Experimental evidence for an intraspecific Janzen-Connell effect mediated by soil biota

The negative effect of soil pathogens on seedling survival varies considerably among conspecific individuals, but the underlying mechanisms are largely unknown. For variation between heterospecifics, a common explanation is the Janzen-Connell effect: negative density dependence in survival due to specialized pathogens aggregating on common hosts. We test whether an intraspecific Janzen-Connell effect exists, i.e., whether the survival chances of one population's seedlings surrounded by a different conspecific population increase with genetic difference, spatial distance, and trait dissimilarity between them. In a shade-house experiment, we grew seedlings of five populations of each of two subtropical tree species (Castanopsis fissa and Canarium album) for which we measured genetic distance using intersimple sequence repeat (ISSR) analysis and eight common traits/characters, and we treated them with soil material or soil biota filtrate collected from different populations. We found that the relative survival rate increased with increasing dissimilarity measured by spatial distance, genetic distance, and trait differences between the seedling and the population around which the soil was collected. This effect disappeared after soil sterilization. Our results provide evidence that genetic variation, trait similarity, and spatial distance can explain intraspecific variation in plant-soil biotic interactions and suggest that limiting similarity also occurs at the intraspecific level.

High speciation rate at temperate latitudes explains unusual diversity gradients in a clade of ectomycorrhizal fungi

Understanding the patterns of biodiversity through time and space is a challenging task. However, phylogeny-based macroevolutionary models allow us to account and measure many of the processes responsible for diversity buildup, namely speciation and extinction. The general latitudinal diversity gradient (LDG) is a well-recognized pattern describing a decline in species richness from the equator polewards. Recent macroecological studies in ectomycorrhizal (EM) fungi have shown that their LDG is shifted, peaking at temperate rather than tropical latitudes. Here we investigate this phenomenon from a macroevolutionary perspective, focusing on a well-sampled group of edible EM mushrooms from the genus Amanita-the Caesar's mushrooms, which follow similar diversity patterns. Our approach consisted in applying a suite of models including (1) nontrait-dependent time-varying diversification (Bayesian analysis of macroevolutionary mixtures [BAMM]), (2) continuous trait-dependent diversification (quantitative-state speciation and extinction [QuaSSE]), and (3) diversity-dependent diversification. In short, results give strong support for high speciation rates at temperate latitudes (BAMM and QuaSSE). We also find some evidence for different diversity-dependence thresholds in "temperate" and "tropical" subclades, and little differences in diversity due to extinction. We conclude that our analyses on the Caesar's mushrooms give further evidence of a temperate-peaking LDG in EM fungi, highlighting the importance and the implications of macroevolutionary processes in explaining diversity gradients in microorganisms.

Equilibrium and non-equilibrium dynamics simultaneously operate in the Galápagos islands

Island biotas emerge from the interplay between colonisation, speciation and extinction and are often the scene of spectacular adaptive radiations. A common assumption is that insular diversity is at a dynamic equilibrium, but for remote islands, such as Hawaii or Galápagos, this idea remains untested. Here, we reconstruct the temporal accumulation of terrestrial bird species of the Galápagos using a novel phylogenetic method that estimates rates of biota assembly for an entire community. We show that species richness on the archipelago is in an ascending phase and does not tend towards equilibrium. The majority of the avifauna diversifies at a slow rate, without detectable ecological limits. However, Darwin's finches form an exception: they rapidly reach a carrying capacity and subsequently follow a coalescent‐like diversification process. Together, these results suggest that avian diversity of remote islands is rising, and challenge the mutual exclusivity of the non‐equilibrium and equilibrium ecological paradigms.

Unifying ecology and macroevolution with individual-based theory

A contemporary goal in both ecology and evolutionary biology is to develop theory that transcends the boundary between the two disciplines, to understand phenomena that cannot be explained by either field in isolation. This is challenging because macroevolution typically uses lineage-based models, whereas ecology often focuses on individual organisms. Here, we develop a new parsimonious individual-based theory by adding mild selection to the neutral theory of biodiversity. We show that this model generates realistic phylogenies showing a slowdown in diversification and also improves on the ecological predictions of neutral theory by explaining the occurrence of very common species. Moreover, we find the distribution of individual fitness changes over time, with average fitness increasing at a pace that depends positively on community size. Consequently, large communities tend to produce fitter species than smaller communities. These findings have broad implications beyond biodiversity theory, potentially impacting, for example, invasion biology and paleontology.

A sampling formula for ecological communities with multiple dispersal syndromes

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.

The importance of ecological costs for the evolution of plant defense against herbivory

Plant defense against herbivory comes at a cost, which can be either direct (reducing resources available for growth and reproduction) or indirect (through reducing ecological performance, for example intraspecific competitiveness). While direct costs have been well studied in theoretical models, ecological costs have received almost no attention. In this study we compare models with a direct trade-off (reduced growth rate) to models with an ecological trade-off (reduced competitive ability), using a combination of adaptive dynamics and simulations. In addition, we study the dependence of the level of defense that can evolve on the type of defense (directly by reducing consumption, or indirectly by inducing herbivore mortality (toxicity)), and on the type of herbivore against which the plant is defending itself (generalists or specialists). We find three major results: First, for both direct and ecological costs, defense only evolves if the benefit to the plant is direct (through reducing consumption). Second, the type of cost has a major effect on the evolutionary dynamics: direct costs always lead to a single optimal strategy against herbivores, but ecological costs can lead to branching and the coexistence of non-defending and defending plants; however, coexistence is only possible when defending against generalist herbivores. Finally, we find that fast-growing plants invest less than slow-growing plants when defending against generalist herbivores, as predicted by the Resource Availability Hypothesis, but invest more than slow-growing plants when defending against specialists. Our results clearly show that assumptions about ecological interactions are crucial for understanding the evolution of defense against herbivores.

When can species abundance data reveal non-neutrality?

Species abundance distributions (SAD) are probably ecology's most well-known empirical pattern, and over the last decades many models have been proposed to explain their shape. There is no consensus over which model is correct, because the degree to which different processes can be discerned from SAD patterns has not yet been rigorously quantified. We present a power calculation to quantify our ability to detect deviations from neutrality using species abundance data. We study non-neutral stochastic community models, and show that the presence of non-neutral processes is detectable if sample size is large enough and/or the amplitude of the effect is strong enough. Our framework can be used for any candidate community model that can be simulated on a computer, and determines both the sampling effort required to distinguish between alternative processes, and a range for the strength of non-neutral processes in communities whose patterns are statistically consistent with neutral theory. We find that even data sets of the scale of the 50 Ha forest plot on Barro Colorado Island, Panama, are unlikely to be large enough to detect deviations from neutrality caused by competitive interactions alone, though the presence of multiple non-neutral processes with contrasting effects on abundance distributions may be detectable.

A new dynamic null model for phylogenetic community structure

Phylogenies are increasingly applied to identify the mechanisms structuring ecological communities but progress has been hindered by a reliance on statistical null models that ignore the historical process of community assembly. Here, we address this, and develop a dynamic null model of assembly by allopatric speciation, colonisation and local extinction. Incorporating these processes fundamentally alters the structure of communities expected due to chance, with speciation leading to phylogenetic overdispersion compared to a classical statistical null model assuming equal probabilities of community membership. Applying this method to bird and primate communities in South America we show that patterns of phylogenetic overdispersion – often attributed to negative biotic interactions – are instead consistent with a species neutral model of allopatric speciation, colonisation and local extinction. Our findings provide a new null expectation for phylogenetic community patterns and highlight the importance of explicitly accounting for the dynamic history of assembly when testing the mechanisms governing community structure.

Estimating the duration of speciation from phylogenies

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. 2014). 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.

The effects of island ontogeny on species diversity and phylogeny

A major goal of island biogeography is to understand how island communities are assembled over time. However, we know little about the influence of variable area and ecological opportunity on island biotas over geological timescales. Islands have limited life spans, and it has been posited that insular diversity patterns should rise and fall with an island's ontogeny. The potential of phylogenies to inform us of island ontogenetic stage remains unclear, as we lack a phylogenetic framework that focuses on islands rather than clades. Here, we present a parsimonious island-centric model that integrates phylogeny and ontogeny into island biogeography and can incorporate a negative feedback of diversity on species origination. This framework allows us to generate predictions about species richness and phylogenies on islands of different ages. We find that peak richness lags behind peak island area, and that endemic species age increases with island age on volcanic islands. When diversity negatively affects rates of immigration and cladogenesis, our model predicts speciation slowdowns on old islands. Importantly, we find that branching times of in situ radiations can be informative of an island's ontogenetic stage. This novel framework provides a quantitative means of uncovering processes responsible for island biogeography patterns using phylogenies.

The reconstructed tree in the lineage-based model of protracted speciation

A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree produced by a given model of diversification. Etienne and Rosindell in Syst Biol 61(2):204-213, (2012) proposed a lineage-based model of diversification, called protracted speciation, where species remain incipient during a random duration before turning good species, and showed that this can explain the slowdown in lineage accumulation observed in real phylogenies. However, they were unable to provide a general likelihood formula. Here, we present a likelihood formula for protracted speciation models, where rates at which species turn good or become extinct can depend both on their age and on time. Our only restrictive assumption is that speciation rate does not depend on species status. Our likelihood formula utilizes a new technique, based on the contour of the phylogenetic tree and first developed by Lambert in Ann Probab 38(1):348-395, (2010). We consider the reconstructed trees spanned by all extant species, by all good extant species, or by all representative species, which are either good extant species or incipient species representative of some good extinct species. Specifically, we prove that each of these trees is a coalescent point process, that is, a planar, ultrametric tree where the coalescence times between two consecutive tips are independent, identically distributed random variables. We characterize the common distribution of these coalescence times in some, biologically meaningful, special cases for which the likelihood reduces to an elegant analytical formula or becomes numerically tractable.

Shifts in pollinator population structure may jeopardize pollination service

Plant-pollinator interactions are among the best known and ubiquitous plant-animal mutualisms and are crucial for ecosystem functioning and the maintenance of biodiversity. Most pollinators are insects with several life-stages (e.g. egg, larva, pupa, adult) and the mutualistic interaction depends on the pollinator surviving these different life-stages. However, to our knowledge, pollinator population structure has been ignored in most theoretical models of plant-pollinator dynamics, and we lack understanding of the role of different life-stages in determining the stability of the mutualism. Here we therefore develop a simple plant-pollinator model with a facultative plant and an obligate pollinator with stage-structure. Our model predicts a globally stable equilibrium when pollinator demography is dominated by adults and a locally stable equilibrium when the plants are strongly dependent on pollination and pollinator demography is dominated by the larval stage. In the latter case, the mutualism is vulnerable to fluctuations in the pollinator population size or structure caused by external factors (e.g. pesticides) reducing larval development and increasing adult mortality. This may cause a sudden collapse rather than gradual decrease of the mutualism, after which the pollination service cannot be recovered by reducing these detrimental external factors, but must be accompanied by large increases in pollinator populations. This highlights the importance of considering population structure in plant-pollinator interactions.

Invasion success in a marginal habitat: an experimental test of competitive ability and drought tolerance in Chromolaena odorata

Climatic niche models based on native-range climatic data accurately predict invasive-range distributions in the majority of species. However, these models often do not account for ecological and evolutionary processes, which limit the ability to predict future range expansion. This might be particularly problematic in the case of invaders that occupy environments that would be considered marginal relative to the climatic niche in the native range of the species. Here, we assess the potential for future range expansion in the shrub Chromolaena odorata that is currently invading mesic savannas (>650 mm MAP) in South Africa that are colder and drier than most habitats in its native range. In a greenhouse experiment we tested whether its current distribution in South Africa can be explained by increased competitive ability and/or differentiation in drought tolerance relative to the native population. We compared aboveground biomass, biomass allocation, water use efficiency and relative yields of native and invasive C. odorata and the resident grass Panicum maximum in wet and dry conditions. Surprisingly, we found little differentiation between ranges. Invasive C. odorata showed no increased competitive ability or superior drought tolerance compared to native C. odorata. Moreover we found that P. maximum was a better competitor than either native or invasive C. odorata. These results imply that C. odorata is unlikely to expand its future range towards more extreme, drier, habitats beyond the limits of its current climatic niche and that the species’ invasiveness most likely depends on superior light interception when temporarily released from competition by disturbance. Our study highlights the fact that species can successfully invade habitats that are at the extreme end of their ranges and thereby contributes towards a better understanding of range expansion during species invasions.

Predicting coexistence of plants subject to a tolerance-competition trade-off

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.

Caught in the middle: Asymmetric competition causes high variance in intermediate trait abundances

In asymmetric competition between two individuals of the same or different species, one individual has a distinct advantage over the other due to a particular beneficial trait. An important trait that induces asymmetric competition is size (body size in animals, height in plants). There is usually a trade-off between fecundity and the trait that leads to competitive superiority (e.g. seed number vs seed size), enabling coexistence of populations with different trait values. These predictions on coexistence are based on classic deterministic models. Here, we explore the behaviour of a stochastic model of asymmetric competition where stochasticity is assumed to be demographic. We derive approximations for the temporal variance and covariance of the population sizes of the coexisting species. The derivations highlight that the variability of the population size of a species strongly depends on the stochastic fluctuations of species with higher trait values, while they are less influenced by species with lower trait values. Particularly, species with intermediate trait values are strongly affected resulting in relatively high variability. As a result these species have a relative high probability of extinction even though they have a larger population size than species with high trait values. We confirm these approximations with individual-based simulations. Thus, our analysis can explain gaps in size distributions as an emergent property of systems with a fecundity-competition trade-off.

The neutral-niche debate: a philosophical perspective

Ecological communities around the world are under threat while a consensus theory of community structure remains elusive. In the last decade ecologists have struggled with two seemingly opposing theories: niche-based theory that explains diversity with species’ differences and the neutral theory of biodiversity that claims that much of the diversity we observe can be explained without explicitly invoking species’ differences. Although ecologists are increasingly attempting to reconcile these two theories, there is still much resistance against the neutral theory of biodiversity. Here we argue that the dispute between the two theories is a classic example of the dichotomy between philosophical perspectives, realism and instrumentalism. Realism is associated with specific, small-scale and detailed explanations, whereas instrumentalism is linked to general, large-scale, but less precise accounts. Recognizing this will help ecologists get both niche-based and neutral theories in perspective as useful tools for understanding biodiversity patterns.

Comment on "Global correlations in tropical tree species richness and abundance reject neutrality"

Ricklefs and Renner (Reports, 27 January 2012, p. 464) showed correlations of species richness and individual abundance within families across continents and claimed that neutral theory predicts no such correlation. However, they did not substantiate this claim quantitatively with a neutral model. Here, we show that neutral theory can be consistent with these correlations and, consequently, that the correlations alone cannot reject neutrality.