Extending genomics to natural communities and ecosystems

Reducing herbivory in mixed planting by genomic prediction of neighbor effects in the field

Genetically diverse populations can increase plant resistance to natural enemies. Yet, beneficial genotype pairs remain elusive due to the occurrence of positive or negative effects of mixed planting on plant resistance, respectively called associational resistance or susceptibility. Here, we identify key genotype pairs responsible for associational resistance to herbivory using the genome-wide polymorphism data of the plant species Arabidopsis thaliana. To quantify neighbor interactions among 199 genotypes grown in a randomized block design, we employ a genome-wide association method named "Neighbor GWAS" and genomic prediction inspired by the Ising model of magnetics. These analyses predict that 823 of the 19,701 candidate pairs can reduce herbivory in mixed planting. We planted three pairs with the predicted effects in mixtures and monocultures, and detected 18-30% reductions in herbivore damage in the mixed planting treatment. Our study shows the power of genomic prediction to assemble genotype mixtures with positive biodiversity effects.

Ecosystem effects of intraspecific variation in a colour polymorphic amphibian

An emerging consensus suggests that evolved intraspecific variation can be ecologically important. However, evidence that evolved trait variation within vertebrates can influence fundamental ecosystem-level processes remains sparse. In this study, we sought to assess the potential for evolved variation in the spotted salamander (Ambystoma maculatum) to affect aquatic ecosystem properties. Spotted salamanders exhibit a conspicuous polymorphism in the colour of jelly encasing their eggs-some females produce clear jelly, while others produce white jelly. Although the functional significance of jelly colour variation remains largely speculative, evidence for differences in fecundity and the morphology of larvae suggests that the colour morphs might differ in the strength or identity of ecological effects. Here, we assessed the potential for frequency variation in spotted salamander colour morphs to influence fundamental physiochemical and ecosystem properties-dissolved organic carbon, conductivity, acidity and primary production-with a mesocosm experiment. By manipulating colour morph frequency across a range of larval densities, we were able to demonstrate that larva density and colour morph variation were ecologically relevant: population density reduced dissolved organic carbon and increased primary production while mesocosms stocked with white morph larvae tended to have higher dissolved organic carbon and conductivity. Thus, while an adaptive significance of jelly coloration remains hypothetical, our results show that colour morphs differentially influence key ecosystem properties-dissolved organic carbon and conductivity.

Complementary roles of two classes of defense chemicals in white spruce against spruce budworm

MAIN CONCLUSION

Monoterpenes and phenolics play distinct roles in defending white spruce trees from insect defoliators. Monoterpenes contribute to the toxicity of the foliage, deterring herbivory, whereas phenolics impede budworm growth. This study demonstrates the complex interplay between monoterpenes and phenolics and their collective influence on the defense strategy of white spruce trees against a common insect defoliator. Long-lived coniferous trees display considerable variations in their defensive chemistry. The impact of these defense phenotype variations on insect herbivores of the same species remains to be thoroughly studied, mainly due to challenges in replicating the comprehensive defense profiles of trees under controlled conditions. This study methodically examined the defensive properties of foliar monoterpenes and phenolics across 80 distinct white spruce families. These families were subsequently grouped into two chemotypes based on their foliar monoterpene concentrations. To understand the separate and combined effects of these classes on tree defenses to the eastern spruce budworm, we conducted feeding experiments using actual defense profiles from representative families. Specifically, we assessed budworm response when exposed to substrates amended with phenolics alone or monoterpenes. Our findings indicate that the ratios and amounts of monoterpenes and phenolics present in the white spruce foliage influence the survival of spruce budworms. Phenotypes associated with complete larval mortality exhibited elevated ratios (ranging from 0.4 to 0.6) and concentrations (ranging from 1143 to 1796 ng mg-1) of monoterpenes. Conversely, families characterized by higher phenolic ratios (ranging from 0.62 to 0.77) and lower monoterpene concentrations (ranging from 419 to 985 ng mg-1) were less lethal to the spruce budworm. Both classes of defense compounds contribute significantly to the overall defensive capabilities of white spruce trees. Monoterpenes appear critical in determining the general toxicity of foliage, while phenolics play a role in slowing budworm development, thereby underscoring their collective importance in white spruce defenses.

Competition-cooperation mechanism between Escherichia coli and Staphylococcus aureus based on systems mapping

Introduction

Interspecies interactions are a crucial driving force of species evolution. The genes of each coexisting species play a pivotal role in shaping the structure and function within the community, but how to identify them at the genome-wide level has always been challenging.

Methods

In this study, we embed the Lotka-Volterra ordinary differential equations in the theory of community ecology into the systems mapping model, so that this model can not only describe how the quantitative trait loci (QTL) of a species directly affects its own phenotype, but also describe the QTL of the species how to indirectly affect the phenotype of its interacting species, and how QTL from different species affects community behavior through epistatic interactions.

Results

By designing and implementing a co-culture experiment for 100 pairs of Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus), we mapped 244 significant QTL combinations in the interaction process of the two bacteria using this model, including 69 QTLs from E. coli and 59 QTLs from S. aureus, respectively. Through gene annotation, we obtained 57 genes in E. coli, among which the genes with higher frequency were ypdC, nrfC, yphH, acrE, dcuS, rpnE, and ptsA, while we obtained 43 genes in S. aureus, among which the genes with higher frequency were ebh, SAOUHSC_00172, capF, gdpP, orfX, bsaA, and phnE1.

Discussion

By dividing the overall growth into independent growth and interactive growth, we could estimate how QTLs modulate interspecific competition and cooperation. Based on the quantitative genetic model, we can obtain the direct genetic effect, indirect genetic effect, and genome-genome epistatic effect related to interspecific interaction genes, and then further mine the hub genes in the QTL networks, which will be particularly useful for inferring and predicting the genetic mechanisms of community dynamics and evolution. Systems mapping can provide a tool for studying the mechanism of competition and cooperation among bacteria in co-culture, and this framework can lay the foundation for a more comprehensive and systematic study of species interactions.

Genomic and transcriptomic analyses reveal polygenic architecture for ecologically important traits in aspen (Populus tremuloides Michx.)

Intraspecific genetic variation in foundation species such as aspen (Populus tremuloides Michx.) shapes their impact on forest structure and function. Identifying genes underlying ecologically important traits is key to understanding that impact. Previous studies, using single-locus genome-wide association (GWA) analyses to identify candidate genes, have identified fewer genes than anticipated for highly heritable quantitative traits. Mounting evidence suggests that polygenic control of quantitative traits is largely responsible for this "missing heritability" phenomenon. Our research characterized the genetic architecture of 30 ecologically important traits using a common garden of aspen through genomic and transcriptomic analyses. A multilocus association model revealed that most traits displayed a highly polygenic architecture, with most variation explained by loci with small effects (likely below the detection levels of single-locus GWA methods). Consistent with a polygenic architecture, our single-locus GWA analyses found only 38 significant SNPs in 22 genes across 15 traits. Next, we used differential expression analysis on a subset of aspen genets with divergent concentrations of salicinoid phenolic glycosides (key defense traits). This complementary method to traditional GWA discovered 1243 differentially expressed genes for a polygenic trait. Soft clustering analysis revealed three gene clusters (241 candidate genes) involved in secondary metabolite biosynthesis and regulation. Our work reveals that ecologically important traits governing higher-order community- and ecosystem-level attributes of a foundation forest tree species have complex underlying genetic structures and will require methods beyond traditional GWA analyses to unravel.

Insights into the Ecological Diversification of the Hymenochaetales based on Comparative Genomics and Phylogenomics With an Emphasis on Coltricia

To elucidate the genomic traits of ecological diversification in the Hymenochaetales, we sequenced 15 new genomes, with attention to ectomycorrhizal (EcM) Coltricia species. Together with published data, 32 genomes, including 31 Hymenochaetales and one outgroup, were comparatively analyzed in total. Compared with those of parasitic and saprophytic members, EcM species have significantly reduced number of plant cell wall degrading enzyme genes, and expanded transposable elements, genome sizes, small secreted proteins, and secreted proteases. EcM species still retain some of secreted carbohydrate-active enzymes (CAZymes) and have lost the key secreted CAZymes to degrade lignin and cellulose, while possess a strong capacity to degrade a microbial cell wall containing chitin and peptidoglycan. There were no significant differences in secreted CAZymes between fungi growing on gymnosperms and angiosperms, suggesting that the secreted CAZymes in the Hymenochaetales evolved before differentiation of host trees into gymnosperms and angiosperms. Nevertheless, parasitic and saprophytic species of the Hymenochaetales are very similar in many genome features, which reflect their close phylogenetic relationships both being white rot fungi. Phylogenomic and molecular clock analyses showed that the EcM genus Coltricia formed a clade located at the base of the Hymenochaetaceae and divergence time later than saprophytic species. And Coltricia remains one to two genes of AA2 family. These indicate that the ancestors of Coltricia appear to have originated from saprophytic ancestor with the ability to cause a white rot. This study provides new genomic data for EcM species and insights into the ecological diversification within the Hymenochaetales based on comparative genomics and phylogenomics analyses.

The Correlation between Genotype Richness of Submerged Macrophytes and Periphyton Biomass: A Mesocosm Study Based on Five Dominant Submerged Macrophytes from Yangtze River

Submerged macrophyte and periphyton are main primary producers which strongly interact with each other in clear water shallow lakes. In this study, the effects of genetic variation of the macrophyte species on periphyton biomass were studied in five submerged species. A two-year mesocosm study was conducted with four levels of genetic diversity (1, 4, 8 and 16 genotypes) for each submerged macrophyte, including 1600 individuals and 320 boxes in 20 mesocosms. Of the five submerged species, only Vallisneria spinulosa showed a positive correlation between its levels of genotype richness and the periphyton biomass. The correlation between genetic distance of genotypes and periphyton biomass was tested, which varied with the difference of seasons and species. In summary, we found that in freshwater mesocosms, the genetic diversity of submerged macrophytes may play a role in regulating the periphyton biomass, but the interaction between genetic diversity of macrophytes and periphyton biomass was not straightforward. This study will provide new insights into the interaction dynamics between the two primary producers in shallow lakes.

Genetic divergence along a climate gradient shapes chemical plasticity of a foundation tree species to both changing climate and herbivore damage

Climate change is threatening the persistence of many tree species via independent and interactive effects on abiotic and biotic conditions. In addition, changes in temperature, precipitation, and insect attacks can alter the traits of these trees, disrupting communities and ecosystems. For foundation species such as Populus, phytochemical traits are key mechanisms linking trees with their environment and are likely jointly determined by interactive effects of genetic divergence and variable environments throughout their geographic range. Using reciprocal Fremont cottonwood (Populus fremontii) common gardens along a steep climatic gradient, we explored how environment (garden climate and simulated herbivore damage) and genetics (tree provenance and genotype) affect both foliar chemical traits and the plasticity of these traits. We found that (1) Constitutive and plastic chemical responses to changes in garden climate and damage varied among defense compounds, structural compounds, and leaf nitrogen. (2) For both defense and structural compounds, plastic responses to different garden climates depended on the climate in which a population or genotype originated. Specifically, trees originating from cool provenances showed higher defense plasticity in response to climate changes than trees from warmer provenances. (3) Trees from cool provenances growing in cool garden conditions expressed the lowest constitutive defense levels but the strongest induced (plastic) defenses in response to damage. (4) The combination of hot garden conditions and simulated herbivory switched the strategy used by these genotypes, increasing constitutive defenses but erasing the capacity for induction after damage. Because Fremont cottonwood chemistry plays a major role in shaping riparian communities and ecosystems, the effects of changes in phytochemical traits can be wide reaching. As the southwestern US is confronted with warming temperatures and insect outbreaks, these results improve our capacity to predict ecosystem consequences of climate change and inform selection of tree genotypes for conservation and restoration purposes.

Simulating selection and evolution at the community level using common garden data

A key issue in evolutionary biology is whether selection acting at levels higher than the individual can cause evolutionary change. If it can, then conceptual and empirical studies must consider how selection operates at multiple levels of biological organization. Here, we test the hypothesis that estimates of broad-sense community heritability, H C 2 , can be used to predict the evolutionary response by community-level phenotypes when community-level selection is imposed. Using an approach informed by classic quantitative genetics, we made three predictions. First, when we imposed community-level selection, we expected a significant change in the average phenotype of arthropod communities associated with individual tree genotypes [we imposed selection by favoring high and low NMDS (nonmetric multidimensional scaling) scores that reflected differences in arthropod species richness, abundance and composition]. Second, we expected H C 2 to predict the magnitude of the community-level response. Third, we expected no significant change in average NMDS scores with community-level selection imposed at random. We tested these hypotheses using three years of common garden data for 102 species comprising the arthropod communities, associated with nine clonally replicated Populus angustifolia genotypes. Each of our predictions were met. We conclude that estimates of H C 2 account for the resemblance among communities sharing common ancestry, the persistence of community composition over time, and the outcome of selection when it occurs at the community level. Our results provide a means for exploring how this process leads to large-scale community evolutionary change, and they identify the circumstances in which selection may routinely act at the community level.

Genetic diversity, viability and conservation value of the global captive population of the Moroccan Royal lions

This study evaluates the diversity of the so-called ‘Moroccan Royal lions’ using genealogical information. Lions are no longer extant in North Africa, but the previous wild population was an important element of the now-recognised northern subspecies (Panthera leo leo) that ranged across West Africa, North Africa and the Middle East into India. The remaining captive population of ‘Moroccan Royal lions’ seems to be significantly endangered by the loss of diversity due to the effective population size decrease. The pedigree file of this captive lion population consisted of 454 individuals, while the reference population included 98 animals (47 males and 51 females). The completeness of the pedigree data significantly decreased with an increasing number of generations. The highest percentage of pedigree completeness (over 70%) was achieved in the first generation of the reference population. Pedigree-based parameters derived from the common ancestor and gene origin were used to estimate the state of diversity. In the reference population, the average inbreeding coefficient was 2.14%, while the individual increase in inbreeding over generations was 2.31%. Overall, the reference population showed lower average inbreeding and average relatedness compared with the pedigree file. The number of founders (47), the effective number of founders (24) and the effective number of ancestors (22) were estimated in the reference population. The effective population size of 14.02 individuals confirms the critically endangered status of the population and rapid loss of diversity in the future. Thus, continuous monitoring of the genetic diversity of the ‘Moroccan Royal lion’ group is required, especially for long-term conservation management purposes, as it would be an important captive group should further DNA studies establish an affinity to P. leo leo.

Tree genotypes affect rock lichens and understory plants: examples of trophic-independent interactions

Genetic variation in foundation tree species can strongly influence communities of trophic‐dependent organisms, such as herbivorous insects, pollinators, and mycorrhizal fungi. However, the extent and manner in which this variation results in unexpected interactions that reach trophic‐independent organisms remains poorly understood, even though these interactions are essential to understanding complex ecosystems. In pinyon–juniper woodland at Sunset Crater (Arizona, USA), we studied pinyon (Pinus edulis) that were either resistant or susceptible to stem‐boring moths (Dioryctria albovittella). Moth herbivory alters the architecture of susceptible trees, thereby modifying the microhabitat beneath their crowns. We tested the hypothesis that this interaction between herbivore and tree genotype extends to affect trophic‐independent communities of saxicolous (i.e., growing on rocks) lichens and bryophytes and vascular plants beneath their crowns. Under 30 pairs of moth‐resistant and moth‐susceptible trees, we estimated percent cover of lichens, bryophytes, and vascular plants. We also quantified the cover of leaf litter and rocks as well as light availability. Four major findings emerged. (1) Compared to moth‐resistant trees, which exhibited monopodial architecture, the microhabitat under the shrub‐like susceptible trees was 60% darker and had 21% more litter resulting in 68% less rock exposure. (2) Susceptible trees had 56% and 87% less cover, 42% and 80% less richness, and 38% and 92% less diversity of saxicolous and plant communities, respectively, compared to resistant trees. (3) Both saxicolous and plant species accumulated at a slower rate beneath susceptible trees, suggesting an environment that might inhibit colonization and/or growth. (4) Both saxicolous and plant communities were negatively affected by the habitat provided by susceptible trees. The results suggest that herbivory of moth‐susceptible trees generated litter at high enough rates to reduce rock substrate availability, thereby suppressing the saxicolous communities. However, our results did not provide a causal pathway explaining the suppression of vascular plants. Nonetheless, the cascading effects of genetic variation in pinyon appear to extend beyond trophic‐dependent moths to include trophic‐independent saxicolous and vascular plant communities that are affected by specific tree–herbivore interactions that modify the local environment. We suggest that such genetically based interactions are common in nature and contribute to the evolution of complex communities.

Intraspecific Genetic Variation and Species Interactions Contribute to Community Evolution

Evolution has been viewed as occurring primarily through selection among individuals. We present a framework based on multilevel selection for evaluating evolutionary change from individuals to communities, with supporting empirical evidence. Essential to this evaluation is the role that interspecific indirect genetic effects play in shaping community organization, in generating variation among community phenotypes, and in creating community heritability. If communities vary in phenotype, and those phenotypes are heritable and subject to selection at multiple levels, then a community view of evolution must be merged with mainstream evolutionary theory. Rapid environmental change during the Anthropocene will require a better understanding of these evolutionary processes, especially selection acting at the community level, which has the potential to eliminate whole communities while favoring others.

High-Temperature-Responsive Poplar lncRNAs Modulate Target Gene Expression via RNA Interference and Act as RNA Scaffolds to Enhance Heat Tolerance

High-temperature stress is a threat to plant development and survival. Long noncoding RNAs (lncRNAs) participate in plant stress responses, but their functions in the complex stress response network remain unknown. Poplar contributes to terrestrial ecological stability. In this study, we identified 204 high-temperature-responsive lncRNAs in an abiotic stress-tolerant poplar (Populus simonii) species using strand-specific RNA sequencing (ssRNA-seq). Mimicking overexpressed and repressed candidate lncRNAs in poplar was used to illuminate their regulation pattern on targets using nano sheet mediation. These lncRNAs were predicted to target 185 genes, of which 100 were cis genes and 119 were trans genes. Gene Ontology enrichment analysis showed that anatomical structure morphogenesis and response to stress and signaling were significantly enriched. Among heat-responsive LncRNAs, TCONS_00202587 binds to upstream sequences via its secondary structure and interferes with target gene transcription. TCONS_00260893 enhances calcium influx in response to high-temperature treatment by interfering with a specific variant/isoform of the target gene. Heterogeneous expression of these two lncRNA targets promoted photosynthetic protection and recovery, inhibited membrane peroxidation, and suppressed DNA damage in Arabidopsis under heat stress. These results showed that lncRNAs can regulate their target genes by acting as potential RNA scaffolds or through the RNA interference pathway.

Key Genes and Genetic Interactions of Plant-Pathogen Functional Modules in Poplar Infected by Marssonina brunnea

Marssonina brunnea, the causative pathogen of Marssonina leaf spot of poplars (MLSP), devastates poplar plantations by forming black spots on leaves and defoliating trees. Although MLSP has been studied for over 30 years, the key genes that function during M. brunnea infection and their effects on plant growth are poorly understood. Here, we used multigene association studies to investigate the effects of key genes in the plant-pathogen interaction pathway, as revealed by transcriptome analysis, on photosynthesis and growth in a natural population of 435 Populus tomentosa individuals. By analyzing transcriptomic changes during three stages of infection, we detected 628 transcription factor genes among the 7,611 differentially expressed genes that might be associated with basal defense responses. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that transcriptomic changes across different stages of infection lead to the reprogramming of metabolic processes possibly related to defense activation. We identified 29,399 common single-nucleotide polymorphisms (SNPs) within 221 full-length genes in plant-pathogen interaction pathways that were significantly associated with photosynthetic and growth traits. We also detected 4,460 significant epistatic pairs associated with stomatal conductance, tree diameter, and tree height. Epistasis analysis uncovered significant interactions between 2,561 SNP-SNP pairs from different functional modules in the plant-pathogen interaction pathway, revealing possible genetic interactions. This analysis revealed many key genes that function during M. brunnea infection and their potential roles in mediating photosynthesis and plant growth, shedding light on genetic interactions between functional modules in the plant-pathogen interaction pathway.

Adaptive capacity in the foundation tree species Populus fremontii: implications for resilience to climate change and non-native species invasion in the American Southwest

Populus fremontii (Fremont cottonwood) is recognized as one of the most important foundation tree species in the southwestern USA and northern Mexico because of its ability to structure communities across multiple trophic levels, drive ecosystem processes and influence biodiversity via genetic-based functional trait variation. However, the areal extent of P. fremontii cover has declined dramatically over the last century due to the effects of surface water diversions, non-native species invasions and more recently climate change. Consequently, P. fremontii gallery forests are considered amongst the most threatened forest types in North America. In this paper, we unify four conceptual areas of genes to ecosystems research related to P. fremontii's capacity to survive or even thrive under current and future environmental conditions: (i) hydraulic function related to canopy thermal regulation during heat waves; (ii) mycorrhizal mutualists in relation to resiliency to climate change and invasion by the non-native tree/shrub, Tamarix; (iii) phenotypic plasticity as a mechanism for coping with rapid changes in climate; and (iv) hybridization between P. fremontii and other closely related Populus species where enhanced vigour of hybrids may preserve the foundational capacity of Populus in the face of environmental change. We also discuss opportunities to scale these conceptual areas from genes to the ecosystem level via remote sensing. We anticipate that the exploration of these conceptual areas of research will facilitate solutions to climate change with a foundation species that is recognized as being critically important for biodiversity conservation and could serve as a model for adaptive management of arid regions in the southwestern USA and around the world.

Mediation of plant-mycorrhizal interaction by a lectin receptor-like kinase

The molecular mechanisms underlying mycorrhizal symbioses, the most ubiquitous and impactful mutualistic plant-microbial interaction in nature, are largely unknown. Through genetic mapping, resequencing and molecular validation, we demonstrate that a G-type lectin receptor-like kinase (lecRLK) mediates the symbiotic interaction between Populus and the ectomycorrhizal fungus Laccaria bicolor. This finding uncovers an important molecular step in the establishment of symbiotic plant-fungal associations and provides a molecular target for engineering beneficial mycorrhizal relationships.

Heritable Phytohormone Profiles of Poplar Genotypes Vary in Resistance to a Galling Aphid

Insect galls are highly specialized structures arising from atypical development of plant tissue induced by insects. Galls provide the insect enhanced nutrition and protection against natural enemies and environmental stresses. Galls are essentially plant organs formed by an intimate biochemical interaction between the gall-inducing insect and its host plant. Because galls are plant organs, their development is likely to be governed by phytohormones involved in normal organogenesis. We characterized concentrations of both growth and defensive phytohormones in ungalled control leaves and galls induced by the aphid Pemphigus betae on narrowleaf cottonwood Populus angustifolia that differ genotypically in resistance to this insect. We found that susceptible trees differed from resistant trees in constitutive concentrations of both growth and defense phytohormones. Susceptible trees were characterized by significantly higher constitutive cytokinin concentrations in leaves, significantly greater ability of aphids to elicit cytokinin increases, and significantly lower constitutive defense phytohormone concentrations than observed in resistant trees. Phytohormone concentrations in both constitutive and induced responses in galled leaves exhibited high broad-sense heritability that, respectively, ranged from 0.39 to 0.93 and from 0.28 to 0.66, suggesting that selection can act upon these traits and that they might vary across the landscape. Increased cytokinin concentrations may facilitate forming strong photosynthate sinks in the galls, a requirement for galling insect success. By characterizing for the first time the changes in 15 phytohormones belonging to five different classes, this study offers a better overview of the signaling alteration occurring in galls that has likely been important for their ecology and evolution. Copyright © 2019 The Author(s). This is an open-access article distributed under the CC BY-NC-ND 4.0 International license .

Plant Part Age and Size Affect Sessile Macrobenthic Assemblages Associated with a Foliose Red Algae Phycodrys rubens in the White Sea

Facilitation by foundation species commonly structures terrestrial and marine communities. Intraspecific variation in individual properties of these strong facilitators can affect the whole suite of the dependent taxa. Marine macroalgae often act as ecosystem engineers, providing shelter and substrate for numerous associated organisms. Epibiosis of foliose red algae, however, remains underexplored, especially in the high latitudes. Here we studied sessile macrobenthic assemblages associated with a foliose red algae Phycodrys rubens in the White Sea (66° N) shallow subtidal, and the effect of individual plant properties on their structure. The blades of P. rubens develop annually, and it is possible to tell the young (usually larger) plant parts from the old ones. We hypothesized that epibenthic community structure depends on plant part age and size. We examined epibiosis on 110 plants at two sites, and the results generally supported our hypotheses. Old plant parts were several times smaller, and had higher total cover than young parts. Sponges strongly dominated the epibiosis on old parts, and young parts were dominated by polychaetes and bryozoans. Plant part surface area negatively correlated with total cover on young parts, while on old parts the relatioship was location-specific. On young parts the relative abundance of a polychaete Circeis armoricana increased with surface area, and the proportion of sponges decreased. The patterns indicate that epibenthic community structure is linked to the demography of an ecosystem engineer.

A mapping framework of competition-cooperation QTLs that drive community dynamics

Genes have been thought to affect community ecology and evolution, but their identification at the whole-genome level is challenging. Here, we develop a conceptual framework for the genome-wide mapping of quantitative trait loci (QTLs) that govern interspecific competition and cooperation. This framework integrates the community ecology theory into systems mapping, a statistical model for mapping complex traits as a dynamic system. It can characterize not only how QTLs of one species affect its own phenotype directly, but also how QTLs from this species affect the phenotype of its interacting species indirectly and how QTLs from different species interact epistatically to shape community behavior. We validated the utility of the new mapping framework experimentally by culturing and comparing two bacterial species, Escherichia coli and Staphylococcus aureus, in socialized and socially isolated environments, identifying several QTLs from each species that may act as key drivers of microbial community structure and function.

Genotypic variation in plant traits shapes herbivorous insect and ant communities on a foundation tree species

Community genetics aims to understand the effects of intraspecific genetic variation on community composition and diversity, thereby connecting community ecology with evolutionary biology. Multiple studies have shown that different plant genotypes harbor different communities of associated organisms, such as insects. Yet, the mechanistic links that tie insect community composition to plant genetics are still not well understood. To shed light on these relationships, we explored variation in both plant traits (e.g., growth, phenology, defense) and herbivorous insect and ant communities on 328 replicated aspen (Populus tremuloides) genets grown in a common garden. We measured traits and visually surveyed insect communities annually in 2014 and 2015. We found that insect communities overall exhibited low heritability and were shaped primarily by relationships among key insects (i.e., aphids, ants, and free-feeders). Several tree traits affected insect communities and the presence/absence of species and functional groups. Of these traits, tree size and foliar phenology were the most important. Larger trees had denser (i.e., number of insects per unit tree size) and more diverse insect communities, while timing of bud break and bud set differentially influenced particular species and insect groups, especially leaf modifying insects. These findings will inform future research directed toward identification of plant genes and genetic regions that underlie the structure of associated insect communities.

Rare genotype advantage promotes survival and genetic diversity of a tropical palm

Negative density dependence, where survival decreases as density increases, is a well-established driver of species diversity at the community level, but the degree to which a similar process might act on the density or frequency of genotypes within a single plant species to maintain genetic diversity has not been well studied in natural systems. In this study, we determined the maternal genotype of naturally dispersed seeds of the palm Oenocarpus bataua within a tropical forest in northwest Ecuador, tracked the recruitment of each seed, and assessed the role of individual-level genotypic rarity on survival. We demonstrate that negative frequency-dependent selection within this species conferred a survival advantage to rare maternal genotypes and promoted population-level genetic diversity. The strength of the observed rare genotype survival advantage was comparable to the effect of conspecific density regardless of genotype. These findings corroborate an earlier, experimental study and implicate negative frequency-dependent selection of genotypes as an important, but currently underappreciated, determinant of plant recruitment and within-species genetic diversity. Incorporating intraspecific genetic variation into studies and theory of forest dynamics may improve our ability to understand and manage forests, and the processes that maintain their diversity.

Heterosis in poplar involves phenotypic stability: cottonwood hybrids outperform their parental species at suboptimal temperatures

Heterosis or hybrid vigor is common in hybrid poplars, and to investigate its occurrence and physiological basis we compared narrowleaf cottonwoods, Populus angustifolia James, prairie cottonwoods, Populus deltoides Bartr. ex Marsh, and their native intersectional hybrids, P. × acuminata Rydb., from Alberta, Canada. Clonal replicates from 10 separate trees from each taxon were raised in growth chambers at different temperatures (T). Growth was similarly vigorous across the taxa at 20 and 24 °C, and morphological and physiological traits of the hybrids were generally intermediate between the parental species, or similar to the larger parent, demonstrating additive inheritance or dominance, respectively. Growth declined at 18 and 15 °C particularly in the parental species, and consequently hybrid vigor was displayed for root and especially leaf growth. Stomatal distributions and chlorophyll indices were intermediate in the hybrids and unaffected by T. Foliar nitrogen (N), net assimilation (Asat), stomatal conductance (gs) and transpiration (E) per unit of leaf area were lower in the hybrids, but the hybrids generally had larger leaf areas. Water-use efficiencies (Asat/gs) were similar across the taxa and reduced with warming, while nitrogen-use efficiencies (Asat/N) increased. δ13C was correlated with leaf mass per area, which varied across the taxa. Photosynthesis (Asat) was correlated with chlorophyll content index, N and/or gs in P. deltoides and the hybrids, but not in P. angustifolia, indicating different physiological limitations. We conclude that heterosis in P. × acuminata results from the compound benefits from multiple dominant traits, and superior growth particularly at suboptimal conditions. This indicates phenotypic stability or environmental adaptability, whereby heterozygosity provides metabolic diversity that allows hybrids to thrive across a broader environmental range.

Large effect quantitative trait loci for salicinoid phenolic glycosides in Populus: Implications for gene discovery

Genomic studies have been used to identify genes underlying many important plant secondary metabolic pathways. However, genes for salicinoid phenolic glycosides (SPGs)—ecologically important compounds with significant commercial, cultural, and medicinal applications—remain largely undescribed. We used a linkage map derived from a full‐sib population of hybrid cottonwoods (Populus spp.) to search for quantitative trait loci (QTL) for the SPGs salicortin and HCH‐salicortin. SSR markers and primer sequences were used to anchor the map to the V3.0 P. trichocarpa genome. We discovered 21 QTL for the two traits, including a major QTL for HCH‐salicortin (R² = .52) that colocated with a QTL for salicortin on chr12. Using the V3.0 Populus genome sequence, we identified 2,983 annotated genes and 1,480 genes of unknown function within our QTL intervals. We note ten candidate genes of interest, including a BAHD‐type acyltransferase that has been potentially linked to PopulusSPGs. Our results complement other recent studies in Populus with implications for gene discovery and the evolution of defensive chemistry in a model genus. To our knowledge, this is the first study to use a full‐sib mapping population to identify QTL intervals and gene lists associated with SPGs.

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.

Codominant grasses differ in gene expression under experimental climate extremes in native tallgrass prairie

Extremes in climate, such as heat waves and drought, are expected to become more frequent and intense with forecasted climate change. Plant species will almost certainly differ in their responses to these stressors. We experimentally imposed a heat wave and drought in the tallgrass prairie ecosystem near Manhattan, Kansas, USA to assess transcriptional responses of two ecologically important C4 grass species, Andropogon gerardii and Sorghastrum nutans. Based on previous research, we expected that S. nutans would regulate more genes, particularly those related to stress response, under high heat and drought. Across all treatments, S. nutans showed greater expression of negative regulatory and catabolism genes while A. gerardii upregulated cellular and protein metabolism. As predicted, S. nutans showed greater sensitivity to water stress, particularly with downregulation of non-coding RNAs and upregulation of water stress and catabolism genes. A. gerardii was less sensitive to drought, although A. gerardii tended to respond with upregulation in response to drought versus S. nutans which downregulated more genes under drier conditions. Surprisingly, A. gerardii only showed minimal gene expression response to increased temperature, while S. nutans showed no response. Gene functional annotation suggested that these two species may respond to stress via different mechanisms. Specifically, A. gerardii tends to maintain molecular function while S. nutans prioritizes avoidance. Sorghastrum nutans may strategize abscisic acid response and catabolism to respond rapidly to stress. These results have important implications for success of these two important grass species under a more variable and extreme climate forecast for the future.

Evolution as an ecosystem process: insights from genomics

Evolution is a fundamental ecosystem process. The study of genomic variation of organisms can not only improve our understanding of evolutionary processes, but also of contemporary and future ecosystem dynamics. We argue that integrative research between the fields of genomics and ecosystem ecology could generate new insights. Specifically, studies of biodiversity and ecosystem functioning, evolutionary rescue, and eco-evolutionary dynamics could all benefit from information about variation in genome structure and the genetic architecture of traits, whereas genomic studies could benefit from information about the ecological context of evolutionary dynamics. We propose new ways to help link research on functional genomic diversity with (reciprocal) interactions between phenotypic evolution and ecosystem change. Despite numerous challenges, we anticipate that the wealth of genomic data being collected on natural populations will improve our understanding of ecosystems.

Intrapopulation Genotypic Variation of Foliar Secondary Chemistry during Leaf Senescence and Litter Decomposition in Silver Birch (Betula pendula)

Abundant secondary metabolites, such as condensed tannins, and their interpopulation genotypic variation can remain through plant leaf senescence and affect litter decomposition. Whether the intrapopulation genotypic variation of a more diverse assortment of secondary metabolites equally persists through leaf senescence and litter decomposition is not well understood. We analyzed concentrations of intracellular phenolics, epicuticular flavonoid aglycones, epicuticular triterpenoids, condensed tannins, and lignin in green leaves, senescent leaves and partly decomposed litter of silver birch, Betula pendula. Broad-sense heritability (H2) and coefficient of genotypic variation (CVG) were estimated for metabolites in senescent leaves and litter using 19 genotypes selected from a B. pendula population in southern Finland. We found that most of the secondary metabolites remained through senescence and decomposition and that their persistence was related to their chemical properties. Intrapopulation H2 and CVG for intracellular phenolics, epicuticular flavonoid aglycones and condensed tannins were high and remarkably, increased from senescent leaves to decomposed litter. The rank of genotypes in metabolite concentrations was persistent through litter decomposition. Lignin was an exception, however, with a diminishing genotypic variation during decomposition, and the concentrations of lignin and condensed tannins had a negative genotypic correlation in the senescent leaves. Our results show that secondary metabolites and their intrapopulation genotypic variation can for the most part remain through leaf senescence and early decomposition, which is a prerequisite for initial litter quality to predict variation in litter decomposition rates. Persistent genotypic variation also opens an avenue for selection to impact litter decomposition in B. pendula populations through acting on their green foliage secondary chemistry. The negative genotypic correlations and diminishing heritability of lignin concentrations may, however, counteract this process.

Arthropod communities on hybrid and parental cottonwoods are phylogenetically structured by tree type: Implications for conservation of biodiversity in plant hybrid zones

Although hybridization in plants has been recognized as an important pathway in plant speciation, it may also affect the ecology and evolution of associated communities. Cottonwood species (Populus angustifolia and P. fremontii) and their naturally occurring hybrids are known to support different plant, animal, and microbial communities, but no studies have examined community structure within the context of phylogenetic history. Using a community composed of 199 arthropod species, we tested for differences in arthropod phylogenetic patterns within and among hybrid and parental tree types in a common garden. Three major patterns emerged. (1) Phylogenetic diversity (PD) was significantly different between arthropod communities on hybrids and Fremont cottonwood when pooled by tree type. (2) Mean phylogenetic distance (MPD) and net relatedness index (NRI) indicated that communities on hybrid trees were significantly more phylogenetically overdispersed than communities on either parental tree type. (3) Community distance (D_pw) indicated that communities on hybrids were significantly different than parental species. Our results show that arthropod communities on parental and hybrid cottonwoods exhibit significantly different patterns of phylogenetic structure. This suggests that arthropod community assembly is driven, in part, by plant-arthropod interactions at the level of cottonwood tree type. We discuss potential hypotheses to explain the effect of plant genetic dissimilarity on arthropod phylogenetic community structure, including the role of competition and environmental filtering. Our findings suggest that cottonwood species and their hybrids function as evolutionarily significant units (ESUs) that affect the assembly and composition of associated arthropod communities and deserve high priority for conservation.

Genetic-based interactions among tree neighbors: identification of the most influential neighbors, and estimation of correlations among direct and indirect genetic effects for leaf disease and growth in Eucalyptus globulus

An individual's genes may influence the phenotype of neighboring conspecifics. Such indirect genetic effects (IGEs) are important as they can affect the apparent total heritable variance in a population, and thus the response to selection. We studied these effects in a large, pedigreed population of Eucalyptus globulus using variance component analyses of Mycosphearella leaf disease, diameter growth at age 2 years, and post-infection diameter growth at ages 4 and 8 years. In a novel approach, we initially modeled IGEs using a factor analytic (FA) structure to identify the most influential neighbor positions, with the FA loadings being position-specific regressions on the IGEs. This involved sequentially comparing FA models for the variance-covariance matrices of the direct and indirect effects of each neighbor. We then modeled IGEs as a distance-based, combined effect of the most influential neighbors. This often increased the magnitude and significance of indirect genetic variance estimates relative to using all neighbors. The extension of a univariate IGEs model to bivariate analyses also provided insights into the genetic architecture of this population, revealing that: (1) IGEs arising from increased probability of neighbor infection were not associated with reduced growth of neighbors, despite adverse fitness effects being evident at the direct genetic level; and (2) the strong, genetic-based competitive interactions for growth, established early in stand development, were highly positively correlated over time. Our results highlight the complexities of genetic-based interactions at the multi-trait level due to (co)variances associated with IGEs, and the marked discrepancy occurring between direct and total heritable variances.

Adaptive evolution and functional innovation of Populus-specific recently evolved microRNAs

Lineage-specific microRNAs (miRNAs) undergo rapid turnover during evolution; however, their origin and functional importance have remained controversial. Here, we examine the origin, evolution, and potential roles in local adaptation of Populus-specific miRNAs, which originated after the recent salicoid-specific, whole-genome duplication. RNA sequencing was used to generate extensive, comparable miRNA and gene expression data for six tissues. A natural population of Populus trichocarpa and closely related species were used to study the divergence rates, evolution, and adaptive variation of miRNAs. MiRNAs that originated in 5' untranslated regions had higher expression levels and their expression showed high correlation with their host genes. Compared with conserved miRNAs, a significantly higher proportion of Populus-specific miRNAs appear to target genes that were duplicated in salicoids. Examination of single nucleotide polymorphisms in Populus-specific miRNA precursors showed high amounts of population differentiation. We also characterized the newly emerged MIR6445 family, which could trigger the production of phased small interfering RNAs from NAC mRNAs, which encode a transcription factor with primary roles in a variety of plant developmental processes. Together, these observations provide evolutionary insights into the birth and potential roles of Populus-specific miRNAs in genome maintenance, local adaptation, and functional innovation.

Morphometric analysis of young petiole galls on the narrow-leaf cottonwood, Populus angustifolia, by the sugarbeet root aphid, Pemphigus betae

An insect-induced gall is a highly specialized structure resulting from atypical development of plant tissue induced by a reaction to the presence and activity of an insect. The insect induces a differentiation of tissues with features and functions of an ectopic organ, providing nutrition and protection to the galling insect from natural enemies and environmental stresses. In this anatomical and cytological study, we characterized how the gall-inducing aphid Pemphigus betae reshapes the leaf morphology of the narrow-leaf cottonwood Populus angustifolia to form a leaf fold gall. Young galls displayed a bend on one side of the midvein toward the center of the leaf and back to create a fold on the abaxial side of the leaf. This fold was formed abaxially by periclinal and anticlinal divisions, effectively eliminating intercellular spaces from the spongy parenchyma. Galls at this stage exhibited both cell hypertrophy and tissue hyperplasia. Cells on the adaxial surface were more numerous and smaller than cells near the abaxial surface were, creating the large fold that surrounds the insect. Mesophyll cells exhibited some features typical of nutritive cells induced by other galling insects, including conspicuous nucleolus, reduced and fragmented vacuole, smaller and degraded chloroplasts, and dense cytoplasm compared to ungalled tissue. Even though aphids feed on the contents of phloem and do not directly consume the gall tissue, they induce changes in the plant vascular system, which lead to nutrient accumulation to support the growing aphid numbers in mature galls.

An improved butanol-HCl assay for quantification of water-soluble, acetone:methanol-soluble, and insoluble proanthocyanidins (condensed tannins)

BACKGROUND

Condensed tannins (CT) are the most abundant secondary metabolite of land plants and can vary in abundance and structure according to tissue type, species, genotype, age, and environmental conditions. Recent improvements to the butanol-HCl assay have separately helped quantification of soluble and insoluble CTs, but have not yet been applied jointly. Our objectives were to combine previous assay improvements to allow for quantitative comparisons of different condensed tannin forms and to test protocols for analyses of condensed tannins in vegetative plant tissues. We also tested if the improved butanol-HCl assay can be used to quantify water-soluble forms of condensed tannins.

RESULTS

Including ~50% acetone in both extraction solvents and final assay reagents greatly improved the extraction and quantification of soluble, insoluble and total condensed tannins. The acetone-based method also extended the linear portion of standard integration curves allowing for more accurate quantification of samples with a broader range of condensed tannin concentrations. Estimates of tannin concentrations determined using the protocol without acetone were lower, but correlated with values from acetone-based methods. With the improved assay, quantification of condensed tannins in water-soluble forms was highly replicable. The relative abundance of condensed tannins in soluble and insoluble forms differed substantially between tissue types.

CONCLUSIONS

The quantification of condensed tannins using the butanol-HCl assay was improved by adding acetone to both extraction and reagent solutions. These improvements will facilitate the quantification of total condensed tannin in tissues containing a range of concentrations, as well as to determine the amount in water-soluble, acetone:MeOH-soluble and insoluble forms. Accurate determination of these three condensed tannin forms is essential for careful investigations of their potentially different physiological and ecological functions.

Integrating Evolutionary Game Theory into Mechanistic Genotype-Phenotype Mapping

Natural selection has shaped the evolution of organisms toward optimizing their structural and functional design. However, how this universal principle can enhance genotype-phenotype mapping of quantitative traits has remained unexplored. Here we show that the integration of this principle and functional mapping through evolutionary game theory gains new insight into the genetic architecture of complex traits. By viewing phenotype formation as an evolutionary system, we formulate mathematical equations to model the ecological mechanisms that drive the interaction and coordination of its constituent components toward population dynamics and stability. Functional mapping provides a procedure for estimating the genetic parameters that specify the dynamic relationship of competition and cooperation and predicting how genes mediate the evolution of this relationship during trait formation.

Genetic variation in NIN1 and C/VIF1 genes is significantly associated with Populus angustifolia resistance to a galling herbivore, Pemphigus betae

The identification of genes associated with ecologically important traits provides information on the potential genetic mechanisms underlying the responses of an organism to its natural environment. In this study, we investigated the genetic basis of host plant resistance to the gall-inducing aphid, Pemphigus betae, in a natural population of 154 narrowleaf cottonwoods (Populus angustifolia). We surveyed genetic variation in two genes putatively involved in sink-source relations and a phenology gene that co-located in a previously identified quantitative trait locus for resistance to galling. Using a candidate gene approach, three major findings emerged. First, natural variation in tree resistance to galling was repeatable. Sampling of the same tree genotypes 20 years after the initial survey in 1986 show that 80% of the variation in resistance was due to genetic differences among individuals. Second, we identified significant associations at the single nucleotide polymorphism and haplotype levels between the plant neutral invertase gene NIN1 and tree resistance. Invertases are a class of sucrose hydrolyzing enzymes and play an important role in plant responses to biotic stress, including the establishment of nutrient sinks. These associations with NIN1 were driven by a single nucleotide polymorphism (NIN1_664) located in the second intron of the gene and in an orthologous sequence to two known regulatory elements. Third, haplotypes from an inhibitor of invertase (C/VIF1) were significantly associated with tree resistance. The identification of genetic variation in these two genes provides a starting point to understand the possible genetic mechanisms that contribute to tree resistance to gall formation. We also build on previous work demonstrating that genetic differences in sink-source relationships of the host influence the ability of P. betae to manipulate the flow of nutrients and induce a nutrient sink.

Intraspecific trait variation across scales: implications for understanding global change responses

Recognition of the importance of intraspecific variation in ecological processes has been growing, but empirical studies and models of global change have only begun to address this issue in detail. This review discusses sources and patterns of intraspecific trait variation and their consequences for understanding how ecological processes and patterns will respond to global change. We examine how current ecological models and theories incorporate intraspecific variation, review existing data sources that could help parameterize models that account for intraspecific variation in global change predictions, and discuss new data that may be needed. We provide guidelines on when it is most important to consider intraspecific variation, such as when trait variation is heritable or when nonlinear relationships are involved. We also highlight benefits and limitations of different model types and argue that many common modeling approaches such as matrix population models or global dynamic vegetation models can allow a stronger consideration of intraspecific trait variation if the necessary data are available. We recommend that existing data need to be made more accessible, though in some cases, new experiments are needed to disentangle causes of variation.

Sequential divergence and the multiplicative origin of community diversity

Phenotypic and genetic variation in one species can influence the composition of interacting organisms within communities and across ecosystems. As a result, the divergence of one species may not be an isolated process, as the origin of one taxon could create new niche opportunities for other species to exploit, leading to the genesis of many new taxa in a process termed "sequential divergence." Here, we test for such a multiplicative effect of sequential divergence in a community of host-specific parasitoid wasps, Diachasma alloeum, Utetes canaliculatus, and Diachasmimorpha mellea (Hymenoptera: Braconidae), that attack Rhagoletis pomonella fruit flies (Diptera: Tephritidae). Flies in the R. pomonella species complex radiated by sympatrically shifting and ecologically adapting to new host plants, the most recent example being the apple-infesting host race of R. pomonella formed via a host plant shift from hawthorn-infesting flies within the last 160 y. Using population genetics, field-based behavioral observations, host fruit odor discrimination assays, and analyses of life history timing, we show that the same host-related ecological selection pressures that differentially adapt and reproductively isolate Rhagoletis to their respective host plants (host-associated differences in the timing of adult eclosion, host fruit odor preference and avoidance behaviors, and mating site fidelity) cascade through the ecosystem and induce host-associated genetic divergence for each of the three members of the parasitoid community. Thus, divergent selection at lower trophic levels can potentially multiplicatively and rapidly amplify biodiversity at higher levels on an ecological time scale, which may sequentially contribute to the rich diversity of life.

Mapping complex traits as a dynamic system

Despite increasing emphasis on the genetic study of quantitative traits, we are still far from being able to chart a clear picture of their genetic architecture, given an inherent complexity involved in trait formation. A competing theory for studying such complex traits has emerged by viewing their phenotypic formation as a "system" in which a high-dimensional group of interconnected components act and interact across different levels of biological organization from molecules through cells to whole organisms. This system is initiated by a machinery of DNA sequences that regulate a cascade of biochemical pathways to synthesize endophenotypes and further assemble these endophenotypes toward the end-point phenotype in virtue of various developmental changes. This review focuses on a conceptual framework for genetic mapping of complex traits by which to delineate the underlying components, interactions and mechanisms that govern the system according to biological principles and understand how these components function synergistically under the control of quantitative trait loci (QTLs) to comprise a unified whole. This framework is built by a system of differential equations that quantifies how alterations of different components lead to the global change of trait development and function, and provides a quantitative and testable platform for assessing the multiscale interplay between QTLs and development. The method will enable geneticists to shed light on the genetic complexity of any biological system and predict, alter or engineer its physiological and pathological states.

Where is the extended phenotype in the wild? The community composition of arthropods on mature oak trees does not depend on the oak genotype

Through a series of common garden experiments, it has been shown that heritable phenotypic differences between individual trees can affect arthropod communities. However, field studies under heterogeneous environmental conditions remain rare. In the present study, we investigated the genetic constitution of 121 mature oak host trees at different trophic levels from 10 sites across Bavaria, southern Germany and their associated insect communities. A total of 23,576 individuals representing 395 species of beetles and true bugs were evaluated. In particular, we determined whether the composition of arthropod communities is related to the oak genotype and whether the strength of the relationships decreases from lower to higher trophic levels, such as for phytophagous, xylophagous, zoophagous, and mycetophagous species. The genetic differentiation of oaks was assessed using eight microsatellite markers. We found no significant influence of the oak genotype on neither the full beetle and true bug community nor on any of the analyzed trophic guilds. In contrast, the community composition of the insects was highly related to the space and climate, such that the community similarity decreased with increases in spatial distance and climatic differences. The relationship with space and climate was much stronger in beetles than in true bugs, particularly in mycetophagous species. Our results suggest that spatial processes override the genetic effects of the host plant in structuring arthropod communities on oak trees. Because we used neutral markers, we cannot exclude the possibility that trait-specific markers may reveal a genetic imprint of the foundation tree species on the composition of the arthropod community. However, based on the strength of the spatial patterns in our data set, we assume that genetic differences among oaks are less important in the structuring of arthropod communities. Future whole-genome studies are required to draw a final conclusion.

Genotype × herbivore effect on leaf litter decomposition in Betula Pendula saplings: ecological and evolutionary consequences and the role of secondary metabolites

Plant genetic variation and herbivores can both influence ecosystem functioning by affecting the quantity and quality of leaf litter. Few studies have, however, investigated the effects of herbivore load on litter decomposition at plant genotype level. We reduced insect herbivory using an insecticide on one half of field-grown Betula Pendula saplings of 17 genotypes, representing random intrapopulation genetic variation, and allowed insects to naturally colonize the other half. We hypothesized that due to induced herbivore defence, saplings under natural herbivory produce litter of higher concentrations of secondary metabolites (terpenes and soluble phenolics) and have slower litter decomposition rate than saplings under reduced herbivory. We found that leaf damage was 89 and 53% lower in the insecticide treated saplings in the summer and autumn surveys, respectively, which led to 73% higher litter production. Litter decomposition rate was also affected by herbivore load, but the effect varied from positive to negative among genotypes and added up to an insignificant net effect at the population level. In contrast to our hypothesis, concentrations of terpenes and soluble phenolics were higher under reduced than natural herbivory. Those genotypes, whose leaves were most injured by herbivores, produced litter of lowest mass loss, but unlike we expected, the concentrations of terpenes and soluble phenolics were not linked to either leaf damage or litter decomposition. Our results show that (1) the genetic and herbivore effects on B. pendula litter decomposition are not mediated through variation in terpene or soluble phenolic concentrations and suggest that (2) the presumably higher insect herbivore pressure in the future warmer climate will not, at the ecological time scale, affect the mean decomposition rate in genetically diverse B. pendula populations. However, (3) due to the significant genetic variation in the response of decomposition to herbivory, evolutionary changes in mean decomposition rate are possible.

Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion

Genetic biodiversity contributes to individual fitness, species' evolutionary potential, and ecosystem stability. Temporal monitoring of the genetic status and trends of wild populations' genetic diversity can provide vital data to inform policy decisions and management actions. However, there is a lack of knowledge regarding which genetic metrics, temporal sampling protocols, and genetic markers are sufficiently sensitive and robust, on conservation-relevant timescales. Here, we tested six genetic metrics and various sampling protocols (number and arrangement of temporal samples) for monitoring genetic erosion following demographic decline. To do so, we utilized individual-based simulations featuring an array of different initial population sizes, types and severity of demographic decline, and DNA markers [single nucleotide polymorphisms (SNPs) and microsatellites] as well as decline followed by recovery. Number of alleles markedly outperformed other indicators across all situations. The type and severity of demographic decline strongly affected power, while the number and arrangement of temporal samples had small effect. Sampling 50 individuals at as few as two time points with 20 microsatellites performed well (good power), and could detect genetic erosion while 80-90% of diversity remained. This sampling and genotyping effort should often be affordable. Power increased substantially with more samples or markers, and we observe that power of 2500 SNPs was nearly equivalent to 250 microsatellites, a result of theoretical and practical interest. Our results suggest high potential for using historic collections in monitoring programs, and demonstrate the need to monitor genetic as well as other levels of biodiversity.