of forest trees exhibit large temporal fluctuations, but little is known about the synchrony of these fluctuations across space, including their sign, magnitude, causes and characteristic scales. These have important implications for metapopulation persistence and theoretical community ecology. Using data from permanent forest plots spanning local, regional and global spatial scales, we measured spatial synchrony in tree population growth rates over sub-decadal and decadal timescales and explored the relationship of synchrony to geographical distance. Synchrony was high at local scales of less than 1 km, with estimated Pearson correlations of approximately 0.6–0.8 between species' population growth rates across pairs of quadrats. Synchrony decayed by approximately 17–44% with each order of magnitude increase in distance but was still detectably positive at distances of 100 km and beyond. Dispersal cannot explain observed large-scale synchrony because typical seed dispersal distances (<100 m) are far too short to couple the dynamics of distant forests on decadal timescales. We attribute the observed synchrony in forest dynamics primarily to the effect of spatially synchronous environmental drivers (the Moran effect), in particular climate, although pests, pathogens and anthropogenic drivers may play a role for some species. [ABSTRACT FROM AUTHOR]

Canopy gaps are widely recognized as being crucial for maintaining the diversity of forest tree communities. But empirical studies have found mixed results because the differences in diversity between individual gaps and non‐gaps are often small and statistically undetectable. One overlooked factor, however, is how small individual gap versus non‐gap differences may accumulate across sites and potentially have a large effect on forest diversity at the plot scale. Our study investigated sapling richness, density, and composition in 124 treefall gaps, and 200 non‐gap sites in the 50‐ha tropical forest plot at Barro Colorado Island (BCI), Panama. Additionally, we analyzed species accumulation curves to understand how species richness increases with increasing stem numbers. We observed that sapling richness and density were only slightly higher in gaps 7 years after formation and statistically indistinguishable from non‐gaps after 12 years. However, species accumulation curves across multiple gaps were substantially higher than those across non‐gaps. Species composition showed small differences between individual gaps and non‐gaps but differed significantly between collections of gaps and non‐gaps. Specifically, 55 species specialized in 7‐year‐old gaps compared with 24 in non‐gaps; of these, 23 gap‐specialized species and zero non‐gap species were pioneers. Our results indicate that tree species richness is higher in gaps because of both higher stem density and the presence of gap‐specialized species. Our study has finally provided compelling evidence to support the idea that gaps enhance the overall diversity of tropical forest tree communities. [ABSTRACT FROM AUTHOR]

There is an urgent need for reliable data on the impacts of deforestation on tropical biodiversity. The city-state of Singapore has one of the most detailed biodiversity records in the tropics, dating back to the turn of the 19th century. In 1819, Singapore was almost entirely covered in primary forest, but this has since been largely cleared. We compiled more than 200 y of records for 10 major taxonomic groups in Singapore (>50,000 individual records; >3,000 species), and we estimated extinction rates using recently developed and novel statistical models that account for “dark extinctions,” i.e., extinctions of undiscovered species. The estimated overall extinction rate was 37% (95% CI [31 to 42%]). Extrapolating our Singapore observations to a future business-as- usual deforestation scenario for Southeast Asia suggests that 18% (95% CI [16 to 22%]) of species will be lost regionally by 2100. Our extinction estimates for Singapore and Southeast Asia are a factor of two lower than previous estimates that also attempted to account for dark extinctions. However, we caution that particular groups such as large mammals, forest-dependent birds, orchids, and butterflies are disproportionately vulnerable. [ABSTRACT FROM AUTHOR]

Hyperdiverse tropical forest tree communities illustrate a fundamental problem in ecology: How can many species coexist given relatively few limiting resources? Neutral theory provides a solution by positing that species have equal fitness and hence drift to extinction slowly. However, neutral theory seriously under‐predicts temporal changes in species abundances. This can be remedied by breaking neutrality and adding temporal environmental stochasticity (TES), but the mechanisms mediating the effects of TES on species richness remain unclear. Here, we make progress by analysing a local community model with species competing for a common resource under TES, to derive formulae partitioning species richness according to different mechanisms.By applying our formulae to generic parameter sets for tropical forest tree communities, we found that when the autocorrelation time of TES was short, the dominant mechanism driving species richness was non‐linear averaging of the interspecific competition term over time, which reduced the typical strength of interspecific competition and boosted richness relative to the neutral case. However, greater immigration to the community resulted in more species and hence weaker non‐linear averaging due to the law of large numbers. In contrast, when the autocorrelation time of TES was long, the dominant mechanism driving species richness was strong selection between changes in environmental conditions, which increased the typical strength of interspecific competition and reduced richness relative to the neutral case.By applying our formulae to a specific parameter set for a tropical forest tree community in Panama, we found that TES had minor effects on species richness because (i) the immigration rate was sufficiently large for non‐linear averaging of the interspecific competition term to be weak and (ii) the autocorrelation time was sufficiently short to suppress the effects of selection.Synthesis. We provide a novel mechanistic explanation of how TES affects tree species richness in tropical forests, in particular how TES often has minor effects on richness despite having substantial effects on temporal changes in species abundances. This provides a deeper insight into why a neutral model with added TES can accurately capture static and dynamic aspects of tree community diversity in the tropics. [ABSTRACT FROM AUTHOR]

A central goal in ecology is to understand what maintains species diversity in local communities. Classic ecological theory1,2 posits that niches dictate the maximum number of species that can coexist in a community and that the richness of observed species will be below this maximum only where immigration is very low. A new alternative theory3,4 is that niches, instead, dictate the minimum number of coexisting species and that the richness of observed species will usually be well above this because of ongoing immigration. We conducted an experimental test to discriminate between these two unified theories using a manipulative field experiment with tropical intertidal communities. We found, consistent with the new theory, that the relationship of species richness to immigration rate stabilized at a low value at low immigration rates and did not saturate at high immigration rates. Our results suggest that tropical intertidal communities have low niche diversity and are typically in a dispersal-assembled regime where immigration is high enough to overfill the niches. Observational data from other studies3,5 suggest that these conclusions may generalize to other ecological systems. Our new experimental approach can be adapted for other systems and be used as a ‘niche detector’ and a tool for assessing when communities are niche versus dispersal assembled.This study shows through a field experiment that tropical intertidal communities switch from a niche- to a dispersal-assembled regime as immigration rates rise. [ABSTRACT FROM AUTHOR]

The question of whether biodiversity conservation and carbon conservation can be synergistic hinges on the form of the biodiversity–productivity relationship (BPR), a fundamental ecological pattern. The stakes are particularly high when it comes to forests, which at a global level comprises a large fraction of both biodiversity and carbon. And yet, in forests, the BPR is relatively poorly understood. In this review, we critically evaluate research on forest BPRs, focussing on the experimental and observational studies of the last 2 decades. We find general support for a positive forest BPR, suggesting that biodiversity and carbon conservation are synergistic to a degree. However, we identify several major caveats: (i) although, on average, productivity may increase with biodiversity, the highest-yielding forests are often monocultures of very productive species; (ii) productivity typically saturates at fewer than ten species; (iii) positive BPRs can be driven by some third variable, in particular stem density, instead of a causal arrow from biodiversity to productivity; (iv) the BPR's sign and magnitude varies across spatial grains and extents, and it may be weak at scales relevant to conservation; and (v) most productivity estimates in forests are associated with large errors. We conclude by explaining the importance of these caveats for both conservation programmes focussed on protection of existing forests and conservation programmes focussed on restoring or replanting forests. [ABSTRACT FROM AUTHOR]

Neutral models in ecology assume that all species are demographically equivalent, such that their abundances differ ultimately because of demographic stochasticity rather than selection. In spite of their simplicity, neutral models have been found to accurately reproduce static patterns of biodiversity for diverse communities. However, the same neutral models have been found to exhibit species abundance dynamics that are far too slow compared to reality, resulting in poor fits to temporally dynamic patterns of biodiversity. Here, we show that one of the root causes of these slow dynamics is the additional assumption that a community has reached an equilibrium with a fixed community size, with species that have a net growth rate close to zero. We removed this additional assumption by constructing and analyzing a neutral model with an expected community size that can change over time and is not necessarily at equilibrium, which thus allows the historical formation of a community to be represented explicitly. Our analysis demonstrated that for the general scenario where a small community rapidly grows in size to a carrying capacity, representing recovery from ecological disturbance or assembly of a new community, the model produced much larger changes in species abundances and much shorter species ages than a neutral model at an equilibrium with fixed community size. In addition, the species abundance distribution was biphasic with a subset of abundant species arising from a founder effect. We confirmed these new results in applications of the new model to the specific scenario of recovery of the Amazon tree community after the end-Cretaceous bolide impact, which involved periods of increasing and decreasing community size. We conclude that incorporating transient dynamics in neutral models improves realism by allowing explicit consideration of how a community is formed over realistic time-scales. • Transient dynamics of a neutral model with varying community size are analyzed. • Formulae are derived specifying expected species richness and species age. • Formulae are derived specifying the species-abundance distribution. • Model gives a biphasic SAD with common species arising from a founder effect. • Model also gives realistic species ages for a tree community at an Amazon scale. [ABSTRACT FROM AUTHOR]

Habitat complexity has been considered a key driver of biodiversity and other ecological phenomena for nearly a century. However, there is still no consensus over the definition of complexity or how to measure it. Up‐to‐date and clear guidance on measuring complexity is urgently needed, particularly given the rise of remote sensing and advent of technologies that allow environments to be scanned at unprecedented spatial extents and resolutions. Here we review how complexity is measured in ecology. We provide a framework for metrics of habitat complexity, and for the related concept of spatial heterogeneity. We focus on the two most commonly used complexity metrics in ecology: fractal dimension and rugosity. We discuss the pros and cons of these metrics using practical examples from our own empirical data and from simulations. Fractal dimension is particularly widely used, and we provide a critical examination of it drawing on research from other scientific fields. We also discuss informational metrics of complexity and their potential benefits. We chart a path forward for research on measuring habitat complexity by presenting, as a guide, sets of essential and desirable criteria that a metric of complexity should possess. Lastly, we discuss the applied significance of our review. [ABSTRACT FROM AUTHOR]

To purchase or authenticate to the full-text of this article, please visit this link: http://dx.doi.org/10.1111/j.1523-1739.2007.00815.x Byline: RYAN CHISHOLM (*), ROBERT TAYLOR ([dagger]) Keywords: Australian mammals; critical weight range; extinction risk; mammal body size; null-hypothesis significance testing Abstract: Abstract: The critical weight range hypothesis for Australian terrestrial mammals states that species in the intermediate size range 35-5500 g are particularly susceptible to extinction. In a 2001 study Cardillo and Bromham found no statistically significant evidence for this hypothesis and suggested that research should instead focus on why small species are resistant to extinction. We used a similar data set of body sizes of Australian mammals grouped by conservation classification, but we used test statistics (mean deviation above and below the median body size) that are more statistically powerful than those of Cardillo and Bromham (quartiles, maxima, and minima of body size distributions). We found strong evidence in favor of the critical weight range hypothesis: the body size distribution of threatened species was more clustered toward the median body size from above and below. This pattern was statistically significant at the continental scale and in the arid zone, but not in the mesic zone. Confusing statistical significance with evidence of no effect, as Cardillo and Bromham did, can have negative implications for conservation biology because it can result in failure to act when action is warranted or provision of incorrect advice that affects policy and planning decisions. Abstract (Spanish): La Prueba de Significancia de la Hipotesis Nula y el Rango de Peso Critico para Mamiferos Australianos Resumen: La hipotesis del rango de peso critico (RPC) para mamiferos australianos terrestres plantea que las especies en el rango de tamano intermedio de 35-5500 g son particularmente susceptibles a la extincion. En un estudio en 2001, Cardillo y Bromham no encontraron evidencia significativa para esta hipotesis y sugirieron que, en su lugar, la investigacion se deberia enfocar al porque las especies pequenas son resistentes a la extincion. Utilizamos un conjunto de datos de tamanos corporales de mamiferos australianos agrupados por clasificacion de conservacion, pero utilizamos pruebas estadisticas (desviacion media por encima y por debajo de la mediana del tamano corporal) que son estadisticamente mas poderosas que utilizadas por Cardillo y Bromham (cuartilas, maximos y minimos de las distribuciones de tamanos corporales). Encontramos fuerte evidencia a favor de la hipotesis RPC: la distribucion del tamano corporal de especies amenazadas estuvo mayormente agrupada hacia la mediana del tamano corporal. Este patron fue estadisticamente significativo en la escala continental y en la zona arida, pero no en la zona mesica. La confusion de la significancia estadistica con la evidencia de no efecto, como hicieron Cardillo y Bromham, puede tener implicaciones negativas para la biologia de la conservacion porque puede resultar en la falta de accion cuando se requiera o en asesoria inadecuada que afecta las decisiones politicas y de planificacion. Author Affiliation: (*)Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, U.S.A., emailchisholm@princeton.edu ([dagger])Department of Environment and Conservation, Dubbo, New South Wales 2830, Australia Article History: Paper submitted February 17, 2007; revised manuscript accepted July 2, 2007.

Estimating the total number of species on Earth has been a longstanding pursuit. Models project anywhere between 2 and 10 million species, and discovery of new species continues to the present day. Despite this, we hypothesized that our current knowledge of phylogenetic diversity (PD) may be almost complete because new discoveries may be less phylogenetically distinct than past discoveries. Focusing on birds, which are well studied, we generated a robust phylogenetic tree for most extant species by combining existing published trees and calculated each discovery's marginal contribution to known PD since the first formal species descriptions in 1758. We found that PD contributions began to plateau in the early 1900s, about half a century earlier than species richness. Relative contributions of each phylogenetic order to known PD shifted over the first 150 years, with a growing contribution of the hyper-diverse perching birds (Passeriformes) in particular, but after the early 1900s this has remained relatively stable. Altogether, this suggests that our knowledge of the evolutionary history of extant birds is mostly complete, with few discoveries of high evolutionary novelty left to be made, and that conclusions of studies using avian phylogenies are likely to be robust to future species discoveries. [ABSTRACT FROM AUTHOR]

A long‐standing puzzle in ecology is coexistence of many species despite relatively few limiting resources. Studies using competitive community models have found that temporal environmental stochasticity (TES) can provide a solution by providing a rare‐species advantage, for example by creating temporal niches. However, this appears to contradict studies using population models, which have found that TES‐induced temporal fluctuations in species abundances increase the chance of species becoming rare and hence increase their extinction risk. Here, we clarified how TES affects species richness by analysing a competitive community model using a novel mean‐field approach. We found that when temporal correlation in TES was weak, the dominant effect of TES was to create temporal niches by decreasing the strength of interspecific competition via a temporal averaging effect, thereby increasing species richness relative to the neutral case without TES. In contrast, when temporal correlation was strong, the dominant effect of TES was to increase the strength of selection and hence interspecific competition, thereby decreasing species richness. Compared with these indirect community effects of TES, the direct effects of TES on species richness via temporal fluctuations in abundances of species populations were relatively minor. [ABSTRACT FROM AUTHOR]

Aim: Research in island biogeography has long focused mainly on present‐day island configurations. Recently, there has been an increasing focus on islands' past histories of land connection, shape and size. Moreover, continental islands (=shelf islands) have received less attention than oceanic islands, and species inventories from extremely small islands are lacking in many datasets. We examine the effects of sea‐level rise since the Last Glacial Maximum (LGM) on bird species diversity and composition of tropical shelf islands in Southeast Asia. Location: Sundaland. Taxon: Birds. Methods: We compiled avifaunal island inventories for 94 islands using an exhaustive literature review of historic surveys of larger islands combined with our own comprehensive island surveys from both small and large islands. Using generalised least‐squares models with spatial autocorrelation, we assessed the importance of traditional biogeographical parameters including area, maximum elevation, distance from mainland and geographical isolation, along with post‐LGM effects of change in island area and duration since isolation. We also compared the species composition on similar‐sized shelf islands from two categories—recently submerged and unsubmerged—using non‐metric multidimensional scaling. Results: Post‐LGM effects on species diversity are minimal and insular diversity is instead well explained by present‐day island characteristics, such as area, distance to mainland and proportion of land surrounding an island within a 10 km radius (Cox and Snell Pseudo‐R2 = 0.803). Avifaunal diversity is similar across recently submerged and unsubmerged small shelf islands. Main conclusion: Avifaunal diversity on tropical shelf islands equilibrates rapidly after isolation, indicating that both extinction and immigration rates are high. In particular, a high immigration rate of dispersive species maintains diversity, especially on small islands. Over‐water dispersal is generally restricted to short distances among Sundaic birds. Consequently, the diversity of an island can be maintained by the presence of large or stepping‐stone islands near it. [ABSTRACT FROM AUTHOR]

Theoretical ecologists have analysed a range of neutral models but few including stage structure. Here we introduce a stage‐structured neutral model, by extending the standard spatial neutral model to have two‐stage classes: a juvenile stage and a reproductive stage. We find that formulas for biodiversity patterns (e.g. species–area relationships and species abundance distributions) of reproductives in the stage‐structured model can be obtained from the corresponding standard formulas via a parameter rescaling, which involves calculating an effective speciation rate parameter and an effective dispersal parameter. This is useful because it means existing knowledge about the non‐stage‐structured model can be transferred to the stage‐structured model, providing that applications focus exclusively on the reproductive stage. One surprising implication is that the presence of a juvenile stage can substantially increase the species richness of reproductive individuals: a juvenile stage with a length fraction k that of the reproductive stage increases reproductive species richness by roughly the same factor. We apply our new formulas to a case study of tropical forest trees in Panama and find that while the stage‐structured model makes different predictions than the standard model, it does not fix known problems with cross‐scale predictions. We speculate that some of our results, in particular the result that the presence of a juvenile stage increases community diversity, likely apply to non‐neutral systems as well. [ABSTRACT FROM AUTHOR]

Bark contributes approximately 20% to the total above‐ground biomass of trees, yet bark is not properly accounted for when estimating carbon sequestered by trees. Current allometric functions estimate tree volume from diameter measured over the bark, and derive bark density and carbon content from estimates for wood. As the bark density of hardwood species is 40%–50% lower than the wood density, but nearly equivalent in conifers, bark carbon is overestimated for most species. The latter is further exacerbated by variation in bark volume with bark surface morphology.Fissured bark volume is overestimated by diameter over bark measurements by up to 40%. The vacant space in fissures can be accounted for by a bark fissure index (BFI). We calculate bark carbon for Australian species from a non‐destructive and effective BFI using bark thickness measured in the field.Bark volume, and in turn bark carbon, scaled inversely with tree size (diameter) so that bark volume comprised 42% of small trees (10 cm diameter at breast height, DBH) but 23% of large trees (50 cm DBH). Our BFI method using a bark thickness gauge (BGM) yielded similar results than using the less time‐efficient contour gauge method (CM) to estimate BFI (bias BGM‐CM −1.3%, non‐significant at p = 0.72). Both BGM and CM had an error of <4% compared to digitized BFI from destructive sampled stem disks. An average of 15 bark gauge measurements per tree estimated bark thickness (and inconsequence BFI) for both fissured and unfissured bark with <20% error relative to the exact value.Using the bark gauge method, BFI can be rapidly measured from large numbers of trees needed for estimating bark carbon at the community level and modelling carbon uptake, storage and cycling in woody biomes. [ABSTRACT FROM AUTHOR]

Bayesian methods have been developed for inferring the true year of extinction of a species from sighting records that have both certain and uncertain sightings. These methods typically make the restrictive assumption that all sighting types (i.e. certain, valid uncertain, invalid uncertain) derive from constant rate Poisson processes.In this study, the constant rate assumption in the homogeneous Poisson process is relaxed by allowing certain and uncertain sightings to follow independent non‐homogeneous Poisson processes. The model can thus identify whether any of the sighting rates were increasing, decreasing or constant. In addition, a change‐point is introduced to model the uncertain sightings, where the sighting rates before and after the change‐point vary.We have used Markov Chain Monte Carlo (MCMC) sampling to generate the posterior distributions for model parameters including species extinction time. The proposed method was applied to the sighting records of the black‐footed ferret Mustela nigripes and the ivory‐billed woodpecker Campephilus principalis (IBW) species.Based on a hypothesis test, the results of the model indicate that the species both went extinct in the years 1988 and 1956 respectively. Moreover, a decline in the certain sighting rate was also inferred for both these species, possibly indicating the decrease in the species abundance as it converges to extinction. Thus, earlier models that assume a constant sighting rate may well be biased. Uncertain sighting rates for the IBW were found to increase before extinction (indicating possibly some additional ecological attention received near extinction) and remained constant after extinction. [ABSTRACT FROM AUTHOR]

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A goal of ecology is to identify the stabilizing mechanisms that maintain species diversity in the face of competitive exclusion and drift. For tropical forest tree communities, it has been hypothesized that high diversity is maintained via Janzen-Connell effects, whereby host-specific natural enemies prevent any one species from becoming too abundant. Here we explore the plausibility of this hypothesis with theoretical models. We confirm a previous result that when added to a model with drift but no competitive exclusion—that is, a neutral model where intrinsic fitnesses are perfectly equalized across species—Janzen-Connell effects maintain very high species richness that scales strongly with community size. However, when competitive exclusion is introduced—that is, when intrinsic fitnesses vary across species—the number of species maintained by Janzen-Connell effects is substantially reduced and scales much less strongly with community size. Because fitness variation is pervasive in nature, we conclude that the potential of Janzen-Connell effects to maintain diversity is probably weak and that the mechanism does not yet provide a sufficient explanation for the observed high diversity of tropical forest tree communities. We also show that, surprisingly, dispersal limitation can further reduce the ability of Janzen-Connell effects to maintain diversity. [ABSTRACT FROM AUTHOR]

Neutral theory proposes that some macroscopic biodiversity patterns can be explained in terms of drift, speciation and immigration, without invoking niches. There are many different varieties of neutral model, all assuming that the fitness of an individual is unrelated to its species identity. Variants that are spatially explicit provide a means for making quantitative predictions about spatial biodiversity patterns.We present software packages that make spatially explicit neutral simulations straightforward and efficient. The packages allow the user to customize both dispersal and landscape structure in a wide variety of ways. We provide a Python package pycoalescence and a functionally equivalent R package rcoalescence. In both packages, the core routines are written in C++ and make use of coalescence methods to optimize performance.We explain the technical details of the packages and give examples for their application, with a particular focus on two scenarios of ecological and evolutionary interest—a landscape with habitat fragmentation, and an archipelago of islands.Spatially explicit neutral models represent an important tool in ecology for understanding the processes of biodiversity generation and predicting outcomes at large scales. The effort required to implement these complex spatially explicit simulations efficiently has thus far been a barrier to entry. Our packages increase the accessibility of these models and encourage further investigation of the primary mechanisms underpinning biodiversity. [ABSTRACT FROM AUTHOR]