Genetic structure of a foundation species: scaling community phenotypes from the individual to the region

Genetic underpinnings of arthropod community distributions in Populus trichocarpa

Community genetics seeks to understand the mechanisms by which natural genetic variation in heritable host phenotypes can encompass assemblages of organisms such as bacteria, fungi, and many animals including arthropods. Prior studies that focused on plant genotypes have been unable to identify genes controlling community composition, a necessary step to predict ecosystem structure and function as underlying genes shift within plant populations. We surveyed arthropods within an association population of Populus trichocarpa in three common gardens to discover plant genes that contributed to arthropod community composition. We analyzed our surveys with traditional single-trait genome-wide association analysis (GWAS), multitrait GWAS, and functional networks built from a diverse set of plant phenotypes. Plant genotype was influential in structuring arthropod community composition among several garden sites. Candidate genes important for higher level organization of arthropod communities had broadly applicable functions, such as terpenoid biosynthesis and production of dsRNA binding proteins and protein kinases, which may be capable of targeting multiple arthropod species. We have demonstrated the ability to detect, in an uncontrolled environment, individual genes that are associated with the community assemblage of arthropods on a host plant, further enhancing our understanding of genetic mechanisms that impact ecosystem structure.

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.

Intraspecific variation in a predator changes intertidal community through effects on a foundation species

Intraspecific variation is an important form of biodiversity that can alter community and ecosystem properties. Recent work demonstrates the community effects of intraspecific variation in predators via altering prey communities and in foundation species via shaping habitat attributes. However, tests of the community effects of intraspecific trait variation in predators acting on foundation species are lacking despite the fact that consumption of foundation species can have strong community effects by shaping habitat structure. Here, we tested the hypothesis that intraspecific foraging differences among populations of mussel-drilling dogwhelk predators (Nucella) differentially alter intertidal communities through effects on foundational mussels. We conducted a 9-month field experiment where we exposed intertidal mussel bed communities to predation from three Nucella populations that exhibit differences in size-selectivity and consumption time for mussel prey. At the end of the experiment, we measured mussel bed structure, species diversity, and community composition. While exposure to Nucella originating from different populations did not significantly alter overall community diversity, we found that differences in Nucella mussel selectivity significantly altered foundational mussel bed structure, which in turn altered the biomass of shore crabs and periwinkle snails. Our study extends the emerging paradigm of the ecological importance of intraspecific variation to include the effects of intraspecific variation on predators of foundation species.

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.

Evidence for the genetic similarity rule at an expanding mangrove range limit

PREMISE

Host-plant genetic variation can shape associated communities of organisms. These community-genetic effects include (1) genetically similar hosts harboring similar associated communities (i.e., the genetic similarity rule) and (2) host-plant heterozygosity increasing associated community diversity. Community-genetic effects are predicted to be less prominent in plant systems with limited genetic variation, such as those at distributional range limits. Yet, empirical evidence from such systems is limited.

METHODS

We sampled a natural population of a mangrove foundation species (Avicennia germinans) at an expanding range limit in Florida, USA. We measured genetic variation within and among 40 host trees with 24 nuclear microsatellite loci and characterized their foliar endophytic fungal communities with internal transcribed spacer (ITS1) gene amplicon sequencing. We evaluated relationships among host-tree genetic variation, host-tree spatial location, and the associated fungal communities.

RESULTS

Genetic diversity was low across all host trees (mean: 2.6 alleles per locus) and associated fungal communities were relatively homogeneous (five sequence variants represented 78% of all reads). We found (1) genetically similar host trees harbored similar fungal communities, with no detectable effect of interhost geographic distance. (2) Host-tree heterozygosity had no detectable effect, while host-tree absolute spatial location affected community alpha diversity.

CONCLUSIONS

This research supports the genetic similarity rule within a range limit population and helps broaden the current scope of community genetics theory by demonstrating that community-genetic effects can occur even at expanding distributional limits where host-plant genetic variation may be limited. Our findings also provide the first documentation of community-genetic effects in a natural mangrove system.

Local Adaptation in Marine Foundation Species at Microgeographic Scales

AbstractNearshore foundation species in coastal and estuarine systems (e.g., salt marsh grasses, mangroves, seagrasses, corals) drive the ecological functions of ecosystems and entire biomes by creating physical structure that alters local abiotic conditions and influences species interactions and composition. The resilience of foundation species and the ecosystem functions they provide depends on their phenotypic and genetic responses to spatial and temporal shifts in environmental conditions. In this review, we explore what is known about the causes and consequences of adaptive genetic differentiation in marine foundation species over spatial scales shorter than dispersal capabilities (i.e., microgeographic scales). We describe the strength of coupling field and laboratory experiments with population genetic techniques to illuminate patterns of local adaptation, and we illustrate this approach by using several foundation species. Among the major themes that emerge from our review include (1) adaptive differentiation of marine foundation species repeatedly evolves along vertical (i.e., elevation or depth) gradients, and (2) mating system and phenology may facilitate this differentiation. Microgeographic adaptation is an understudied mechanism potentially underpinning the resilience of many sessile marine species, and this evolutionary mechanism likely has particularly important consequences for the ecosystem functions provided by foundation species.

Defining codominance in plant communities

Species dominance and biodiversity in plant communities have received considerable attention and characterisation. However, species codominance, while often alleged, is seldom defined or quantified. Codominance is a common phenomenon and is likely to be an important driver of community structure, ecosystem function and the stability of both. Here we review the use of the term 'codominance' and find inconsistencies in its use, suggesting that the scientific community currently lacks a universal understanding of codominance. We address this issue by: (1) qualitatively defining codominance as mostly shared abundance that is distinctively isolated within a subset of a community, and (2) presenting a novel metric for quantifying the degree to which relative abundances are shared among a codominant subset of plant species, while also accounting for the remaining species within a plant community. Using both simulated and real-world data, we then demonstrate the process of applying the codominance metric to compare communities and to generate a quantitatively defensible subset of species to consider codominant within a community. We show that our metric effectively distinguishes the degree of codominance between four types of grassland ecosystems as well as simulated ecosystems with varying degrees of abundance sharing among community members. Overall, we make the case that increased research focusses on the conditions under which codominance occurs and the consequences for species coexistence, community structure and ecosystem function that would considerably advance the fields of community and ecosystem ecology.

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.

Incorporating Ploidy Diversity into Ecological and Community Genetics

Studies in ecological and community genetics have advanced our understanding of the role of intraspecific diversity in structuring communities and ecosystems. However, in near-shore marine communities, these studies have mostly been restricted to seagrasses, marsh plants, and oysters. Yet, macroalgae are critically important ecosystem engineers in these communities. Greater intraspecific diversity in a macroalgal ecosystem engineer should result in higher primary and secondary production and community resilience. The paucity of studies investigating the consequences of macroalgal intraspecific genetic variation might be due, in part, to the complexity of macroalgal life cycles. The majority of macroalgae have seemingly subtle, but in actuality, profoundly different life cycles than the more typical animal and angiosperm models. Here, we develop a novel genetic diversity metric, P_HD , that incorporates the ratio of gametophytic to sporophytic thalli in natural populations. This metric scales from 0 to 1 like many common genetic diversity metrics, such as genotypic richness, enabling comparisons among metrics. We discuss P_HD and examples from the literature, with specific reference to the widespread, red seaweed Agarophyton vermiculophyllum. We also discuss a sex diversity metric, P_FM , which also scales from 0 to 1, but fewer studies have identified males and females in natural populations. Nevertheless, by incorporating these novel metrics into the repertoire of diversity metrics, we can explore the role of genetic diversity in community and ecosystem dynamics with an emphasis on the unique biology of many macroalgae, as well as other haplodiplontic taxa such as ferns, foraminiferans, and some fungi.

Demystifying dominant species

The pattern of a few abundant species and many rarer species is a defining characteristic of communities worldwide. These abundant species are often referred to as dominant species. Yet, despite their importance, the term dominant species is poorly defined and often used to convey different information by different authors. Based on a review of historical and contemporary definitions we develop a synthetic definition of dominant species. This definition incorporates the relative local abundance of a species, its ubiquity across the landscape, and its impact on community and ecosystem properties. A meta-analysis of removal studies shows that the loss of species identified as dominant by authors can significantly impact ecosystem functioning and community structure. We recommend two metrics that can be used jointly to identify dominant species in a given community and provide a roadmap for future avenues of research on dominant species. In our review, we make the case that the identity and effects of dominant species on their environments are key to linking patterns of diversity to ecosystem function, including predicting impacts of species loss and other aspects of global change on ecosystems.

Experimental drought reduces genetic diversity in the grassland foundation species Bouteloua eriopoda

Understanding the resistance and resilience of foundation plant species to climate change is a critical issue because the loss of these species would fundamentally reshape communities and ecosystem processes. High levels of population genetic diversity may buffer foundation species against climate disruptions, but the strong selective pressures associated with climatic shifts may also rapidly reduce such diversity. We characterized genetic diversity and its responsiveness to experimental drought in the foundation plant, black grama grass (Bouteloua eriopoda), which dominates many western North American grasslands and shrublands. Previous studies suggested that in arid ecosystems, black grama reproduces largely asexually via stolons, and thus is likely to have low genetic variability, which might limit its potential to respond to climate disruptions. Using genotyping-by-sequencing, we demonstrated unexpectedly high genetic variability among black grama plants in a 1 ha site within the Sevilleta National Wildlife Refuge in central New Mexico, suggesting some level of sexual reproduction. Three years of experimental, growing season drought reduced black grama survival and biomass (the latter by 96%), with clear genetic differentiation (higher F_ST) between plants succumbing to drought and those remaining alive. Reduced genetic variability in the surviving plants in drought plots indicated that the experimental drought had forced black grama populations through selection bottlenecks. These results suggest that foundation grass species, such as black grama, may experience rapid evolutionary change if future climates include more severe droughts.

Natural hybridisation among Quercus glabrescens, Q. rugosa and Q. obtusata (Fagaceae): Microsatellites and secondary metabolites markers

Natural hybridisation has significant ecological, genetic and evolutionary consequences altering morphological and chemical characters of individuals. Quercus glabrescens, Q. rugosa and Q. obtusata are white oak species well separated by their morphological characters when they occur in allopatry in Mexican temperate forests. However, in sympatry, individuals with atypical morphology have been observed, suggesting hybridisation events. In this study, we determined, with microsatellites and secondary metabolites, if interspecific gene flow occurs when these three oak species coexist in sympatry. In total, 180 individuals belonging to seven populations [three allopatric (one for each parental species) and four sympatric sites] were analysed. Allopatric populations represent well-defined genetic groups and the sympatric populations showed genetic evidence of hybridisation between Q. glabrescens × Q. rugosa and Q. glabrescens × Q. obtusata. The hybridisation percentage varied between sites and combination of involved species. We registered the presence of unique flavonoid compounds for Q. glabrescens (caffeic acid and flavonol 2), Q. rugosa (flavonol 5) and Q. obtusata (flavonol 1). Three compounds (quercetin rhamnoside, flavonol 3 and alkyl coumarate) were expressed in all taxa. Finally, the hybrid genotypes identified in this study (Q. glabrescens × Q. rugosa and Q. glabrescens × Q. obtusata) showed specific chemical profiles, resulting from a combination of those of their parental species. These results show that hybridisation events between these oak species alter chemical expression of secondary metabolites, creating a mosaic of resources and conditions that provide the substrate for different combinations of foliar-associated species such as herbivores, endophytic fungi or epiphyte plants.

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.

Effects of Intraspecific Genetic Variation and Prior Herbivory in an Old-Field Plant on the Abundance of the Specialist Aphid Uroleucon nigrotuberculatum (Hemiptera: Aphididae)

Intraspecific genetic variation in plants can contribute to the diversity and abundance of associated insects, though many questions remain about why some genotypes support more insects than others. Since plant secondary metabolites, which may be induced after insect attack, may potentially vary among genotypes, these compounds provide a possible explanation for insect abundance variation in plants with substantial genetic variation. In this study, we examined four genotypes of the old-field plant species Solidago altissima (L.; Asterales: Asteraceae) and asked if the abundance of the specialist aphid Uroleucon nigrotuberculatum (Olive; Hemiptera: Aphididae) was affected by genotype and previous foliage damage by a specialist beetle. We hypothesized that different genotypes and prior herbivory would result in different quantities of terpenes produced by S. altissima, and that terpenes would affect aphid abundance. We found evidence of foliar terpene induction in a greenhouse environment, and significant differences in terpene production among genotypes in a field setting, though prior damage had little effect on aphid abundance in the field. There were significant effects of genotypes on aphid abundance, as well as genotype effects on terpenes and foliar nutrients (leaf N and C:N). Noteworthy was a change in the allocation of particular terpenes among genotypes that related to aphid abundance. Our analyses demonstrated that phytochemicals, and especially terpenes, related to aphid abundance. This study adds to a previous finding that variation in leaf terpenes in S. altissima provides a partial explanation for variable abundance among genotypes of a specialist aphid, and suggests that differences in the allocation of compounds is important.

Genetic variation in foundation species governs the dynamics of trophic interactions

Various studies have demonstrated that the foundation species genetic diversity can have direct effects that extend beyond the individual or population level, affecting the dependent communities. Additionally, these effects may be indirectly extended to higher trophic levels throughout the entire community. Quercus castanea is an oak species with characteristics of foundation species beyond presenting a wide geographical distribution and being a dominant element of Mexican temperate forests. In this study, we analyzed the influence of population (He) and individual (HL) genetic diversity of Q. castanea on its canopy endophagous insect community and associated parasitoids. Specifically, we studied the composition, richness (S) and density of leaf-mining moths (Lepidoptera: Tischeridae, Citheraniidae), gall-forming wasps (Hymenoptera: Cynipidae), and canopy parasitoids of Q. castanea. We sampled 120 trees belonging to six populations (20/site) through the previously recognized gradient of genetic diversity. In total, 22 endophagous insect species belonging to three orders (Hymenoptera, Lepidoptera, and Diptera) and 20 parasitoid species belonging to 13 families were identified. In general, we observed that the individual genetic diversity of the host plant (HL) has a significant positive effect on the S and density of the canopy endophagous insect communities. In contrast, He has a significant negative effect on the S of endophagous insects. Additionally, indirect effects of HL were observed, affecting the S and density of parasitoid insects. Our results suggest that genetic variation in foundation species can be one of the most important factors governing the dynamics of tritrophic interactions that involve oaks, herbivores, and parasitoids.

Genetic variation of a foundation rockweed species affects associated communities

Genetic variation in a foundation species may affect the composition of associated communities as well as modify ecosystem function. While the ecological consequences of genetic diversity of foundation species have been widely reported, the ability of individual genotypes to support dissimilar communities has been documented only in forest ecosystems. Here, for the first time in a marine ecosystem, we test whether the different genotypes of the rockweed Fucus vesiculosus harbor distinct community phenotypes and whether the genetic similarity of individual genotypes or their defensive compound content can explain the variation of the associated communities. We reared replicated genotypes in a common garden in the sea and analyzed their associated communities of periphytic algae and invertebrates as well as determined their contents of defense compounds, phlorotannins, and genetic distance based on neutral molecular markers. The periphytic community was abundant in mid-summer and its biovolume, diversity and community composition varied among the rockweed genotypes. The diversity of the periphytic community decreased with its increasing biovolume. In autumn, when grazers were abundant, periphytic community biomass was lower and less variable among rockweed genotypes, indicating different relative importance of bottom-up regulation through heritable variation of the foundation species and top-down regulation through grazing intensity. Similarly, composition of the invertebrate community varied among the rockweed genotypes. Although the genotype explained about 10-18% of the variation in associated communities, the variation was explained neither by the genetic distance nor the phlorotannin content. Thus, neither neutral genetic markers nor a single phenotypic trait could provide a mechanistic understanding of the genetic basis of community specificity. Therefore, a more comprehensive mapping of quantitative trait variation is needed to understand the underlying mechanisms. The community specificity implies that genetic variation within a foundation species is crucial for the biodiversity and assembly of associated organisms and, thus, for the functioning of associated communities. The result highlights the importance of ensuring the genetic variation of foundation species as a conservation target.

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.

Genetically based latitudinal clines in Artemisia californica drive parallel clines in arthropod communities

Intraspecific variation in plant traits has been clearly shown to drive the structure of associated arthropod communities at the spatial scale of individual plant populations. Nevertheless, it is largely unknown whether plant trait variation among populations drives landscape-scale variation in arthropod communities, and how the strength of such plant genetic effects compares to, and interacts with, those of environmental variation. We documented the structure of arthropod communities on Artemisia californica for two consecutive years in a common garden of plants sourced from five populations along a 5° latitudinal gradient and grown under precipitation treatments approximating the four-fold difference between the north and south range margins for this species. Previous study of plant traits from this garden documented clinal genetic variation, suggesting local adaptation to this environmental gradient, as well as effects of precipitation manipulation that were consistent among populations (i.e., no genotype-by-environment interaction). Within the common garden, arthropod density, evenness, and diversity increased clinally with population source latitude, and arthropod community composition (i.e., species relative abundance) showed a north-south divide. The 2.6-fold cline of northward increase in arthropod density in the common garden was mirrored by a 6.4-fold increase in arthropod density on wild plants sampled along the species range. In contrast to the strong influence of plant genotype, the precipitation manipulation only influenced arthropod community composition, and plant genetic effects on arthropods operated independently of precipitation regime (no genotype-by-environment interaction). Accordingly, we conclude that the strongest driver of landscape-level variation in arthropod communities in this foundational plant species is not variation in the abiotic environment itself, but rather variation in plant traits underlain by the evolutionary process of plant local adaptation.

Genetic diversity affects ecological performance and stress response of marine diatom populations

Genetic diversity is considered an important factor, stabilizing ecological functions when organisms are faced with changing environmental conditions. Although well known from terrestrial systems, documentations of this relationship from marine organisms, and particularly planktonic microorganisms, are still limited. Here we experimentally tested the effects of genotypic diversity on ecologically relevant cellular parameters (growth, primary production, particulate organic carbon, particulate organic nitrogen, particulate organic phosphorus and biogenic silica) at optimal and suboptimal salinity conditions in a marine phytoplankton species. Multiple clonal genotyped and phenotypically characterized isolates of the diatom Skeletonema marinoi from the Baltic Sea were grown in monocultures and mixes of 5 and 20 clones at native (5 psu) and reduced (3 psu) salinities and respective parameters were compared. Re-genotyping of 30 individuals from each population at five microsatellite loci at the end of the experiment confirmed maintenance of genotypic richness. Although a diversity effect on growth was not detected, primary production and particulate organic nutrients were positively affected by increased diversity independent of salinity condition. Under salinity stress, highest values of primary production and particulate organic nitrogen content were measured at the high diversity level. The observed diversity effects emphasize the importance of genetic diversity of phytoplankton populations for ecological functions.

Cryptic eco-evolutionary dynamics

Natural systems harbor complex interactions that are fundamental parts of ecology and evolution. These interactions challenge our inclinations and training to seek the simplest explanations of patterns in nature. Not least is the likelihood that some complex processes might be missed when their patterns look similar to predictions for simpler mechanisms. Along these lines, theory and empirical evidence increasingly suggest that environmental, ecological, phenotypic, and genetic processes can be tightly intertwined, resulting in complex and sometimes surprising eco-evolutionary dynamics. The goal of this review is to temper inclinations to unquestioningly seek the simplest explanations in ecology and evolution, by recognizing that some eco-evolutionary outcomes may appear very similar to purely ecological, purely evolutionary, or even null expectations, and thus be cryptic. We provide theoretical and empirical evidence for observational biases and mechanisms that might operate among the various links in eco-evolutionary feedbacks to produce cryptic patterns. Recognition that cryptic dynamics can be associated with outcomes like stability, resilience, recovery, or coexistence in a dynamically changing world provides added impetus for finding ways to study them.

Plant-herbivore interactions in a trispecific hybrid swarm of Populus: assessing support for hypotheses of hybrid bridges, evolutionary novelty and genetic similarity

Natural systems of hybridizing plants are powerful tools with which to assess evolutionary processes between parental species and their associated arthropods. Here we report on these processes in a trispecific hybrid swarm of Populus trees. Using field observations, common garden experiments and genetic markers, we tested the hypothesis that genetic similarities among hosts underlie the distributions of 10 species of gall-forming arthropods and their ability to adapt to new host genotypes.

KEY FINDINGS

the degree of genetic relatedness among parental species determines whether hybridization is primarily bidirectional or unidirectional; host genotype and genetic similarity strongly affect the distributions of gall-forming species, individually and as a community. These effects were detected observationally in the wild and experimentally in common gardens; correlations between the diversity of host genotypes and their associated arthropods identify hybrid zones as centres of biodiversity and potential species interactions with important ecological and evolutionary consequences. These findings support both hybrid bridge and evolutionary novelty hypotheses. However, the lack of parallel genetic studies on gall-forming arthropods limits our ability to define the host of origin with their subsequent shift to other host species or their evolution on hybrids as their final destination.

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.

Landscape genetic connectivity in a riparian foundation tree is jointly driven by climatic gradients and river networks

Fremont cottonwood (Populus fremonti) is a foundation riparian tree species that drives community structure and ecosystem processes in southwestern U.S. ecosystems. Despite its ecological importance, little is known about the ecological and environmental processes that shape its genetic diversity, structure, and landscape connectivity. Here, we combined molecular analyses of 82 populations including 1312 individual trees dispersed over the species' geographical distribution. We reduced the data set to 40 populations and 743 individuals to eliminate admixture with a sibling species, and used multivariate restricted optimization and reciprocal causal modeling to evaluate the effects of river network connectivity and climatic gradients on gene flow. Our results confirmed the following: First, gene flow of Fremont cottonwood is jointly controlled by the connectivity of the river network and gradients of seasonal precipitation. Second, gene flow is facilitated by mid-sized to large rivers, and is resisted by small streams and terrestrial uplands, with resistance to gene flow decreasing with river size. Third, genetic differentiation increases with cumulative differences in winter and spring precipitation. Our results suggest that ongoing fragmentation of riparian habitats will lead to a loss of landscape-level genetic connectivity, leading to increased inbreeding and the concomitant loss of genetic diversity in a foundation species. These genetic effects will cascade to a much larger community of organisms, some of which are threatened and endangered.

Climate relicts and their associated communities as natural ecology and evolution laboratories

Climate relicts, marginal populations that have become isolated via climate-driven range shifts, preserve ecological and evolutionary histories that can span millennia. Studies point to climate relicts as 'natural laboratories' for investigating how long-term environmental change impacts species and populations. However, we propose that such research should be expanded to reveal how climate change affects 'interacting' species in ways that reshape community composition and evolution. Biotic interactions and their community and ecosystem effects are often genetically based and driven by associations with foundation species. We discuss evolution in climate relicts within the context of the emerging fields of community and ecosystem genetics, exploring the idea that foundation relicts are also natural community and ecosystem laboratories and windows to future landscapes.

Genetic sorting of subordinate species in grassland modulated by intraspecific variation in dominant species

Genetic variation in a single species can have predictable and heritable effects on associated communities and ecosystem processes, however little is known about how genetic variation of a dominant species affects plant community assembly. We characterized the genetic structure of a dominant grass (Sorghastrum nutans) and two subordinate species (Chamaecrista fasciculata, Silphium integrifolium), during the third growing season in grassland communities established with genetically distinct (cultivated varieties or local ecotypes) seed sources of the dominant grasses. There were genetic differences between subordinate species growing in the cultivar versus local ecotype communities, indicating that intraspecific genetic variation in the dominant grasses affected the genetic composition of subordinate species during community assembly. A positive association between genetic diversity of S. nutans, C. fasciculata, and S. integrifolium and species diversity established the role of an intraspecific biotic filter during community assembly. Our results show that intraspecific variation in dominant species can significantly modulate the genetic composition of subordinate species.

Effects of plant genotype and insect dispersal rate on the population dynamics of a forest pest

It has been shown that plant genotype can strongly affect not only individual herbivore performance, but also community composition and ecosystem function. Few studies, however, have addressed how plant genotype affects herbivore population dynamics. In this paper, we used a simulation modeling approach to ask how the genetic composition of a forest influences pest outbreak dynamics, using the example of aspen (Populus tremuloides) and forest tent caterpillars (FTC; Malacosoma disstria). Specifically, we examined how plant genotype, the relative size of genotypic patches, and the rate of insect dispersal between them, affect the frequency, amplitude, and duration of outbreaks. We found that coupling two different genotypes does not necessarily result in an averaging of insect dynamics. Instead, depending on the ratio of patch sizes, when dispersal rates are moderate, outbreaks in the two-genotype case may be more or less severe than in forests of either genotype alone. Thresholds for different dynamic behaviors were similar for all genotypic combinations. Thus, the qualitative behavior of a stand of two different genotypes can be predicted based on the response of the insect to each genotype, the relative sizes of the two patches, and the scale of insect dispersal.

Genetic and environmental determinants of insect herbivore community structure in a Betula pendula population

A number of recent studies have shown that intraspecific genetic variation of plants may have a profound effect on the herbivorous communities which depend on them. However less is known about the relative importance of intraspecific variation compared to other ecological factors, for example environmental variation or the effects of herbivore damage. We randomly selected 22 Betula pendula genotypes from a local population (< 0.9 ha), cloned them and planted cloned seedlings on two study sites separated at a regional scale (distance between sites about 30 km) to examine an insect community of 23-27 species on these genotypes. B. pendula genotypes did not differ in their species richness, but the total mean abundance and the structure of the insect herbivore community was significantly affected by the genotype, which could account for up to 27% of the total variation in community structure. B. pendula genotype accounted for two to four times more variation in the arthropod community structure than did environmental (block) variation on a local scale, while on a regional scale, genotypic and environmental (site) variation accounted for 4-14% of the arthropod community structure. The genetic effects were modified by environmental variation on both a local and regional scale over one study year, and locally, the largest part of the variation (38%) could be explained by the genotype × environment (block) interactions. Suppression of insect herbivores during one growing season led to changed arthropod community structure in the following growing season, but this effect was minimal and could explain only 4% of the total variation in insect community structure. Our results suggest that both genetic and environmental factors are important determinants of the community structure of herbivorous insects. Together these mechanisms appear to maintain the high diversity of insects in B. pendula forest ecosystems.

Relationship between fish size and metabolic rate in the oxyconforming inanga Galaxias maculatus reveals size-dependent strategies to withstand hypoxia

The relationship between metabolic rate and body size in animals is unlikely to be a constant but is instead shaped by a variety of intrinsic (i.e., physiological) and extrinsic (i.e., environmental) factors. This study examined the effect of environmental oxygen tension on oxygen consumption as a function of body mass in the galaxiid fish, inanga (Galaxias maculatus). As an oxyconformer, this fish lacks overt intrinsic regulation of oxygen consumption, eliminating this as a factor affecting the scaling relationship at different oxygen tensions. The relationship between oxygen consumption rate and body size was best described by a power function, with an exponent of 0.82, higher than the theoretical values of 0.66 or 0.75. The value of this exponent was significantly altered by environmental P(O2), first increasing as P(O2) decreased and then declining at the lowest P(O2) tested. These data suggest that the scaling exponent is species specific and regulated by extrinsic factors. Furthermore, the external P(O2) at which fish lost equilibrium was related to fish size, an effect explained by the scaling of anaerobic capacity with fish mass. Therefore, although bigger fish were forced to depress aerobic metabolism more rapidly than small fish when exposed to progressive hypoxia, they were better able to enact anaerobic metabolism, potentially extending their survival in hypoxia.

Can elevated CO2 and ozone shift the genetic composition of aspen (Populus tremuloides) stands?

The world's forests are currently exposed to increasing concentrations of carbon dioxide (CO2) and ozone (O3). Both pollutants can potentially exert a selective effect on plant populations. This, in turn, may lead to changes in ecosystem properties, such as carbon sequestration. Here, we report how elevated CO2 and O3 affect the genetic composition of a woody plant population via altered survival. Using data from the Aspen free-air CO2 enrichment (FACE) experiment (in which aspen clones were grown in factorial combinations of CO2 and O3), we develop a hierarchical Bayesian model of survival. We also examine how survival differences between clones could affect pollutant responses in the next generation. Our model predicts that the relative abundance of the tested clones, given equal initial abundance, would shift under either elevated CO2 or O3 as a result of changing survival rates. Survival was strongly affected by between-clone differences in growth responses. Selection could noticeably decrease O3 sensitivity in the next generation, depending on the heritability of growth responses and the distribution of seed production. The response to selection by CO2, however, is likely to be small. Our results suggest that the changing atmospheric composition could shift the genotypic composition and average pollutant responses of tree populations over moderate timescales.

Rapid phytochemical analysis of birch (Betula) and poplar (Populus) foliage by near-infrared reflectance spectroscopy

Poplar (Populus) and birch (Betula) species are widely distributed throughout the northern hemisphere, where they are foundation species in forest ecosystems and serve as important sources of pulpwood. The ecology of these species is strongly linked to their foliar chemistry, creating demand for a rapid, inexpensive method to analyze phytochemistry. Our study demonstrates the feasibility of using near-infrared reflectance spectroscopy (NIRS) as an inexpensive, high-throughput tool for determining primary (e.g., nitrogen, sugars, starch) and secondary (e.g., tannins, phenolic glycosides) foliar chemistry of Populus and Betula species, and identifies conditions necessary for obtaining reliable quantitative data. We developed calibrations with high predictive power (residual predictive deviations ≤ 7.4) by relating phytochemical concentrations determined with classical analytical methods (e.g., spectrophotometric assays, liquid chromatography) to NIR spectra, using modified partial least squares regression. We determine that NIRS, although less sensitive and precise than classical methods for some compounds, provides useful predictions in a much faster, less expensive manner than do classical methods.

Genetic effects of tank-forming bromeliads on the associated invertebrate community in a tropical forest ecosystem

Within the area of community genetics there is an expanding volume of literature demonstrating how within-species genetic variation in temperate trees can have important effects on structuring animal and plant communities. The influence of intraspecific genetic variation on associated communities in relatively more complex ecosystems is only starting to be appreciated. Within tropical forests, epiphytic bromeliad plants often grow high in the canopy and create unique nutrient-rich microhabitats on which many invertebrate and vertebrate species depend. We investigated the influence of within-species genetic variation in the bromeliad Aechmea bracteata on the invertebrate microhabitat community. We found that more genetically similar bromeliad plants were host to more similar communities of juvenile-stage invertebrates, but not adult invertebrates. We discuss possible mechanisms for this, including differential survival and active female oviposition choice. Our work shows that the impact of within-species genetic variation on associated ecological communities may be more general than previously considered. These results agree with recent research suggesting that within-species genetic variation may perform a supporting ecosystem service for maintaining community and ecological processes.

Genetic variation in a tropical tree species influences the associated epiphytic plant and invertebrate communities in a complex forest ecosystem

Genetic differences among tree species, their hybrids and within tree species are known to influence associated ecological communities and ecosystem processes in areas of limited species diversity. The extent to which this same phenomenon occurs based on genetic variation within a single tree species, in a diverse complex ecosystem such as a tropical forest, is unknown. The level of biodiversity and complexity of the ecosystem may reduce the impact of a single tree species on associated communities. We assessed the influence of within-species genetic variation in the tree Brosimum alicastrum (Moraceae) on associated epiphytic and invertebrate communities in a neotropical rainforest. We found a significant positive association between genetic distance of trees and community difference of the epiphytic plants growing on the tree, the invertebrates living among the leaf litter around the base of the tree, and the invertebrates found on the tree trunk. This means that the more genetically similar trees are host to more similar epiphyte and invertebrate communities. Our work has implications for whole ecosystem conservation management, since maintaining sufficient genetic diversity at the primary producer level will enhance species diversity of other plants and animals.

Forward from the crossroads of ecology and evolution

Community genetics is a synthesis of community ecology and evolutionary biology. It examines how genetic variation within a species affects interactions among species to change ecological community structure and diversity. The use of community genetics approaches has greatly expanded in recent years and the evidence for ecological effects of genetic diversity is growing. The goal of current community genetics research is to determine the circumstances in which, and the mechanisms by which community genetic effects occur and is the focus of the papers in this special issue. We bring a new group of researchers into the community genetics fold. Using a mixture of empirical research, literature reviews and theoretical development, we introduce novel concepts and methods that we hope will enable us to develop community genetics into the future.

Community genetics: what have we accomplished and where should we be going?

Research in community genetics seeks to understand how the dynamic interplay between ecology and evolution shapes simple and complex communities and ecosystems. A community genetics perspective, however, may not be necessary or informative for all studies and systems. To better understand when and how intraspecific genetic variation and microevolution are important in community and ecosystem ecology, we suggest future research should focus on three areas: (i) determining the relative importance of intraspecific genetic variation compared with other ecological factors in mediating community and ecosystem properties; (ii) understanding the importance of microevolution in shaping ecological dynamics in multi-trophic communities; and (iii) deciphering the phenotypic and associated genetic mechanisms that drive community and ecosystem processes. Here, we identify key areas of research that will increase our understanding of the ecology and evolution of complex communities but that are currently missing in community genetics. We then suggest experiments designed to meet these current gaps.

Analytic theories of allometric scaling

During the 13 years since it was first advanced, the fractal network theory (FNT), an analytic theory of allometric scaling, has been subjected to a wide range of methodological, mathematical and empirical criticisms, not all of which have been answered satisfactorily. FNT presumes a two-variable power-law relationship between metabolic rate and body mass. This assumption has been widely accepted in the past, but a growing body of evidence during the past quarter century has raised questions about its general validity. There is now a need for alternative theories of metabolic scaling that are consistent with empirical observations over a broad range of biological applications. In this article, we briefly review the limitations of FNT, examine the evidence that the two-variable power-law assumption is invalid, and outline alternative perspectives. In particular, we discuss quantum metabolism (QM), an analytic theory based on molecular-cellular processes. QM predicts the large variations in scaling exponent that are found empirically and also predicts the temperature dependence of the proportionality constant, issues that have eluded models such as FNT that are based on macroscopic and network properties of organisms.

Controlling for non-independence in comparative analysis of patterns across populations within species

How do we quantify patterns (such as responses to local selection) sampled across multiple populations within a single species? Key to this question is the extent to which populations within species represent statistically independent data points in our analysis. Comparative analyses across species and higher taxa have long recognized the need to control for the non-independence of species data that arises through patterns of shared common ancestry among them (phylogenetic non-independence), as have quantitative genetic studies of individuals linked by a pedigree. Analyses across populations lacking pedigree information fall in the middle, and not only have to deal with shared common ancestry, but also the impact of exchange of migrants between populations (gene flow). As a result, phenotypes measured in one population are influenced by processes acting on others, and may not be a good guide to either the strength or direction of local selection. Although many studies examine patterns across populations within species, few consider such non-independence. Here, we discuss the sources of non-independence in comparative analysis, and show why the phylogeny-based approaches widely used in cross-species analyses are unlikely to be useful in analyses across populations within species. We outline the approaches (intraspecific contrasts, generalized least squares, generalized linear mixed models and autoregression) that have been used in this context, and explain their specific assumptions. We highlight the power of 'mixed models' in many contexts where problems of non-independence arise, and show that these allow incorporation of both shared common ancestry and gene flow. We suggest what can be done when ideal solutions are inaccessible, highlight the need for incorporation of a wider range of population models in intraspecific comparative methods and call for simulation studies of the error rates associated with alternative approaches.

Spatial location dominates over host plant genotype in structuring an herbivore community

Recent work has shown a potential role for both host plant genotype and spatial context in structuring insect communities. In this study, we use three separate data sets on herbivorous insects on oak (Quercus robur) to estimate the relative effects of host plant genotype (G), location (E), and the G x E interaction on herbivore community structure: a common garden experiment replicated at the landscape scale (approximately 5 km2); two common gardens separated at the regional scale (approximately 10 000 km2); and survey data on wild trees in various spatial settings. Our experiments and survey reveal that, at the landscape scale, the insect community is strongly affected by the spatial setting, with 32% of the variation in species richness explained by spatial connectivity. In contrast, G and G x E play minor roles in structuring the insect community. Results remained similar when extending the spatial scale of the study from the more local (landscape) level to the regional level. We conclude that in our study system, spatial processes play a major role in structuring these insect communities at both the landscape and regional scales, whereas host plant genotype seems of secondary importance.

Drought negatively affects communities on a foundation tree: growth rings predict diversity

Understanding how communities respond to extreme climatic events is important for predicting the impact of climate change on biodiversity. The plant vigor and stress hypotheses provide a theoretical framework for understanding how arthropods respond to stress, but are rarely tested at the community level. Following a record drought, we compared the communities of arthropods on pinyon pine (Pinus edulis) that exhibited a gradient in physical traits related to environmental stress (e.g., growth rate, branch dieback, and needle retention). Six patterns emerged that show how one of the predicted outcomes of climate change in the southwestern USA (i.e., increased drought severity) alters the communities of a foundation tree species. In accordance with the plant vigor hypothesis, increasing tree stress was correlated with an eight to tenfold decline in arthropod species richness and abundance. Trees that were more similar in their level of stress had more similar arthropod communities. Both foliage quantity and quality contributed to arthropod community structure. Individual species and feeding groups differed in their responses to plant stress, but most were negatively affected. Arthropod richness (r(2) = 0.48) and abundance (r(2) = 0.48) on individual trees were positively correlated with the tree's radial growth during drought. This relationship suggests that tree ring analysis may be used as a predictor of arthropod diversity, which is similar to findings with ectomycorrhizal fungi. A contrast of our findings on arthropod abundance with published data on colonization by mutualistic fungi on the same trees demonstrates that at low stress these two communities respond differently, but at high stress both are negatively affected. These results suggest that the effect of extreme climatic events such as drought on foundation tree species are likely to decrease multi-trophic diversity and shift arthropod community composition, which in turn could cascade to affect other associated taxa.