A novel approach to understanding bird communities using informed diversity estimates at local and regional scales in northern California and southern Oregon

Assessment and preservation of biodiversity has been a central theme of conservation biology since the discipline's inception. However, when diversity estimates are based purely on measures of presence–absence, or even abundance, they do not directly assess in what way focal habitats support the life history needs of individual species making up biological communities. Here, we move beyond naïve measures of occurrence and introduce the concept of “informed diversity” indices which scale estimates of avian species richness and community assemblage by two critical phases of their life cycle: breeding and molt. We tested the validity of the “informed diversity” concept using bird capture data from multiple locations in northern California and southern Oregon to examine patterns of species richness among breeding, molting, and naïve (based solely on occurrence) bird communities at the landscape and local scales using linear regression, community similarity indices, and a Detrended Correspondence Analysis (DCA). At the landscape scale, we found a striking pattern of increased species richness for breeding, molting, and naïve bird communities further inland and at higher elevations throughout the study area. At the local scale, we found that some sites with species‐rich naïve communities were in fact species‐poor when informed by breeding status, indicating that naïve richness may mask more biologically meaningful patterns of diversity. We suggest that land managers use informed diversity estimates instead of naïve measures of diversity to identify ecologically valuable wildlife habitat.     

Experience matters: prior exposure to plant toxins enhances diversity of gut microbes in herbivores

For decades, ecologists have hypothesised that exposure to plant secondary compounds (PSCs) modifies herbivore‐associated microbial community composition. This notion has not been critically evaluated in wild mammalian herbivores on evolutionary timescales. We investigated responses of the microbial communities of two woodrat species (Neotoma bryanti and N. lepida). For each species, we compared experienced populations that independently converged to feed on the same toxic plant (creosote bush, Larrea tridentata) to naïve populations with no exposure to creosote toxins. The addition of dietary PSCs significantly altered gut microbial community structure, and the response was dependent on previous experience. Microbial diversity and relative abundances of several dominant phyla increased in experienced woodrats in response to PSCs; however, opposite effects were observed in naïve woodrats. These differential responses were convergent in experienced populations of both species. We hypothesise that adaptation of the foregut microbiota to creosote PSCs in experienced woodrats drives this differential response.     

Genetic variation for sensitivity to a thyme monoterpene in associated plant species

Recent studies have shown that plant allelochemicals can have profound effects on the performance of associated species, such that plants with a history of co-existence with “chemical neighbour” plants perform better in their presence compared to naïve plants. This has cast new light on the complexity of plant–plant interactions and plant communities and has led to debates on whether plant communities are more co-evolved than traditionally thought. In order to determine whether plants may indeed evolve in response to other plants’ allelochemicals it is crucial to determine the presence of genetic variation for performance under the influence of specific allelochemicals and show that natural selection indeed operates on this variation. We studied the effect of the monoterpene carvacrol—a dominant compound in the essential oil of Thymus pulegioides—on three associated plant species originating from sites where thyme is either present or absent. We found the presence of genetic variation in both naïve and experienced populations for performance under the influence of the allelochemical but the response varied among naïve and experienced plant. Plants from experienced populations performed better than naïve plants on carvacrol soil and contained significantly more seed families with an adaptive response to carvacrol than naïve populations. This suggests that the presence of T. pulegioides can act as a selective agent on associated species, by favouring genotypes which perform best in the presence of its allelochemicals. The response to the thyme allelochemical varied from negative to neutral to positive among the species. The different responses within a species suggest that plant–plant interactions can evolve; this has implications for community dynamics and stability.     

Genetic costructure in a meta‐community under threat of habitat fragmentation

Habitat fragmentation increasingly threatens the services provided by natural communities and ecosystem worldwide. An understanding of the eco‐evolutionary processes underlying fragmentation‐compromised communities in natural settings is lacking, yet critical to realistic and sustainable conservation. Through integrating the multivariate genetic, biotic and abiotic facets of a natural community module experiencing various degrees of habitat fragmentation, we provide unique insights into the processes underlying community functioning in real, natural conditions. The focal community module comprises a parasitic butterfly of conservation concern and its two obligatory host species, a plant and an ant. We show that both historical dispersal and ongoing habitat fragmentation shape population genetic diversity of the butterfly Phengaris alcon and its most limited host species (the plant Gentiana pneumonanthe). Genetic structure of each species was strongly driven by geographical structure, altitude and landscape connectivity. Strikingly, however, was the strong degree of genetic costructure among the three species that could not be explained by the spatial variables under study. This finding suggests that factors other than spatial configuration, including co‐evolutionary dynamics and shared dispersal pathways, cause parallel genetic structure among interacting species. While the exact contribution of co‐evolution and shared dispersal routes on the genetic variation within and among communities deserves further attention, our findings demonstrate a considerable degree of genetic parallelism in natural meta‐communities. The significant effect of landscape connectivity on the genetic diversity and structure of the butterfly also suggests that habitat fragmentation may threaten the functioning of the community module on the long run.     

How community adaptation affects biodiversity–ecosystem functioning relationships

Evidence is growing that evolutionary dynamics can impact biodiversity–ecosystem functioning (BEF) relationships. However the nature of such impacts remains poorly understood. Here we use a modelling approach to compare random communities, with no trait evolutionary fine‐tuning, and co‐adapted communities, where traits have co‐evolved, in terms of emerging biodiversity–productivity, biodiversity–stability and biodiversity–invasion relationships. Community adaptation impacted most BEF relationships, sometimes inverting the slope of the relationship compared to random communities. Biodiversity–productivity relationships were generally less positive among co‐adapted communities, with reduced contribution of sampling effects. The effect of community‐adaptation, though modest regarding invasion resistance, was striking regarding invasion tolerance: co‐adapted communities could remain very tolerant to invasions even at high diversity. BEF relationships are thus contingent on the history of ecosystems and their degree of community adaptation. Short‐term experiments and observations following recent changes may not be safely extrapolated into the future, once eco‐evolutionary feedbacks have taken place.     

Evidence for rapid evolutionary change in an invasive plant in response to biological control

We present evidence that populations of an invasive plant species that have become re‐associated with a specialist herbivore in the exotic range through biological control have rapidly evolved increased antiherbivore defences compared to populations not exposed to biocontrol. We grew half‐sib families of the invasive plant Lythrum salicaria sourced from 17 populations near Ottawa, Canada, that differed in their history of exposure to a biocontrol agent, the specialist beetle Neogalerucella calmariensis. In a glasshouse experiment, we manipulated larval and adult herbivory to examine whether a population's history of biocontrol influenced plant defence and growth. Plants sourced from populations with a history of biocontrol suffered lower defoliation than naïve, previously unexposed populations, strongly suggesting they had evolved higher resistance. Plants from biocontrol‐exposed populations were also larger and produced more branches in response to herbivory, regrew faster even in the absence of herbivory and were better at compensating for the impacts of herbivory on growth (i.e. they exhibited increased tolerance). Furthermore, resistance and tolerance were positively correlated among genotypes with a history of biocontrol but not among naïve genotypes. Our findings suggest that biocontrol can rapidly select for increased defences in an invasive plant and may favour a mixed defence strategy of resistance and tolerance without an obvious cost to plant vigour. Although rarely studied, such evolutionary responses in the target species have important implications for the long‐term efficacy of biocontrol programmes.     

Predator–prey naïveté, antipredator behavior,and the ecology of predator invasions

We present a framework for explaining variation in predator invasion success and predator impacts on native prey that integrates information about predator–prey naïveté, predator and prey behavioral responses to each other, consumptive and non‐consumptive effects of predators on prey, and interacting effects of multiple species interactions. We begin with the ‘naïve prey’ hypothesis that posits that naïve, native prey that lack evolutionary history with non‐native predators suffer heavy predation because they exhibit ineffective antipredator responses to novel predators. Not all naïve prey, however, show ineffective antipredator responses to novel predators. To explain variation in prey response to novel predators, we focus on the interaction between prey use of general versus specific cues and responses, and the functional similarity of non‐native and native predators. Effective antipredator responses reduce predation rates (reduce consumptive effects of predators, CEs), but often also carry costs that result in non‐consumptive effects (NCEs) of predators. We contrast expected CEs versus NCEs for non‐native versus native predators, and discuss how differences in the relative magnitudes of CEs and NCEs might influence invasion dynamics. Going beyond the effects of naïve prey, we discuss how the ‘naïve prey’, ‘enemy release’ and ‘evolution of increased competitive ability’ (EICA) hypotheses are inter‐related, and how the importance of all three might be mediated by prey and predator naïveté. These ideas hinge on the notion that non‐native predators enjoy a ‘novelty advantage’ associated with the naïveté of native prey and top predators. However, non‐native predators could instead suffer from a novelty disadvantage because they are also naïve to their new prey and potential predators. We hypothesize that patterns of community similarity and evolution might explain the variation in novelty advantage that can underlie variation in invasion outcomes. Finally, we discuss management implications of our framework, including suggestions for managing invasive predators, predator reintroductions and biological control.     

Ecosystem productivity is associated with bacterial phylogenetic distance in surface marine waters

Understanding the link between community diversity and ecosystem function is a fundamental aspect of ecology. Systematic losses in biodiversity are widely acknowledged but the impact this may exert on ecosystem functioning remains ambiguous. There is growing evidence of a positive relationship between species richness and ecosystem productivity for terrestrial macro‐organisms, but similar links for marine micro‐organisms, which help drive global climate, are unclear. Community manipulation experiments show both positive and negative relationships for microbes. These previous studies rely, however, on artificial communities and any links between the full diversity of active bacterial communities in the environment, their phylogenetic relatedness and ecosystem function remain hitherto unexplored. Here, we test the hypothesis that productivity is associated with diversity in the metabolically active fraction of microbial communities. We show in natural assemblages of active bacteria that communities containing more distantly related members were associated with higher bacterial production. The positive phylogenetic diversity–productivity relationship was independent of community diversity calculated as the Shannon index. From our long‐term (7‐year) survey of surface marine bacterial communities, we also found that similarly, productive communities had greater phylogenetic similarity to each other, further suggesting that the traits of active bacteria are an important predictor of ecosystem productivity. Our findings demonstrate that the evolutionary history of the active fraction of a microbial community is critical for understanding their role in ecosystem functioning.     

Transgenerational soil‐mediated differences between plants experienced or naïve to a grass invasion

Invasive species may undergo rapid change as they invade. Native species persisting in invaded areas may also experience rapid change over this short timescale relative to native populations in uninvaded areas. We investigated the response of the native Achillea millefolium to soil from Holcus lanatus‐invaded and uninvaded areas, and we sought to determine whether differential responses between A. millefolium from invaded (invader experienced) and uninvaded (invader naïve) areas were mediated by soil community changes. Plants grown from seed from experienced and naïve areas responded differently to invaded and uninvaded soil with respect to germination time, biomass, and height. Overall, experienced plants grew faster and taller than their naïve counterparts. Naïve native plants showed negative feedbacks with their home soil and positive feedbacks with invaded soil; experienced plants were less responsive to soil differences. Our results suggest that native plants naïve to invasion may be more sensitive to soil communities than experienced plants, consistent with recent studies. While differences between naïve and experienced plants are transgenerational, our design cannot differentiate between differences that are genetically based, plastic, or both. Regardless, our results highlight the importance of seed source and population history in restoration, emphasizing the restoration potential of experienced seed sources.     

Richness, structure and functioning in metazoan parasite communities

Ecosystem functioning, characterized by components such as productivity and stability, has been extensively linked with diversity in recent years, mainly in plant ecology. The aim of our study was thus to quantify general relationships between diversity, community structure and ecosystem functions in metazoan parasite communities. We used data on parasite communities from 15 species of marine fish hosts from coastal Chile. The volumetric abundance (volume of all parasite species per individual host, in mm³) was used as a surrogate for productivity. Species diversity was measured using both species richness and evenness, while community structure was estimated using the co‐occurrence indices V‐ratio, C‐score and a new C‐score_s index standardized for the number of host replicates. After correcting for fish size, 47% of host species show no relationship, 13% show a hump shaped curve and 40% show positive monotonic relationships between productivity and parasite richness across all host individuals in a sample. We obtained a logarithmically decreasing relationship between evenness and productivity for all fish species, and propose a ‘dominance‐resistance’ hypothesis based on immunity to explain this pattern. The stability of the parasite community, measured as the coefficient of variation in productivity among individual hosts, was strongly and positively related to mean species richness across the 15 host species. The C‐score_s index, based on the number of checkerboard units in the host‐parasite presence/absence matrix, increases linearly with mean productivity across the 15 host species, suggesting that parasite communities tend to be more structured when they are more productive. This is the likely reason why linear relationships between richness and productivity were not observed consistently in all fish species. Parasite communities provide some clear patterns for the diversity–ecosystem functioning debate in ecology, although other factors, such as the history of community assembly, may also influence these patterns.     

Responses of a native plant species from invaded and uninvaded areas to allelopathic effects of an invader

Invaders exert new selection pressures on the resident species, for example, through competition for resources or by using novel weapons. It has been shown that novel weapons aid invasion but it is unclear whether native species co‐occurring with invaders have adapted to tolerate these novel weapons. Those resident species which are able to adapt to new selective agents can co‐occur with an invader while others face a risk of local extinction. We ran a factorial common garden experiment to study whether a native plant species, Anthriscus sylvestris, has been able to evolve a greater tolerance to the allelochemicals exerted by the invader, Lupinus polyphyllus. Lupinus polyphyllus produces allelochemicals which potentially act as a novel, strong selective agent on A. sylvestris. We grew A. sylvestris seedlings collected from uninvaded (naïve) and invaded (experienced) sites growing alone and in competition with L. polyphyllus in pots filled with soil with and without activated carbon. Because activated carbon absorbs allelochemicals, its addition should improve especially naïve A. sylvestris performance in the presence of the invader. To distinguish the allelochemicals absorption and fertilizing effects of activated carbon, we grew plants also in a mixture of soil and fertilizer. A common garden experiment indicated that the performances of naïve and experienced A. sylvestris seedlings did not differ when grown with L. polyphyllus. The addition of activated carbon, which reduces interference by allelochemicals, did not induce differences in their performances although it had a positive effect on the aboveground biomass of A. sylvestris. Together, these results suggest that naïve and experienced A. sylvestris plants tolerated equally the invader L. polyphyllus and thus the tolerance has not occurred over the course of invasion.     

Dispersal and seed limitation affect diversity and productivity of montane grasslands

So far, seed limitation as a local process, and dispersal limitation as a regional process have been largely neglected in biodiversity–ecosystem functioning research. However, these processes can influence both local plant species diversity and ecosystem processes, such as biomass production. We added seeds of 60 species from the regional species pool to grassland communities at 20 montane grassland sites in Germany. In these sites, plant species diversity ranged from 10 to 34 species m⁻² and, before manipulation, diversity was not related to aboveground biomass, which ranged from 108 to 687 g m⁻². One year after seed addition, local plant species richness had increased on average by six species m⁻² (29%) compared with control plots, and this increase was highest in grasslands with intermediate productivity. The increased diversity after adding seeds was associated with an average increase of aboveground biomass of 36 g m⁻² (14.8%) compared with control plots. Thus, our results demonstrate that a positive relationship between changes in species richness and productivity, as previously reported from experimental plant communities, also holds for natural grassland ecosystems. Our results show that local plant communities are dispersal limited and a hump‐shaped model appears to be the limiting outline of the natural diversity–productivity relationship. Hence, the effects of dispersal on local diversity can substantially affect the functioning of natural ecosystems.     

Trait convergence and trait divergence in herbaceous plant communities: Mechanisms and consequences

In landscapes subject to intensive agriculture, both soil fertility and vegetation disturbance are capable of impacting strongly, evenly and simultaneously on the herbaceous plant cover and each tends to impose uniformity on the traits of constituent species. In more natural and ancient grasslands greater spatial and temporal variation in both productivity and disturbance occurs and both factors have been implicated in the maintenance of species‐richness in herbaceous communities. However, empirical data suggest that disturbance is the more potent driver of trait differentiation and species co‐existence at a local scale. This may arise from the great diversity in opportunities for establishment, growth or reproduction that arise when the intensity of competition is reduced by damage to the vegetation. In contrast to the diversifying effects of local disturbances, productivity‐related plant traits (growth rate, leaf longevity, leaf chemistry, leaf toughness, decomposition rate) appear to be less variable on a local scale. This difference in the effects of the productivity and disturbance filters arises from the relative constancy of productivity within the community and the diversity in agency and in spatial and temporal scales exhibited by disturbance events. Also, evolutionary responses to disturbances involve minor adaptive shifts in phenological and regenerative traits and are more likely to occur as micro‐evolutionary steps than the shifts in linked traits in the core physiology associated with the capacity to exploit productive and unproductive habitats. During the assembly of a community and over its subsequent lifespan filters with diversifying and convergent effects may operate simultaneously on recruitment from the local species pool and impose contrasted effects on the similarity of the trait values exhibited by co‐existing species. Moreover, as a consequence of the frequent association of productivity with the convergence filter, an additional difference is predicted in terms of the effects of the two filters on ecosystem functioning. Convergence in traits selected by the productivity filter will exert effects on both the plant community and the ecosystem while divergent effects of the disturbance filter will be restricted to the plant community.     

First Documentation of Cultural Transmission of Predator Recognition by Larval Amphibians

Predation is a pervasive selective agent shaping a prey's behaviour, morphology and life history. To survive, prey animals have to respond adaptively to predation threats and this can be achieved through learned predator recognition. Cultural transmission of predator recognition is likely a widespread means of learning in social animals, including mammals, birds and fishes. However, no studies have investigated the cultural transmission of predator recognition in amphibians. In our study, we examined whether naïve woodfrog (Rana sylvatica) tadpoles can acquire the recognition of the odour of a predatory tiger salamander (Ambystoma tigrinum) from experienced conspecifics. After conditioning some tutors to recognize salamander odour, we paired naïve observer tadpoles with either a salamander‐naïve or salamander‐experienced tutor and exposed the pairs to either salamander odour or a water control. Observers were subsequently tested alone for a response to salamander odour. We found that when given salamander odour, observer tadpoles that were paired with a salamander‐experienced tutor successfully learned to recognize the salamander odour as a threat, whereas the observers paired with salamander‐naïve tutors did not. Likewise, tadpoles exposed to the water control did not learn to recognize the salamander regardless of whether they were paired with a naïve or experienced tutor. This is the first study demonstrating cultural transmission of predator recognition in an amphibian species.     

Diversity of plant evolutionary lineages promotes arthropod diversity

Large‐scale habitat destruction and climate change result in the non‐random loss of evolutionary lineages, reducing the amount of evolutionary history represented in ecological communities. Yet, we have limited understanding of the consequences of evolutionary history on the structure of food webs and the services provided by biological communities. Drawing on 11 years of data from a long‐term plant diversity experiment, we show that evolutionary history of plant communities – measured as phylogenetic diversity – strongly predicts diversity and abundance of herbivorous and predatory arthropods. Effects of plant species richness on arthropods become stronger when phylogenetic diversity is high. Plant phylogenetic diversity explains predator and parasitoid richness as strongly as it does herbivore richness. Our findings indicate that accounting for evolutionary relationships is critical to understanding the severity of species loss for food webs and ecosystems, and for developing conservation and restoration policies.     

Host functional and phylogenetic composition rather than host diversity structure plant–herbivore networks

Declining plant diversity alters ecological networks, such as plant–herbivore interactions. However, our knowledge of the potential mechanisms underlying effects of plant species loss on plant–herbivore network structure is still limited. We used DNA barcoding to identify herbivore–host plant associations along declining levels of tree diversity in a large‐scale, subtropical biodiversity experiment. We tested for effects of tree species richness, host functional and phylogenetic diversity, and host functional (leaf trait) and phylogenetic composition on species, phylogenetic and network composition of herbivore communities. We found that phylogenetic host composition and related palatability/defence traits but not tree species richness significantly affected herbivore communities and interaction network complexity at both the species and community levels. Our study indicates that evolutionary dependencies and functional traits of host plants determine the composition of higher trophic levels and corresponding interaction networks in species‐rich ecosystems. Our findings highlight that characteristics of the species lost have effects on ecosystem structure and functioning across trophic levels that cannot be predicted from mere reductions in species richness.     

Does complementary resource use enhance ecosystem functioning? A model of light competition in plant communities

Recent experiments on grassland ecosystems have shown that biodiversity can enhance ecosystem processes such as plant biomass production. Functional complementarity is generally regarded as the main class of mechanisms generating these effects of biodiversity on ecosystem functioning. Although intuitively appealing and supported by some data, the complementarity hypothesis has been little explored theoretically using mechanistic approaches. Here, we present a simple dynamical model for a light-limited terrestrial ecosystem to assess the effects of species diversity on light competition and total biomass in plant communities. Our model shows that competitive relaxation (reduction in average light competition intensity) due to differences in foliar architecture among species enhances total plant biomass in mixtures, but that competitive imbalance (generated by the variance of the average light competition intensity experienced by different species) can either reinforce the effect of competitive relaxation or counteract it and contribute to reducing total plant biomass. Thus, complementary resource use is not enough to increase total plant biomass in species-rich communities; competitive balance among species also plays an important role. We propose an operational measure of light-use complementarity using empirical field data on light absorption to test the presence of complementarity in natural plant communities.     

Plant diversity and root traits benefit physical properties key to soil function in grasslands

Plant diversity loss impairs ecosystem functioning, including important effects on soil. Most studies that have explored plant diversity effects belowground, however, have largely focused on biological processes. As such, our understanding of how plant diversity impacts the soil physical environment remains limited, despite the fundamental role soil physical structure plays in ensuring soil function and ecosystem service provision. Here, in both a glasshouse and a long‐term field study, we show that high plant diversity in grassland systems increases soil aggregate stability, a vital structural property of soil, and that root traits play a major role in determining diversity effects. We also reveal that the presence of particular plant species within mixed communities affects an even wider range of soil physical processes, including hydrology and soil strength regimes. Our results indicate that alongside well‐documented effects on ecosystem functioning, plant diversity and root traits also benefit essential soil physical properties.     

Environmental and biotic drivers of soil microbial β‐diversity across spatial and phylogenetic scales

Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β‐diversity) along ecological gradients. Here, we characterize soil microbial β‐diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are shaped by abiotic processes and biotic interactions with plants. We characterized microbial and plant communities using DNA metabarcoding of soil samples distributed across and within eighteen plots along an elevation gradient in the French Alps. The recovered taxa were placed onto phylogenies to estimate microbial and plant β‐diversity at different phylogenetic grains (i.e. resolution). We then modeled microbial β‐diversities with respect to plant β‐diversities and environmental dissimilarities across plots (landscape scale) and with respect to plant β‐diversities and spatial distances within plots (plot scale). At the landscape scale, fungal and archaeal β‐diversities were mostly related to plant β‐diversity, while bacterial β‐diversities were mostly related to environmental dissimilarities. At the plot scale, we detected a modest covariation of bacterial and fungal β‐diversities with plant β‐diversity; as well as a distance–decay relationship that suggested the influence of ecological drift on microbial communities. In addition, the covariation between fungal and plant β‐diversity at the plot scale was highest at fine or intermediate phylogenetic grains hinting that biotic interactions between those clades depends on early‐evolved traits. Altogether, we show how multiple ecological processes determine soil microbial community assembly at different spatial scales and how the strength of these processes change among microbial clades. In addition, we emphasized the imprint of microbial and plant evolutionary history on today's microbial community structure.