The concept of alternative stable states has long been a dominant framework for studying the influence of historical contingency in community assembly. This concept focuses on stable states, yet many real communities are kept in a transient state by disturbance, and the utility of predictions for stable states in explaining transient states remains unclear. Using a simple model of plant community assembly, we show that the conditions under which historical contingency affects community assembly can differ greatly for stable versus transient states. Differences arise because the contribution of such factors as mortality rate, environmental heterogeneity and plant-soil feedback to historical contingency changes as community assembly proceeds. We also show that transient states can last for a long time relative to immigration rate and generation time. These results argue for a conceptual shift of focus from alternative stable states to alternative transient states for understanding historical contingency in community assembly.

Summary 1.A plant that causes specific changes to soil biota may either positively or negatively affect the performance of the plant that subsequently grows in that location. These effects, known as plant-soil feedback, can affect plant species diversity at multiple spatial scales. 2. It has been hypothesized that positive plant-soil feedback reduces alpha (local) diversity by allowing dominance by early-arriving species, but increases gamma (regional) diversity by promoting community divergence (increased beta diversity) through the emergence of alternative stable states. In contrast, negative plant-soil feedback has been thought to increase alpha diversity by allowing local species coexistence, but to reduce gamma diversity by promoting community convergence (reduced beta diversity). Although widely accepted, these hypotheses do not consider the possibility that plant species differ in their effect on, and their response to, a given other species via soil biota. In reality, plant-soil interactions can be complex, with the strength of the interactions variable between plant species. Using a basic simulation model of plant community assembly, we investigated how complex plant-soil interactions might affect plant diversity during succession. 3. When we included only positive or negative intraspecific plant-soil feedback in the model, with no variation in the strength of interspecific plant-soil interactions, results were consistent with the conventional hypotheses. When we allowed the strength of plant-soil interactions to differ between species, plant-soil interactions enhanced alpha diversity initially and beta and gamma diversity subsequently. Diversity enhancement occurred not necessarily because alternative stable states emerged, but primarily because complex plant-soil interactions lengthened the time during which local species composition changed. Due to the longer time for changes in species composition, the high level of beta and gamma diversity at the early stage of succession was maintained for a long time despite eventual community convergence. Thus, diversity enhancement was often transient, though long-lasting, making the conventional concept of alternative stable states inadequate for explaining diversity. 4. Synthesis. Based on these findings, we propose the new hypothesis that complex plant-soil interactions enhance plant species diversity by delaying community convergence. This hypothesis highlights the role of plant-soil interactions as a driver of long-lasting transient dynamics of community assembly.

Lifelong infection of the gastric mucosa by Helicobacter pylori can lead to peptic ulcers and gastric cancer. However, how the bacteria maintain chronic colonization in the face of constant mucus and epithelial cell turnover in the stomach is unclear. Here, we present a new model of how H . pylori establish and persist in stomach, which involves the colonization of a specialized microenvironment, or microniche, deep in the gastric glands. Using quantitative three-dimensional (3D) confocal microscopy and passive CLARITY technique (PACT), which renders tissues optically transparent, we analyzed intact stomachs from mice infected with a mixture of isogenic, fluorescent H . pylori strains with unprecedented spatial resolution. We discovered that a small number of bacterial founders initially establish colonies deep in the gastric glands and then expand to colonize adjacent glands, forming clonal population islands that persist over time. Gland-associated populations do not intermix with free-swimming bacteria in the surface mucus, and they compete for space and prevent newcomers from establishing in the stomach. Furthermore, bacterial mutants deficient in gland colonization are outcompeted by wild-type (WT) bacteria. Finally, we found that host factors such as the age at infection and T-cell responses control bacterial density within the glands. Collectively, our results demonstrate that microniches in the gastric glands house a persistent H . pylori reservoir, which we propose replenishes the more transient bacterial populations in the superficial mucosa.

Two morphological types ("righty" and "lefty") have been discovered in several fish species and are referred to as a typical example of antisymmetry. It has been suggested, first, that this dimorphism (called laterality) is inheritable; second, that the frequencies of laterality in each species fluctuate around 0.5; and third, that predators mainly exploit prey of the opposite laterality; that is, lefty and righty predators prey on righties and lefties, respectively. The latter is defined as "cross predation"; the antonym "parallel predation" means predation within the same laterality. We hypothesized that cross predation drives alternation of the survival and reproductive advantages between two morphological types, leading to frequency-dependent selection that maintains the dimorphism. To investigate this, we constructed mathematical models of population dynamics of one prey/one predator systems and three-trophic-level systems with omnivory. Mathematical analysis and computer simulations explained the behavior of the laterality frequency in nature well, insofar as cross predation dominated over parallel predation. Furthermore, the simulations showed that when only one of the morphological types exists in a species, the other type can invade. This suggests that dimorphism is maintained in all interacting species.

Non-native plants may be unpalatable or toxic, but have oviposition cues similar to native plants used by insects. The herbivore will then oviposit on the plant, but the offspring will be unable to develop. While such instances have been described previously, the fitness costs at the population level in the wild due to the presence of the lethal host have not been quantified, for this or other related systems. We quantified the fitness cost in the field for the native butterfly Pieris macdunnoughii in the presence of the non-native crucifer Thlaspi arvense, based on the spatial distributions of host plants, female butterflies and eggs in the habitat and the survival of the larvae in the wild. We found that 2.9% of eggs were laid on T. arvense on average, with a survival probability of 0, yielding a calculated fitness cost of 3.0% (95% confidence interval 1.7-3.6%) due to the presence of the non-native in the plant community. Survival probability to the pre-pupal stage for eggs laid on two native crucifers averaged 1.6% over 2 years. The magnitude of the fitness cost will vary temporally and spatially as a function of the relative abundance of the non-native plant. We propose that the fine-scale spatial structure of the plant community relative to the butterflies' dispersal ability, combined with the females' broad habitat use, contributes to the fitness costs associated with the non-native plant and the resulting evolutionary trap.