Tree inventory data from permanent plots in French forest reserves.

We present a data set resulting from the first round of a national monitoring program of forest reserves. It contains 9538 permanent plots, distributed across 111 study sites in mainland France (including Corsica). Notably focusing on dead wood measurement, this protocol has primarily been applied in strict forest reserves and special nature reserves (sensu Bollmann & Braunisch 2013), with 68% (6494) of the plots being currently located in strict forest reserves (unmanaged) and 24.7% (2363 plots) in forests unmanaged for at least 50 years. Sites cover a large variety of ecological conditions, from lowland to subalpine forests, but with an underrepresentation of Mediterranean forests (Table 1). The protocol assesses all the stages of a tree's life cycle, from seedling to decomposed lying dead wood. On each plot, a combination of three sampling techniques was used: (1) fixed-area inventory for regeneration, standing dead trees, living trees, and coarse woody debris (CWD) with diameter over 30 cm; (2) transect lines for CWD with diameter <30 cm; and (3) fixed-angle plot method for living trees with diameter at breast height (DBH) >30 cm (using a relascopic angle of 3%). Measurements include exact tree location (azimuth, distance), species, diameter(s), tree-related microhabitats, decay stage and bark cover, and seedling cover. With ongoing climate change, the program network can also provide important information to monitor changes in forest ecosystems. It can also be used as forest management monitoring or conservation status assessment. These data are freely available for noncommercial scientific use (Creative Commons Attribution 4.0 CC BY SA 4.0) with attribution, and this paper must be cited if this material is reused.

Pólya-splitting distributions as stationary solutions of multivariate birth-death processes under extended neutral theory.

Multivariate count distributions are crucial for the inference of ecological processes underpinning biodiversity. In particular, neutral theory provides useful null distributions allowing the evaluation of adaptation or natural selection. In this paper, we build a broader family of multivariate distributions: the Polya-splitting distributions. We show that they emerge naturally as stationary distributions of a multivariate birth-death process. This family of distributions is a consistent extension of non-zero sum neutral models based on a master equation approach. It allows considering both total abundance of the community and relative abundances of species. We emphasize that this family is large enough to encompass various dependence structures among species. We also introduce the strong closure under addition property that can be useful to generate nested multi-level dependence structures. Although all Pólya splitting distributions do not share this property, we provide numerous example verifying it. They include the previously known example with independent species, and also new ones with alternative dependence structures. Overall, we advocate that Polya-splitting distribution should become a part of the classic toolbox for the analysis of multivariate count data in ecology, providing alternative approaches to joint species distribution framework. Comparatively, our approach allows to model dependencies between species at the observation level, while the classical JSDM's model dependencies at the latent process strata.

Assessing metacommunity processes through signatures in spatiotemporal turnover of community composition.

Although metacommunity ecology has been a major field of research in the last decades, with both conceptual and empirical outputs, the analysis of the temporal dynamics of metacommunities has only emerged recently and consists mostly of repeated static analyses. Here we propose a novel analytical framework to assess metacommunity processes using path analyses of spatial and temporal diversity turnovers. We detail the principles and practical aspects of this framework and apply it to simulated datasets to illustrate its ability to decipher the respective contributions of entangled drivers of metacommunity dynamics. We then apply it to four empirical datasets. Empirical results support the view that metacommunity dynamics may be generally shaped by multiple ecological processes acting in concert, with environmental filtering being variable across both space and time. These results reinforce our call to go beyond static analyses of metacommunities that are blind to the temporal part of environmental variability.

Analyzing snapshot diversity patterns with the Neutral Theory can show functional groups' effects on community assembly.

A central question of community ecology is to understand how the interplay between processes of the Neutral Theory (e.g., immigration and ecological drift) and niche-based processes (e.g., environmental filtering, intra- and interspecific density dependence) shape species diversity in competitive communities. The articulation between these two categories of mechanisms can be studied through the lens of the intermediate organizational level of "functional groups" (FGs), defined as clusters of species with similar traits. Indeed, FGs stress ecological differences among species and are thus likely to unravel non-neutral interactions within communities. Here we presented a novel approach to explore how FGs affect species coexistence by comparing species and functional diversity patterns. Our framework considers the Neutral Theory as a mechanistic null hypothesis. It assesses how much the functional diversity deviates from species diversity in communities, and compares this deviation, called the "average functional deviation," to a neutral baseline. We showed that the average functional deviation can indicate reduced negative density dependence or environmental filtering among FGs. We validated our framework using simulations illustrating the two situations. We further analyzed tropical tree communities in Western Ghats, India. Our analysis of the average functional deviation revealed environmental filtering between deciduous and evergreen FGs along a broad rainfall gradient. By contrast, we did not find clear evidence for reduced density dependence among FGs. We predict that applying our approach to new case studies where environmental gradients are milder and FGs are more clearly associated to resource partitioning should reveal the missing pattern of reduced density dependence among FGs.

Abundance-based detectability in a spatially-explicit metapopulation: a case study on a vulnerable beetle species in hollow trees.

In many fragmented habitats, the detectability of a population in a habitat patch closely depends on the local abundance of individuals. However, metapopulation studies rarely connect abundance and detectability. We propose a framework for using abundance-based estimates of detectability in the analysis of a spatially-explicit stochastic patch occupancy model (SPOM). We illustrate our approach with the example of Tenebrio opacus, a beetle inhabiting hollows in old trees, and have based it on a 6-year monitoring programme of adult beetles in an area harbouring a high density of old oaks. We validated our abundance-based methodology by showing that the estimates of detectability were positively and significantly correlated with those obtained from presence/absence data (Pearson r = 0.54, p < 2E-16) in our study system. We further showed that the height of the hollow on the tree and the area of its entrance hole, the living status and girth of the host tree, and the time of survey significantly affected the detectability of beetle populations. Median detectability was 51% for one survey. The SPOM analysis revealed a high but heterogeneous extinction risk among trees, suggesting a metapopulation dynamics between the "classic" and "mainland-island" paradigms. However, it also indicated unexplained beetle colonization of trees in our study, despite the fact that we included limited detectability in our estimation procedure. This may have been due to the cryptic larval stage of T. opacus and may thus invalidate the use of a classic SPOM in our study system.

Ecological versatility and the assembly of multiple competitors: cautionary notes for assembly inferences.

The role of niche differences and competition is invoked when one finds coexisting species to be more dissimilar in trait composition than expected at random in community assembly studies. This approach has been questioned as competition has been hypothesized to either lead to communities assembled by similar or dissimilar species, depending on whether species similarity reflects fitness or niche differences, respectively. A current problem is that the arguments used to draw relationships between competition and species similarity are based on pairwise theoretical examples, while in nature competition can occurs among a constellation of species with different levels of versatility in resources used. By versatility we mean the documented ability of some species to escape competition for commonly used resources by changing for marginal and unused resources. Thus, a versatile species will have the ability to decrease niche overlap with all other species when facing strong competitors. When these species are embedded in multiple interactions the role of pairwise niche and fitness differences could be reduced due to indirect effects and thus competition would not be detectable. Here we developed a coexistence theory where competition occurs simultaneously among multiple species with different levels of versatility and then used it in a simulation to unravel patterns of species similarity during community assembly. We found that simulated communities can be assembled by species with more, less or equal similarity compared to a null model when using a mean distance based metric (SES.MPD). However, contrasting these varied results, we consistently found species overdispersion using a nearest neighbor-based metric (SES.MNTD), even when species differences reflected more directly their competitive abilities than their niche differences. Strong tendency to overdispersion emerged when high ecological versatility promoted large niche differences and enabled coexistence. This is because versatility to use marginal resources compensates possible fitness differences among species. Our findings provide mounting evidence of the important role of minimum niche differences and versatility in resource consumption for species embedded in multiple direct and indirect interactions.

The effects of archipelago spatial structure on island diversity and endemism: predictions from a spatially-structured neutral model.

Islands are particularly suited to testing hypotheses about the ecological and evolutionary mechanisms underpinning community assembly. Yet the complex spatial arrangements of real island systems have received little attention from both empirical studies and theoretical models. Here, we investigate the extent to which the spatial structure of archipelagos affects species diversity and endemism. We start by proposing a new spatially structured neutral model that explicitly considers archipelago structure, and then investigate its predictions under a diversity of scenarios. Our results suggest that considering the spatial structure of archipelagos is crucial to understanding their diversity and endemism, with structured island systems acting both as "museums" and "cradles" of biodiversity. These dynamics of diversification may change the traditionally expected pattern of decrease in species richness with distance from the mainland, even potentially leading to increasing patterns for taxa with high speciation rates in archipelagos off species-poor continental areas. Our results also predict that, within spatially structured archipelagos, metapopulation dynamics and evolutionary processes can generate higher diversity on islands more centrally placed than at the periphery. We derive from our results a set of theoretical predictions, potentially testable with empirical data.

The evolution of the competition-dispersal trade-off affects α- and ß-diversity in a heterogeneous metacommunity.

Difference in dispersal ability is a key driver of species coexistence in metacommunities. However, the available frameworks for interpreting species diversity patterns in natura often overlook trade-offs and evolutionary constraints associated with dispersal. Here, we build a metacommunity model accounting for dispersal evolution and a competition-dispersal trade-off. Depending on the distribution of carrying capacities among communities, species dispersal values are distributed either around a single strategy (evolutionarily stable strategy, ESS), or around distinct strategies (evolutionary branching, EB). We show that limited dispersal generates spatial aggregation of dispersal traits in ESS and EB scenarios, and that the competition-dispersal trade-off strengthens the pattern in the EB scenario. Importantly, individuals in larger (respectively (resp.) smaller) communities tend to harbour lower (resp. higher) dispersal, especially under the EB scenario. We explore how dispersal evolution affects species diversity patterns by comparing those from our model to the predictions of a neutral metacommunity model. The most marked difference is detected under EB, with distinctive values of both α- and ß-diversity (e.g. the dissimilarity in species composition between small and large communities was significantly larger than neutral predictions). We conclude that, from an empirical perspective, jointly assessing community carrying capacity with species dispersal strategies should improve our understanding of diversity patterns in metacommunities.

Intraspecific genetic variation and species coexistence in plant communities.

Many studies report that intraspecific genetic variation in plants can affect community composition and coexistence. However, less is known about which traits are responsible and the mechanisms by which variation in these traits affect the associated community. Focusing on plant-plant interactions, we review empirical studies exemplifying how intraspecific genetic variation in functional traits impacts plant coexistence. Intraspecific variation in chemical and architectural traits promotes species coexistence, by both increasing habitat heterogeneity and altering competitive hierarchies. Decomposing species interactions into interactions between genotypes shows that genotype × genotype interactions are often intransitive. The outcome of plant-plant interactions varies with local adaptation to the environment and with dominant neighbour genotypes, and some plants can recognize the genetic identity of neighbour plants if they have a common history of coexistence. Taken together, this reveals a very dynamic nature of coexistence. We outline how more traits mediating plant-plant interactions may be identified, and how future studies could use population genetic surveys of genotype distribution in nature and methods from trait-based ecology to better quantify the impact of intraspecific genetic variation on plant coexistence.

A neutral theory for interpreting correlations between species and genetic diversity in communities.

Spatial patterns of biological diversity have been extensively studied in ecology and population genetics, because they reflect the forces acting on biodiversity. A growing number of studies have found that genetic (within-species) and species diversity can be correlated in space (the so-called species-gene diversity correlation [SGDC]), which suggests that they are controlled by nonindependent processes. Positive SGDCs are generally assumed to arise from parallel responses of genetic and species diversity to variation in site size and connectivity. However, this argument implicitly assumes a neutral model that has yet to be developed. Here, we build such a model to predict SGDC in a metacommunity. We describe how SGDC emerges from competition within sites and variation in connectivity and carrying capacity among sites. We then introduce the formerly ignored mutation process, which affects genetic but not species diversity. When mutation rate is low, our model confirms that variation in the number of migrants among sites creates positive SGDCs. However, when considering high mutation rates, interactions between mutation, migration, and competition can produce negative SGDCs. Neutral processes thus do not always contribute positively to SGDCs. Our approach provides empirical guidelines for interpreting these novel patterns in natura with respect to evolutionary and ecological forces shaping metacommunities.