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Biodiversity accumulates hierarchically by means of ecological and evolutionary processes and feedbacks. Within ecological communities drift, dispersal, speciation, and selection operate simultaneously to shape patterns of biodiversity. Reconciling the relative importance of these is hindered by current models and inference methods, which tend to focus on a subset of processes and their resulting predictions. Here we introduce Massive Eco-evolutionary Synthesis Simulations (MESS), a unified mechanistic model of community assembly, rooted in classic island biogeography theory, which makes temporally explicit joint predictions across three biodiversity data axes: i) species richness and abundances; ii) population genetic diversities; and iii) trait variation in a phylogenetic context. Using simulations we demonstrate that each data axis captures information at different timescales, and that integrating these axes enables discriminating among previously unidentifiable community assembly models. MESS is unique in generating predictions of community-scale genetic diversity, and in characterizing joint patterns of genetic diversity, abundance, and trait values. MESS unlocks the full potential for investigation of biodiversity processes using multi-dimensional community data including a genetic component, such as might be produced by contemporary eDNA or metabarcoding studies. We combine with supervised machine learning to fit the parameters of the model to real data and infer processes underlying how biodiversity accumulates, using communities of tropical trees, arthropods, and gastropods as case studies that span a range of data availability scenarios, and spatial and taxonomic scales., Funding was provided by grants from FAPESP (BIOTA, 2013/50297-0 to MJH and AC Carnaval), the Synthesis Centre of iDiv (DFG FZT 118), NASA through the Dimensions of Biodiversity Program (DOB 1343578) and the National Science Foundation (DEB-1253710 to MJH; DEB 1745562 to AC Carnaval; DBI 1927319 to AJR). IO was supported by the Mina Rees Dissertation Fellowship in the Sciences provided by the Graduate Center of the City University of New York. MR was supported by the Bioinformatics and Computational Biology Fellowship through the Institute for Bioinformatics and Evolutionary Studies at the University of Idaho. AJR was supported by the Santa Fe Institute Omidyar Fellowship. JR was supported by fellowships from the Natural Environment Research Council (NERC) (NE/I021179, NE/L011611/1). RSE was supported by an NWO-VICI grant. This work is a contribution to Imperial College’s Grand Challenges in Ecosystems and the Environment initiative, through JR.

Molecular phylogenies have been increasingly recognized as an important source of information on species diversification. For many models of macroevolution, analytical likelihood formulas have been derived to infer macroevolutionary parameters from phylogenies. A few years ago, a general framework to numerically compute such likelihood formulas was proposed, which accommodates models that allow speciation and/or extinction rates to depend on diversity. This framework calculates the likelihood as the probability of the diversification process being consistent with the phylogeny from the root to the tips. However, while some readers found the framework presented in Etienne et al. (Proc R Soc Lond B Biol Sci 279(1732):1300–1309, 2012) convincing, others still questioned it (personal communication), despite numerical evidence that for special cases the framework yields the same (i.e., within double precision) numerical value for the likelihood as analytical formulas do that were independently derived for these special cases. Here we prove analytically that the likelihoods calculated in the new framework are correct for all special cases with known analytical likelihood formula. Our results thus add substantial mathematical support for the overall coherence of the general framework.

The development of neutral community theory has shown that the assumption of species neutrality, although implausible on the level of individual species, can lead to reasonable predictions on the community level. While Hubbell's neutral model and several of its variants have been analyzed in quite some detail, the comparison of theoretical predictions with empirical abundance data is often hindered by technical problems. Only for a few models the exact solution of the stationary abundance distribution is known and sufficiently simple to be applied to data. For other models approximate solutions have been proposed, but their accuracy is questionable. Here, we argue that many of these technical problems can be overcome by replacing the assumption of constant community size (the zero-sum constraint) by the assumption of independent species abundances. We present a general sampling formula for community abundance data under this assumption. We show that for the few models for which an exact solution with zero-sum constraint is known, our independent-species approach leads to very similar parameter estimates as the zero-sum models, for six frequently studied tropical forest community samples. We show that our general sampling formula can be easily confronted to a much wider range of data sets (very large data sets, relative abundance data, presence-absence data, and sets of multiple samples) for a large class of models, including non-neutral ones. We provide an R package, called SADISA (Species Abundance Distributions under the Independent Species Assumption), to facilitate the use of the sampling formula. This article is protected by copyright. All rights reserved.

International audience; Over the past decade, the neutral theory of biodiversity has stirred up community assembly theory considerably by suggesting that stochasticity in the form of ecological drift is an important factor determining community composition and community turnover. The neutral theory assumes that all species within a community are functionally equivalent (the neutrality assumption), and therefore applies best to communities of trophically similar species. Evidently, trophically similar species may still differ in dispersal ability, and therefore may not be completely functionally equivalent. Here we present a new sampling formula that takes into account the partitioning of a community into two guilds that differ in immigration rate. We show that, using this sampling formula, we can accurately detect a subdivision into guilds from species abundance distributions, given ecological data about dispersal ability. We apply our sampling formula to tropical tree data from Barro Colorado Island, Panama. Tropical trees are divided depending on their dispersal mode, where biotically dispersed trees are grouped as one guild, and abiotically dispersed trees represent another guild. We find that breaking neutrality by adding guild structure to the neutral model significantly improves the fit to data and provides a better understanding of community assembly on BCI. Our findings are thus an important step towards an integration of neutral and niche theory.

Ecological trade-offs between species are often invoked to explain species coexistence in ecological communities. However, few mathematical models have been proposed for which coexistence conditions can be characterized explicitly in terms of a trade-off. Here we present a model of a plant community which allows such a characterization. In the model plant species compete for sites where each site has a fixed stress condition. Species differ both in stress tolerance and competitive ability. Stress tolerance is quantified as the fraction of sites with stress conditions low enough to allow establishment. Competitive ability is quantified as the propensity to win the competition for empty sites. We derive the deterministic, discrete-time dynamical system for the species abundances. We prove the conditions under which plant species can coexist in a stable equilibrium. We show that the coexistence conditions can be characterized graphically, clearly illustrating the trade-off between stress tolerance and competitive ability. We compare our model with a recently proposed, continuous-time dynamical system for a tolerance-fecundity trade-off in plant communities, and we show that this model is a special case of the continuous-time version of our model., Comment: To be published in Journal of Mathematical Biology. 30 pages, 5 figures, 5 appendices

International audience; Speciation is not instantaneous but takes time. The protracted birth-death diversification model incorporates this fact and predicts the often observed slowdown of lineage accumulation toward the present. The mathematical complexity of the protracted speciation model has barred estimation of its parameters until recently a method to compute the likelihood of phylogenetic branching times under this model was outlined (Lambert et al. ). Here, we implement this method and study using simulated phylogenies of extant species how well we can estimate the model parameters (rate of initiation of speciation, rate of extinction of incipient and good species, and rate of completion of speciation) as well as the duration of speciation, which is a combination of the aforementioned parameters. We illustrate our approach by applying it to a primate phylogeny. The simulations show that phylogenies often do not contain enough information to provide unbiased estimates of the speciation-initiation rate and the extinction rate, but the duration of speciation can be estimated without much bias. The estimate of the duration of speciation for the primate clade is consistent with literature estimates. We conclude that phylogenies combined with the protracted speciation model provide a promising way to estimate the duration of speciation.

International audience; The roles of species richness, resource use, and resource availability are central to many hypotheses explaining the diversityinvasion phenomenon but are generally not investigated together. Here, we created a large diversity gradient of soil microbial communities by either assembling communities of pure bacterial strains or removing the diversity of a natural soil. Using data on the resource-use capacities of the soil communities and an invader that were gathered from 71 carbon sources, we quantified the niches available to both constituents by using the metrics community niche and remaining niche available to the invader. A strong positive relationship between species richness and community niche across both experiments indicated the presence of resource complementarity. Moreover, community niche and the remaining niche available to the invader predicted invader abundance well. This suggested that increased competition in communities of higher diversity limits community invasibility and underscored the importance of resource availability as a key mechanism through which diversity hinders invasions. As a proof of principle, we subjected selected invaded communities to a resource pulse, which progressively uncoupled the link between soil microbial diversity and invasion and allowed the invader to rebound after nearly being eliminated in some communities. Our results thus show that (1) resource competition suppresses invasion, (2) biodiversity increases resource competition and decreases invasion through niche preemption, and (3) resource pulses that cannot be fully used, even by diverse communities, are favorable to invasion.

The mathematical structure of the two models is summarized in Table 1. The metacommunity composition inside a niche is given by Hubbell’s metacommunity distribution. The model of CP10 imposes the zero-sum constraint, whereas our model does not. Hence, the two models differ only in the sizes of the metacommunity niches. The absolute niche sizes (i.e. the number of individuals in a niche) are infinite in both models; the relative niche sizes (i.e. the fraction of individuals in a niche) are fixed in the model of CP10, and are randomly distributed in our model. This distribution tends to the fixed niche sizes of CP10’s model for high diversity, so that the two models coincide for highly diverse metacommunities. The local community is a sample from the metacommunity, that can be taken with or without dispersal limitation. For both models, the local community SAD inside a niche is given by the Ewens (without dispersal limitation; Ewens 1972) or the Etienne (with dispersal limitation; Etienne 2005) distribution. The models only differ in the niche sizes: fixed in the model of CP10, and randomly distributed in our model. Again, the latter distribution tends to the fixed niche sizes of CP10’s model when the diversity in the local community is high, so that the two models coincide for highly diverse communities.

aeres : ACL; International audience; Hubbell's neutral theory claims that ecological patterns such as species abundance distributions can be explained by a stochastic model based on simple assumptions. One of these assumptions, the point mutation assumption, states that every individual has the same probability to speciate. Etienne et al. have argued that other assumptions on the speciation process could be more realistic, for example, that every species has the same probability to speciate (Etienne, et al. in Oikos 116:241-258, 2007). They introduced a number of neutral community models with a different speciation process, and conjectured formulas for their stationary species abundance distribution. Here we study a generalised neutral community model, encompassing these modified models, and derive its stationary distribution, thus proving the conjectured formulas.

The zero-sum assumption is one of the ingredients of the standard neutral model of biodiversity by Hubbell. It states that the community is saturated all the time, which in this model means that the total number of individuals in the community is constant over time, and therefore introduces a coupling between species abundances. It was shown recently that a neutral model with independent species, and thus without any coupling between species abundances, has the same sampling formula (given a fixed number of individuals in the sample) as the standard model [Etienne, R.S., Alonso, D., McKane, A.J., 2007. The zero-sum assumption in neutral biodiversity theory. J. Theor. Biol. 248, 522-536]. The equilibria of both models are therefore equivalent from a practical point of view. Here we show that this equivalence can be extended to a class of neutral models with density-dependence on the community-level. This result can be interpreted as robustness of the model, i.e. insensitivity of the model to the precise interaction of the species in a neutral community. It can also be interpreted as a lack of resolution, as different mechanisms of interactions between neutral species cannot be distinguished using only a single snapshot of species abundance data. (C) 2008 Elsevier Ltd. All rights reserved.

The neutral theory of S. P. Hubbell postulates a two-scale hierarchical framework consisting of a metacommunity following the speciation - drift equilibrium characterized by the "biodiversity number'' theta, and local communities following the migration - drift equilibrium characterized by the "migration rate'' m ( or the "fundamental dispersal number'' I). While Etienne's sampling formula allows simultaneous estimation of h and m from a single sample of a local community, its applicability to a network of ( rather small) samples is questionable. We de. ne here an alternative two-stage approach estimating h from an adequate subset of the individuals sampled in the field ( using Ewens' sampling formula) and m from community samples ( using Etienne's sampling formula). We compare its results with the simultaneous estimation of theta and m ( one-stage estimation), for simulated neutral samples and for 50 1-ha plots of evergreen forest in South India. The one-stage approach exhibits problems of bias and of poor differentiability between high-theta, low-m and low-theta, high-m solution domains. Conversely, the two-stage approach yielded reasonable estimates and is to be preferred when several small, scattered plots are available instead of a single large one.