Optimal foraging by herbivores maintains polymorphism in defence in a natural plant population

The evolution of chemodiversity in plants-From verbal to quantitative models

Plants harbour a great chemodiversity, that is diversity of specialised metabolites (SMs), at different scales. For instance, individuals can produce a large number of SMs, and populations can differ in their metabolite composition. Given the ecological and economic importance of plant chemodiversity, it is important to understand how it arises and is maintained over evolutionary time. For other dimensions of biodiversity, that is species diversity and genetic diversity, quantitative models play an important role in addressing such questions. Here, we provide a synthesis of existing hypotheses and quantitative models, that is mathematical models and computer simulations, for the evolution of plant chemodiversity. We describe each model's ingredients, that is the biological processes that shape chemodiversity, the scales it considers and whether it has been formalized as a quantitative model. Although we identify several quantitative models, not all are dynamic and many influential models have remained verbal. To fill these gaps, we outline our vision for the future of chemodiversity modelling. We identify quantitative models used for genetic variation that may be adapted for chemodiversity, and we present a flexible framework for the creation of individual-based models that address different scales of chemodiversity and combine different ingredients that bring this chemodiversity about.

Density-Dependent Seed Predation of Quercus wutaishanica by Rodents in Response to Different Seed States

The predation and/or dispersal of Quercus seeds by rodents play an important role in the creation of the tree species. The present study examined the effects of community habitats on the predation and dispersal of Quercus wutaishanica seeds by rodents. We released seeds with densities set at 2, 4, 8, 16, and 32 seed square meter with litter cover, soil burial, and bare ground in the Liupan Mountains National Nature Reserve in the Ningxia Hui Autonomous Region, northwest China. The results showed that (1) the litter cover and soil burial significantly increased the seed survival probability compared with bare ground treatments, especially the predation in situ (PIS) (p < 0.05). Both the scatter hoarding (SH) and larder hoarding (LH) for litter cover and soil burial were significantly increased compared with bare ground (p < 0.05). (2) The large seeds are preferentially predated after dispersal and their long-distance dispersal (>5 m) was significantly greater than that of small seeds (p < 0.05), while small seeds are more likely to be preyed on in situ or during short-distance dispersal (<3 m). (3) The Q. wutaishanica seed predation by rodents increased at a high density rather than at a low density, indicating a negative density-dependent predation. These findings provide insights into the ecological characteristics of Quercus tree regeneration and shed light on the coexistence between rodents and different-sized seeds.

Neighbor GWAS: incorporating neighbor genotypic identity into genome-wide association studies of field herbivory

An increasing number of field studies have shown that the phenotype of an individual plant depends not only on its genotype but also on those of neighboring plants; however, this fact is not taken into consideration in genome-wide association studies (GWAS). Based on the Ising model of ferromagnetism, we incorporated neighbor genotypic identity into a regression model, named "Neighbor GWAS". Our simulations showed that the effective range of neighbor effects could be estimated using an observed phenotype when the proportion of phenotypic variation explained (PVE) by neighbor effects peaked. The spatial scale of the first nearest neighbors gave the maximum power to detect the causal variants responsible for neighbor effects, unless their effective range was too broad. However, if the effective range of the neighbor effects was broad and minor allele frequencies were low, there was collinearity between the self and neighbor effects. To suppress the false positive detection of neighbor effects, the fixed effect and variance components involved in the neighbor effects should be tested in comparison with a standard GWAS model. We applied neighbor GWAS to field herbivory data from 199 accessions of Arabidopsis thaliana and found that neighbor effects explained 8% more of the PVE of the observed damage than standard GWAS. The neighbor GWAS method provides a novel tool that could facilitate the analysis of complex traits in spatially structured environments and is available as an R package at CRAN ( https://cran.rproject.org/package=rNeighborGWAS ).

Herbivore-mediated negative frequency-dependent selection underlies a trichome dimorphism in nature

Negative frequency-dependent selection (NFDS) has been shown to maintain polymorphism in a diverse array of traits. The action of NFDS has been confirmed through modeling, experimental approaches, and genetic analyses. In this study, we investigated NFDS in the wild using morph-frequency changes spanning a 20-year period from over 30 dimorphic populations of Datura wrightii. In these populations, plants either possess glandular (sticky) or non-glandular (velvety) trichomes, and the ratio of these morphs varies substantially among populations. Our method provided evidence that NFDS, rather than drift or migration, is the primary force maintaining this dimorphism. Most populations that were initially dimorphic remained dimorphic, and the overall mean and variance in morph frequency did not change over time. Furthermore, morph-frequency differences were not related to geographic distances. Together, these results indicate that neither directional selection, drift, or migration played a substantial role in determining morph frequencies. However, as predicted by negative frequency-dependent selection, we found that the rare morph tended to increase in frequency, leading to a negative relationship between the change in the frequency of the sticky morph and its initial frequency. In addition, we found that morph-frequency change over time was significantly correlated with the damage inflicted by two herbivores: Lema daturaphila and Tupiochoris notatus. The latter is a specialist on the sticky morph and damage by this herbivore was greatest when the sticky morph was common. The reverse was true for L. daturaphila, such that damage increased with the frequency of the velvety morph. These findings suggest that these herbivores contribute to balancing selection on the observed trichome dimorphism.

Stochastic optimal switching model for migrating population dynamics

An optimal switching control formalism combined with the stochastic dynamic programming is, for the first time, applied to modelling life cycle of migrating population dynamics with non-overlapping generations. The migration behaviour between habitats is efficiently described as impulsive switching based on stochastic differential equations, which is a new standpoint for modelling the biological phenomenon. The population dynamics is assumed to occur so that the reproductive success is maximized under an expectation. Finding the optimal migration strategy ultimately reduces to solving an optimality equation of the quasi-variational type. We show an effective linkage between our optimality equation and the basic reproduction number. Our model is applied to numerical computation of optimal migration strategy and basic reproduction number of an amphidromous fish Plecoglossus altivelis altivelis in Japan as a target species.

Plant Secondary Metabolite Diversity and Species Interactions

Ever since the first plant secondary metabolites (PSMs) were isolated and identified, questions about their ecological functions and diversity have been raised. Recent advances in analytical chemistry and complex data computation, as well as progress in chemical ecology from mechanistic to functional and evolutionary questions, open a new box of hypotheses. Addressing these hypotheses includes the measurement of complex traits, such as chemodiversity, in a context-dependent manner and allows for a deeper understanding of the multifunctionality and functional redundancy of PSMs. Here we review a hypothesis framework that addresses PSM diversity on multiple ecological levels (α, β, and γ chemodiversity), its variation in space and time, and the potential agents of natural selection. We use the concept of chemical information transfer as mediator of antagonistic and mutualistic interaction to interpret functional and microevolutionary studies and create a hypothesis framework for understanding chemodiversity as a factor driving ecological processes.

Sensory deficiencies affect resource selection and associational effects at two spatial scales

Many insect species have limited sensory abilities and may not be able to perceive the quality of different resource types while approaching patchily distributed resources. These restrictions may lead to differences in selection rates between separate patches and between different resource types within a patch, which may have consequences for associational effects between resources. In this study, we used an oviposition assay containing different frequencies of apple and banana substrates divided over two patches to compare resource selection rates of wild-type Drosophila melanogaster at the between- and within-patch scales. Next, we compared the wild-type behavior with that of the olfactory-deficient strain Orco 2 and the gustatory-deficient strain Poxn ΔM22-B5 and found comparable responses to patch heterogeneity and similarly strong selection rates for apple at both scales for the wild-type and olfactory-deficient flies. Their oviposition behavior translated into associational susceptibility for apple and associational resistance for banana. The gustatory-deficient flies, on the other hand, no longer had a strong selection rate for apple, strongly differed in between- and within-patch selection rates from the wild-type flies, and caused no associational effects between the resources. Our study suggests that differences in sensory capabilities can affect resource selection at different search behavior scales in different ways and in turn underlie associational effects between resources at different spatial scales.

Does genomic variation in a foundation species predict arthropod community structure in a riparian forest?

Understanding how genetic variation within a foundation species determines the structure of associated communities and ecosystem processes has been an emerging frontier in ecology. Previous studies in common gardens identified close links between intraspecific variation and multispecies community structure, and these findings are now being evaluated directly in the complex natural ecosystem. In this study, we examined to what extent genomic variation in a foundation tree species explains the structure of associated arthropod communities in the field, comparing with spatial, temporal and environmental factors. In a continuous mixed forest, arthropods were surveyed on 85 mature alders (Alnus hirsuta) in 2 years. Moreover, we estimated Nei's genetic distance among the alders based on 1,077 single nucleotide polymorphisms obtained from restricted-site-associated DNA sequencing of the alders' genome. In both years, we detected significant correlations between genetic distance and dissimilarity of arthropod communities. A generalized dissimilarity modelling indicated that the genetic distance of alder populations was the most important predictor to explain the variance of arthropod communities. Among arthropod functional groups, carnivores were consistently correlated with genetic distance of the foundation species in both years. Furthermore, the extent of year-to-year changes in arthropod communities was more similar between more genetically closed alder populations. This study demonstrates that the genetic similarity rule would be primarily prominent in community assembly of plant-associated arthropods under temporally and spatially variable environments in the field.