Indirect effects drive coevolution in mutualistic networks

Evolutionary emergence of plant and pollinator polymorphisms in consumer-resource mutualisms

Mutualism is considered a major driver of biodiversity, as it enables extensive codiversification in terrestrial communities. An important case is flowering plants and their pollinators, where convergent selection on plant and pollinator traits is combined with divergent selection to minimize niche overlap within each group. In this article, we study the emergence of polymorphisms in communities structured trophically: plants are the primary producers of resources required by the primary consumers, the servicing pollinators. We model natural selection on traits affecting mutualism between plants and pollinators and competition within these two trophic levels. We show that phenotypic diversification is favored by broad plant niches, suggesting that bottom-up trophic control leads to codiversification. Mutualistic generalism, i.e., tolerance to differences in plant and pollinator traits, promotes a cascade of evolutionary branching favored by bottom-up plant competition dependent on similarity and top-down mutualistic services that broaden plant niches. Our results predict a strong positive correlation between the diversity of plant and pollinator phenotypes, which previous work has partially attributed to the trophic dependence of pollinators on plants.

Macroevolution of the plant-hummingbird pollination system

Plant-hummingbird interactions are considered a classic example of coevolution, a process in which mutually dependent species influence each other's evolution. Plants depend on hummingbirds for pollination, whereas hummingbirds rely on nectar for food. As a step towards understanding coevolution, this review focuses on the macroevolutionary consequences of plant-hummingbird interactions, a relatively underexplored area in the current literature. We synthesize prior studies, illustrating the origins and dynamics of hummingbird pollination across different angiosperm clades previously pollinated by insects (mostly bees), bats, and passerine birds. In some cases, the crown age of hummingbirds pre-dates the plants they pollinate. In other cases, plant groups transitioned to hummingbird pollination early in the establishment of this bird group in the Americas, with the build-up of both diversities coinciding temporally, and hence suggesting co-diversification. Determining what triggers shifts to and away from hummingbird pollination remains a major open challenge. The impact of hummingbirds on plant diversification is complex, with many tropical plant lineages experiencing increased diversification after acquiring flowers that attract hummingbirds, and others experiencing no change or even a decrease in diversification rates. This mixed evidence suggests that other extrinsic or intrinsic factors, such as local climate and isolation, are important covariables driving the diversification of plants adapted to hummingbird pollination. To guide future studies, we discuss the mechanisms and contexts under which hummingbirds, as a clade and as individual species (e.g. traits, foraging behaviour, degree of specialization), could influence plant evolution. We conclude by commenting on how macroevolutionary signals of the mutualism could relate to coevolution, highlighting the unbalanced focus on the plant side of the interaction, and advocating for the use of species-level interaction data in macroevolutionary studies.

Reviving collapsed plant-pollinator networks from a single species

Mutualistic ecological networks can suddenly transition to undesirable states due to small changes in environmental conditions. Recovering from such a collapse can be difficult as restoring the original environmental conditions may be infeasible. Additionally, such networks can also exhibit a phenomenon known as hysteresis, whereby the system could exhibit multiple states under the same environmental conditions, implying that ecological networks may not recover. Here, we attempted to revive collapsed mutualistic networks to a high-functioning state from a single species, using concepts from signal propagation theory and an eco-evolutionary model based on network structures of 115 empirical plant-pollinator networks. We found that restoring the environmental conditions rarely aided in recovery of collapsed networks, but a positive relationship between recovering pollinator density and network nestedness emerged, which was qualitatively supported by empirical plant-pollinator restoration data. In contrast, network resurrection from a collapsed state in undesirable environmental conditions where restoration has minimal impacts could be readily achieved by perturbing a single species or a few species that control the response of the dynamical networks. Additionally, nestedness in networks and a moderate amount of trait variation could aid in the revival of networks even in undesirable environmental conditions. Our work suggests that focus should be applied to a few species whose dynamics could be steered to resurrect entire networks from a collapsed state and that network architecture could play a crucial role in reviving collapsed plant-pollinator networks.

Plant diversity drives positive microbial associations in the rhizosphere enhancing carbon use efficiency in agricultural soils

Expanding and intensifying agriculture has led to a loss of soil carbon. As agroecosystems cover over 40% of Earth's land surface, they must be part of the solution put in action to mitigate climate change. Development of efficient management practices to maximize soil carbon retention is currently limited, in part, by a poor understanding of how plants, which input carbon to soil, and microbes, which determine its fate there, interact. Here we implement a diversity gradient by intercropping undersown species with barley in a large field trial, ranging from one to eight undersown species. We find that increasing plant diversity strengthens positive associations within the rhizosphere soil microbial community in relation to negative associations. These associations, in turn, enhance community carbon use efficiency. Jointly, our results highlight how increasing plant diversity in agriculture can be used as a management strategy to enhance carbon retention potential in agricultural soils.

Collective intelligence facilitates emergent resource partitioning through frequency-dependent learning

Deciding where to forage must not only account for variations in habitat quality but also where others might forage. Recent studies have suggested that when individuals remember recent foraging outcomes, negative frequency-dependent learning can allow them to avoid resources exploited by others (indirect competition). This process can drive the emergence of consistent differences in resource use (resource partitioning) at the population level. However, indirect cues of competition can be difficult for individuals to sense. Here, we propose that information pooling through collective decision-making-i.e. collective intelligence-can allow populations of group-living animals to more effectively partition resources relative to populations of solitary animals. We test this hypothesis by simulating (i) individuals preferring to forage where they were recently successful and (ii) cohesive groups that choose one resource using a majority rule. While solitary animals can partially avoid indirect competition through negative frequency-dependent learning, resource partitioning is more likely to emerge in populations of group-living animals. Populations of larger groups also better partition resources than populations of smaller groups, especially in environments with more choices. Our results give insight into the value of long- versus short-term memory, home range sizes and the evolution of specialization, optimal group sizes and territoriality. This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.

Asynchronous Life Histories Generate Uneven Arms Races and Impact the Maintenance of Mutualisms

AbstractMutualisms constitute a diverse class of ecologically important interactions, yet their ecological and evolutionary stability remain topics of debate in coevolutionary theory. Recent theoretical and empirical work has suggested that coevolutionary arms races may be involved in the maintenance of mutualistic interactions, sustaining mutually beneficial outcomes for interacting species while producing exaggerated traits. Here we present an individual-based model that evaluates how asynchronous life histories-that is, partners with different average lifespans-change the dynamics of trait coevolution, the expected fitness outcomes for species involved, and the dynamics of selection differentials across time for each species. Results indicate that a longer-lived mutualist will consistently "lose" an otherwise balanced coevolutionary arms race, being outpaced in both the mean trait value and fitness outcome compared with a shorter-lived partner. Furthermore, linear selection differentials on mutualistic traits become increasingly divergent as life histories become increasingly asynchronous, with the longer-lived species experiencing persistent directional selection and the shorter-lived species experiencing weaker, more inconsistent selection. These results suggest that asynchronous life histories can complicate the maintenance of mutualistic interactions via coevolutionary arms races and that detecting coevolution via selection differentials may be difficult when life histories are sufficiently divergent.

The Hierarchical Coevolutionary Units of Ecological Networks

In ecological networks, cohesive groups of species may shape the evolution of interactions, serving as coevolutionary units. Ranging across network scales, from motifs to isolated components, elucidating which cohesive groups are more determinant for coevolution remains a challenge in ecology. We address this challenge by integrating 376 empirical mutualistic and antagonistic networks and coevolutionary models. We identified cohesive groups at four network scales containing a significant proportion of potential direct coevolutionary effects. Cohesive groups displayed hierarchical organisation, and potential coevolutionary effects overflowing lower-scale groups were contained by higher-scale groups, underscoring the hierarchy's impact. However, indirect coevolutionary effects blurred group boundaries and hierarchy, particularly under strong selection from ecological interactions. Thus, under strong selection, indirect effects render networks themselves, and not cohesive groups, as the likely coevolutionary units of ecological systems. We hypothesise hierarchical cohesive groups to also shape how other forms of direct and indirect effects propagate in ecological systems.

The coevolutionary consequences of biodiversity change

Coevolutionary selection is a powerful process shaping species interactions and biodiversity. Anthropogenic global environmental change is reshaping planetary biodiversity, including by altering the structure and intensity of interspecific interactions. However, remarkably little is understood of how coevolutionary selection is changing in the process. Here, we outline three interrelated pathways - change in evolutionary potential, change in community composition, and shifts in interaction trait distributions - that are expected to redirect coevolutionary selection under biodiversity change. Assessing how both ecological and evolutionary rules governing species interactions are disrupted under anthropogenic global change is of paramount importance to understand the past, present, and future of Earth's biodiversity.

Coevolutionary hotspots favour dispersal and fuel biodiversity in mutualistic landscapes under environmental changes

Mutualistic interactions are key to sustaining Earth's biodiversity. Yet, we are only beginning to understand how coevolution in mutualistic assemblages can shape the distribution and persistence of species across landscapes. Here, we combine the geographic mosaic theory of coevolution with metacommunity dynamics to understand how geographically structured selection can shape patterns of richness, dispersal, extinction and persistence of mutualistic species. In this model, species may experience strong or weak reciprocal selection imposed by mutualisms within each patch (i.e. hotspots and coldspots, respectively). Using numerical simulations, we show that mutualistic coevolution leads to a concentration of species richness at hotspots. Such an effect occurs because hotspots sustain higher rates of colonization and lower rates of extinction than coldspots, whether the environment changes or not. Importantly, under environmental changes, coldspots fail to sustain a positive colonization-to-extinction balance. Rather, species persistence within coldspots relies on hotspots acting as biodiversity sources and enhancing population dispersal across the landscape. In fact, even a few hotspots in the landscape can fuel the spatial network of dispersal of populations in the metacommunity. Our study highlights that coevolutionary hotspots can act as biodiversity sources, favouring colonization and allowing species to expand their distribution across landscapes even in changing environments. This article is part of the theme issue 'Diversity-dependence of dispersal: interspecific interactions determine spatial dynamics'.

Unraveling emergent network indeterminacy in complex ecosystems: A random matrix approach

Indeterminacy of ecological networks-the unpredictability of ecosystem responses to persistent perturbations-is an emergent property of indirect effects a species has on another through interaction chains. Thus, numerous indirect pathways in large, complex ecological communities could make forecasting the long-term outcomes of environmental changes challenging. However, a comprehensive understanding of ecological structures causing indeterminacy has not yet been reached. Here, using random matrix theory (RMT), we provide mathematical criteria determining whether network indeterminacy emerges across various ecological communities. Our analytical and simulation results show that indeterminacy intricately depends on the characteristics of species interaction. Specifically, contrary to conventional wisdom, network indeterminacy is unlikely to emerge in large competitive and mutualistic communities, while it is a common feature in top-down regulated food webs. Furthermore, we found that predictable and unpredictable perturbations can coexist in the same community and that indeterminate responses to environmental changes arise more frequently in networks where predator-prey relationships predominate than competitive and mutualistic ones. These findings highlight the importance of elucidating direct species relationships and analyzing them with an RMT perspective on two fronts: It aids in 1) determining whether the network's responses to environmental changes are ultimately indeterminate and 2) identifying the types of perturbations causing less predictable outcomes in a complex ecosystem. In addition, our framework should apply to the inverse problem of network identification, i.e., determining whether observed responses to sustained perturbations can reconstruct their proximate causalities, potentially impacting other fields such as microbial and medical sciences.

Connections between soil microbes, land use and European climate: Insights for management practices

Soil microbial biomass and activity strongly depend on land use, vegetation cover, climate, and soil physicochemical properties. In most cases, this dependence was assessed by one-to-one correlations while by employing network analysis, information about network robustness and the balance between stochasticity and determinism controlling connectivity, was revealed. In this study, we further elaborated on the hypothesis of Smith et al. (2021) that cropland soils depended more on climate variables and therefore are more vulnerable to climate change. We used the same dataset with that of Smith et al. (2021) that contains seasonal microbial, climate and soil variables collected from 881 soil points representing the main land uses in Europe: forests, grassland, cropland. We examined complete (both direct and indirect relationships) and incomplete networks (only direct relationships) and recorded higher robustness in the former. Partial Least Square results showed that on average more than 45% of microbial attributes' variability was predicted by climate and habitat drivers denoting medium to strong effect of habitat filtering. Network architecture slightly affected by season or land use type; it followed the core/periphery structure with positive and negative interactions and no hub nodes. Microbial attributes (biomass, activity and their ratio) mostly belong to core block together with Soil Organic Carbon (SOC), while climate and soil variables to periphery block with the exception of cropland networks, denoting the higher dependence between microbial and climate variables in these latter. All complete networks appeared robust except for cropland and forest in summer, a finding that disagrees with our initial hypothesis about cropland. Networks' connectivity was controlled stronger by stochasticity in forest than in croplands. The lack of human interventions in forest soils increase habitat homogeneity enhancing the influence of stochastic agents such as microbial unlimited dispersal and/or stochastic extinction. The increased stochasticity implies the necessity for proactive management actions.

Thermal performance of ecosystems: Modeling how physiological responses to temperature scale up in communities

Understanding how ecosystems respond to their environmental temperature is a major challenge. Thermodynamic constraints on species' metabolic rates are expected to affect ecosystem characteristics, but species interactions and interspecific variation in physiological thermal response curves (TRC) may obscure ecosystem-level responses to temperature. As a result, macroecological patterns related to temperature are still poorly understood. We investigate how physiological TRC scale up to ecosystem-level thermal responses by modifying the Tangled Nature (TaNa) model, a stochastic network model of ecology and evolution. We include new parameterizations that make reproduction, death, and mutation temperature-dependent. We find that ecosystem survival probability depends on how the minimum fitness required for species survival varies with temperature. The thermal response of ecosystem survival probability is the only ecosystem property that is sensitive to interspecific variation in TRC. Species richness scales up directly from the TRC of mutation rate, and average species population sizes are inversely related to mutation rate, with Species Abundance Distributions (SADs) exhibiting more rare species in warmer temperatures. Interactions between species are also inversely related to mutation, with positive interactions occurring more frequently in colder temperatures. The abundance of surviving ecosystems is not sensitive to temperature. This work helps clarify the specific relationships between physiological responses to temperature and ecosystem-level repercussions when species are interacting and adapting to their thermal environments.

Costs of being a diet generalist for the protist predator Dictyostelium discoideum

Consumers range from specialists that feed on few resources to generalists that feed on many. Generalism has the clear advantage of having more resources to exploit, but the costs that limit generalism are less clear. We explore two understudied costs of generalism in a generalist amoeba predator, Dictyostelium discoideum, feeding on naturally co-occurring bacterial prey. Both involve costs of combining prey that are suitable on their own. First, amoebas exhibit a reduction in growth rate when they switched to one species of prey bacteria from another compared to controls that experience only the second prey. The effect was consistent across all six tested species of bacteria. These switching costs typically disappear within a day, indicating adjustment to new prey bacteria. This suggests that these costs are physiological. Second, amoebas usually grow more slowly on mixtures of prey bacteria compared to the expectation based on their growth on single prey. There were clear mixing costs in three of the six tested prey mixtures, and none showed significant mixing benefits. These results support the idea that, although amoebas can consume a variety of prey, they must use partially different methods and thus must pay costs to handle multiple prey, either sequentially or simultaneously.

Evolutionary plant-pollinator responses to anthropogenic land-use change: impacts on ecosystem services

Agricultural intensification at field and landscape scales, including increased use of agrochemicals and loss of semi-natural habitats, is a major driver of insect declines and other community changes. Efforts to understand and mitigate these effects have traditionally focused on ecological responses. At the same time, adaptations to pesticide use and habitat fragmentation in both insects and flowering plants show the potential for rapid evolution. Yet we lack an understanding of how such evolutionary responses may propagate within and between trophic levels with ensuing consequences for conservation of species and ecological functions in agroecosystems. Here, we review the literature on the consequences of agricultural intensification on plant and animal evolutionary responses and interactions. We present a novel conceptualization of evolutionary change induced by agricultural intensification at field and landscape scales and emphasize direct and indirect effects of rapid evolution on ecosystem services. We exemplify by focusing on economically and ecologically important interactions between plants and pollinators. We showcase available eco-evolutionary theory and plant-pollinator modelling that can improve predictions of how agricultural intensification affects interaction networks, and highlight available genetic and trait-focused methodological approaches. Specifically, we focus on how spatial genetic structure affects the probability of propagated responses, and how the structure of interaction networks modulates effects of evolutionary change in individual species. Thereby, we highlight how combined trait-based eco-evolutionary modelling, functionally explicit quantitative genetics, and genomic analyses may shed light on conditions where evolutionary responses impact important ecosystem services.

Imprints of indirect interactions on a resource-mediated ant-plant network across different levels of network organization

Indirect interactions are pivotal in the evolution of interacting species and the assembly of populations and communities. Nevertheless, despite recently being investigated in plant-animal mutualism at the community level, indirect interactions have not been studied in resource-mediated mutualisms involving plant individuals that share different animal species as partners within a population (i.e., individual-based networks). Here, we analyzed an individual-based ant-plant network to evaluate how resource properties affect indirect interaction patterns and how changes in indirect links leave imprints in the network across multiple levels of network organization. Using complementary analytical approaches, we described the patterns of indirect interactions at the micro-, meso-, and macro-scale. We predicted that plants offering intermediate levels of nectar quantity and quality interact with more diverse ant assemblages. The increased number of ant species would cause a higher potential for indirect interactions in all scales evaluated. We found that nectar properties modified patterns of indirect interactions of plant individuals that share mutualistic partners, leaving imprints across different network scales. To our knowledge, this is the first study tracking indirect interactions in multiple scales within an individual-based network. We show that functional traits of interacting species, such as nectar properties, may lead to changes in indirect interactions, which could be tracked across different levels of the network organization evaluated.

Mutualisms drive plant trait evolution beyond interaction-related traits

Mutualisms have driven the evolution of extraordinary structures and behavioural traits, but their impact on traits beyond those directly involved in the interaction remains unclear. We addressed this gap using a highly evolutionarily replicated system - epiphytes in the Rubiaceae forming symbioses with ants. We employed models that allow us to test the influence of discrete mutualistic traits on continuous non-mutualistic traits. Our findings are consistent with mutualism shaping the pace of morphological evolution, strength of selection and long-term mean of non-mutualistic traits in function of mutualistic dependency. While specialised and obligate mutualisms are associated with slower trait change, less intimate, facultative and generalist mutualistic interactions - which are the most common - have a greater impact on non-mutualistic trait evolution. These results challenge the prevailing notion that mutualisms solely affect the evolution of interaction-related traits via stabilizing selection and instead demonstrate a broader role for mutualisms in shaping trait evolution.

Coexistence mechanism of ecological specialists and generalists based on a network dimension reduction method

As an ecological strategy for species coexistence, some species adapt to a wide range of habitats, while others specialize in particular environments. Such 'generalists' and 'specialists' achieve normal ecological balance through a complex network of interactions between species. However, the role of these interactions in maintaining the coexistence of generalist and specialist species has not been elucidated within a general theoretical framework. Here, we analyze the ecological mechanism for the coexistence of specialist and generalist species in a class of mutualistic and competitive interaction ecosystems based on the network dimension reduction method. We find that ecological specialists and generalists can be identified based on the number of their respective interactions. We also find, using real-world empirical network simulations, that the removal of ecological generalists can lead to the collapse of local ecosystems, which is rarely observed with the loss of ecological specialists.

Geography, phylogeny and host switch drive the coevolution of parasitic Gyrodactylus flatworms and their hosts

BACKGROUND

Gyrodactylus is a lineage of monogenean flatworm ectoparasites exhibiting many features that make them a suitable model to study the host-parasite coevolutionary dynamics. Previous coevolutionary studies of this lineage mainly relied on low-power datasets (a small number of samples and a single molecular marker) and (now) outdated algorithms.

METHODS

To investigate the coevolutionary relationship of gyrodactylids and their fish hosts in high resolution, we used complete mitogenomes (including two newly sequenced Gyrodactylus species), a large number of species in the single-gene dataset, and four different coevolutionary algorithms.

RESULTS

The overall coevolutionary fit between the parasites and hosts was consistently significant. Multiple indicators confirmed that gyrodactylids are generally highly host-specific parasites, but several species could parasitize either multiple (more than 5) or phylogenetically distant fish hosts. The molecular dating results indicated that gyrodactylids tend to evolve towards high host specificity. Speciation by host switch was identified as a more important speciation mode than co-speciation. Assuming that the ancestral host belonged to Cypriniformes, we inferred four major host switch events to non-Cypriniformes hosts (mostly Salmoniformes), all of which occurred deep in the evolutionary history. Despite their relative rarity, these events had strong macroevolutionary consequences for gyrodactylid diversity. For example, in our dataset, 57.28% of all studied gyrodactylids parasitized only non-Cypriniformes hosts, which implies that the evolutionary history of more than half of all included lineages could be traced back to these major host switch events. The geographical co-occurrence of fishes and gyrodactylids determined the host use by these gyrodactylids, and geography accounted for most of the phylogenetic signal in host use.

CONCLUSIONS

Our findings suggest that the coevolution of Gyrodactylus flatworms and their hosts is largely driven by geography, phylogeny, and host switches.

The Role of Indirect Effects in Coevolution along the Mutualism-Antagonism Continuum

AbstractThe web of interactions in a community drives the coevolution of species. Yet it is unclear how the outcome of species interactions influences the coevolutionary dynamics of communities. This is a pressing matter, as changes to the outcome of interactions may become more common with human-induced global change. Here, we combine network and evolutionary theory to explore coevolutionary outcomes in communities harboring mutualistic and antagonistic interactions. We show that as the ratio of mutualistic to antagonistic interactions decreases, selection imposed by direct partners outweighs that imposed by indirect partners. This weakening of indirect effects results in communities composed of species with dissimilar traits and fast rates of adaptation. These changes are more pronounced when specialist consumers are the first species to engage in antagonistic interactions. Hence, a shift in the outcome of species interactions may reverberate across communities and alter the direction and speed of coevolution.

Microeukaryotic plankton evolutionary constraints in a subtropical river explained by environment and bacteria along differing taxonomic resolutions

Microeukaryotic plankton communities are keystone components for keeping aquatic primary productivity. Currently, variations in microeukaryotic plankton diversity have often been explained by local ecological factors but not by evolutionary constraints. We used amplicon sequencing of 100 water samples across five years to investigate the ecological preferences of the microeukaryotic plankton community in a subtropical riverine ecosystem. We found that microeukaryotic plankton diversity was less associated with bacterial abundance (16S rRNA gene copy number) than bacterial diversity. Further, environmental effects exhibited a larger influence on microeukaryotic plankton community composition than bacterial community composition, especially at fine taxonomic levels. The evolutionary constraints of microeukaryotic plankton community increased with decreasing taxonomic resolution (from 97% to 91% similarity levels), but not significant change from 85% to 70% similarity levels. However, compared with the bacterial community, the evolutionary constraints were shown to be more affected by environmental variables. This study illustrated possible controlling environmental and bacterial drivers of microeukaryotic diversity and community assembly in a subtropical river, thereby indirectly reflecting on the quality status of the water environment by providing new clues on the microeukaryotic community assembly.

Rate-induced tipping in complex high-dimensional ecological networks

In an ecosystem, environmental changes as a result of natural and human processes can cause some key parameters of the system to change with time. Depending on how fast such a parameter changes, a tipping point can occur. Existing works on rate-induced tipping, or R-tipping, offered a theoretical way to study this phenomenon but from a local dynamical point of view, revealing, e.g., the existence of a critical rate for some specific initial condition above which a tipping point will occur. As ecosystems are subject to constant disturbances and can drift away from their equilibrium point, it is necessary to study R-tipping from a global perspective in terms of the initial conditions in the entire relevant phase space region. In particular, we introduce the notion of the probability of R-tipping defined for initial conditions taken from the whole relevant phase space. Using a number of real-world, complex mutualistic networks as a paradigm, we find a scaling law between this probability and the rate of parameter change and provide a geometric theory to explain the law. The real-world implication is that even a slow parameter change can lead to a system collapse with catastrophic consequences. In fact, to mitigate the environmental changes by merely slowing down the parameter drift may not always be effective: Only when the rate of parameter change is reduced to practically zero would the tipping be avoided. Our global dynamics approach offers a more complete and physically meaningful way to understand the important phenomenon of R-tipping.

Rapid bacteria-phage coevolution drives the emergence of multiscale networks

Interactions between species catalyze the evolution of multiscale ecological networks, including both nested and modular elements that regulate the function of diverse communities. One common assumption is that such complex pattern formation requires spatial isolation or long evolutionary timescales. We show that multiscale network structure can evolve rapidly under simple ecological conditions without spatial structure. In just 21 days of laboratory coevolution, Escherichia coli and bacteriophage Φ21 coevolve and diversify to form elaborate cross-infection networks. By measuring ~10,000 phage-bacteria infections and testing the genetic basis of interactions, we identify the mechanisms that create each component of the multiscale pattern. Our results demonstrate how multiscale networks evolve in parasite-host systems, illustrating Darwin's idea that simple adaptive processes can generate entangled banks of ecological interactions.

Nectar robbing by bees affects the reproductive fitness of the distylous plant Tirpitzia sinensis (Linaceae)

Nectar robbing can affect plant reproductive success directly by influencing female and male fitness, and indirectly by affecting pollinator behavior. Flowers have morphological and chemical features that may protect them from nectar robbers. Previous studies on nectar robbing have focused mainly on homotypic plants. It remains unclear how nectar robbing affects the reproductive success of distylous plants, and whether defense strategies of two morphs are different. Nectar-robbing rates on the long- and short-styled morph (L-morph, S-morph) of the distylous Tirpitzia sinensis were investigated. We compared floral traits, the temporal pattern of change in nectar volume and sugar concentration, nectar secondary metabolites, and sugar composition between robbed and unrobbed flowers of two morphs. We tested direct effects of nectar robbing on female and male components of plant fitness and indirect effects of nectar robbing via pollinators. Nectar-robbing rates did not differ between the two morphs. Flowers with smaller sepals and petals were more easily robbed. The floral tube diameter and thickness were greater in L-morphs than in S-morphs, and the nectar rob holes were significantly smaller in L-morphs than in S-morphs. Nectar robbing significantly decreased nectar replenishment rate but did not affect nectar sugar concentration or sugar composition. After robbery, the quantities and diversity of secondary compounds in the nectar of S-morphs increased significantly and total relative contents of secondary compounds in L-morphs showed no obvious changes. Nectar robbing could decrease female fitness by decreasing pollen germination rate and thus decreasing seed set. Nectar robbing had no significant effects on male fitness. Robbed flowers were less likely to be visited by hawkmoth pollinators, especially in S-morphs. These results suggest that nectar robbing could directly and indirectly decrease the female fitness of T. sinensis, and different morphs have evolved different defense mechanisms in response to nectar-robbing pressure.

The role of intra-guild indirect interactions in assembling plant-pollinator networks

Understanding the assembly of plant-pollinator communities has become critical to their conservation given the rise of species invasions, extirpations, and species' range shifts. Over the course of assembly, colonizer establishment produces core interaction patterns, called motifs, which shape the trajectory of assembling network structure. Dynamic assembly models can advance our understanding of this process by linking the transient dynamics of colonizer establishment to long-term network development. In this study, we investigate the role of intra-guild indirect interactions and adaptive foraging in shaping the structure of assembling plant-pollinator networks by developing: 1) an assembly model that includes population dynamics and adaptive foraging, and 2) a motif analysis tracking the intra-guild indirect interactions of colonizing species throughout their establishment. We find that while colonizers leverage indirect competition for shared mutualistic resources to establish, adaptive foraging maintains the persistence of inferior competitors. This produces core motifs in which specialist and generalist species coexist on shared mutualistic resources which leads to the emergence of nested networks. Further, the persistence of specialists develops richer and less connected networks which is consistent with empirical data. Our work contributes new understanding and methods to study the effects of species' intra-guild indirect interactions on community assembly.

More Than the Sum of Its Parts: Unlocking the Power of Network Structure for Understanding Organization and Function in Microbiomes

Plant and soil microbiomes are integral to the health and productivity of plants and ecosystems, yet researchers struggle to identify microbiome characteristics important for providing beneficial outcomes. Network analysis offers a shift in analytical framework beyond "who is present" to the organization or patterns of coexistence between microbes within the microbiome. Because microbial phenotypes are often significantly impacted by coexisting populations, patterns of coexistence within microbiomes are likely to be especially important in predicting functional outcomes. Here, we provide an overview of the how and why of network analysis in microbiome research, highlighting the ways in which network analyses have provided novel insights into microbiome organization and functional capacities, the diverse network roles of different microbial populations, and the eco-evolutionary dynamics of plant and soil microbiomes.

Conspicuous coloration of toxin-resistant predators implicates additional trophic interactions in a predator-prey arms race

Antagonistic coevolution between natural enemies can produce highly exaggerated traits, such as prey toxins and predator resistance. This reciprocal process of adaptation and counter-adaptation may also open doors to other evolutionary novelties not directly involved in the phenotypic interface of coevolution. We tested the hypothesis that predator-prey coevolution coincided with the evolution of conspicuous coloration on resistant predators that retain prey toxins. In western North America, common garter snakes (Thamnophis sirtalis) have evolved extreme resistance to tetrodotoxin (TTX) in the coevolutionary arms race with their deadly prey, Pacific newts (Taricha spp.). TTX-resistant snakes can retain large amounts of ingested TTX, which could serve as a deterrent against the snakes' own predators if TTX toxicity and resistance are coupled with a conspicuous warning signal. We evaluated whether arms race escalation covaries with bright red coloration in snake populations across the geographic mosaic of coevolution. Snake colour variation departs from the neutral expectations of population genetic structure and covaries with escalating clines of newt TTX and snake resistance at two coevolutionary hotspots. In the Pacific Northwest, bright red coloration fits an expected pattern of an aposematic warning to avian predators: TTX-resistant snakes that consume highly toxic newts also have relatively large, reddish-orange dorsal blotches. Snake coloration also seems to have evolved with the arms race in California, but overall patterns are less intuitively consistent with aposematism. These results suggest that interactions with additional trophic levels can generate novel traits as a cascading consequence of arms race coevolution across the geographic mosaic.

Evidence for hunter-gatherer impacts on raven diet and ecology in the Gravettian of Southern Moravia

The earlier Gravettian of Southern Moravia-the Pavlovian-is notable for the many raven bones (Corvus corax) documented in its faunal assemblages. On the basis of the rich zooarchaeological and settlement data from the Pavlovian, previous work suggested that common ravens were attracted by human domestic activities and subsequently captured by Pavlovian people, presumably for feathers and perhaps food. Here, we report independent δ15N, δ13C and δ34S stable isotope data obtained from 12 adult ravens from the Pavlovian key sites of Předmostí I, Pavlov I and Dolní Věstonice I to test this idea. We show that Pavlovian ravens regularly fed on larger herbivores and especially mammoths, aligning in feeding preferences with contemporaneous Gravettian foragers. We argue that opportunistic-generalist ravens were encouraged by human settlement and carcass provisioning. Our data may thus provide surprisingly early evidence for incipient synanthropism among Palaeolithic ravens. We suggest that anthropogenic manipulation of carrion supply dynamics furnished unique contexts for the emergence of human-oriented animal behaviours, in turn promoting novel human foraging opportunities-dynamics which are therefore important for understanding early hunter-gatherer ecosystem impacts.

Indirect effects shape species fitness in coevolved mutualistic networks

Ecological interactions are one of the main forces that sustain Earth's biodiversity. A major challenge for studies of ecology and evolution is to determine how these interactions affect the fitness of species when we expand from studying isolated, pairwise interactions to include networks of interacting species^1-4. In networks, chains of effects caused by a range of species have an indirect effect on other species they do not interact with directly, potentially affecting the fitness outcomes of a variety of ecological interactions (such as mutualism)^5-7. Here we apply analytical techniques and numerical simulations to 186 empirical mutualistic networks and show how both direct and indirect effects alter the fitness of species coevolving in these networks. Although the fitness of species usually increased with the number of mutualistic partners, most of the fitness variation across species was driven by indirect effects. We found that these indirect effects prevent coevolving species from adapting to their mutualistic partners and to other sources of selection pressure in the environment, thereby decreasing their fitness. Such decreases are distributed in a predictable way within networks: peripheral species receive more indirect effects and experience higher reductions in fitness than central species. This topological effect was also evident when we analysed an empirical study of an invasion of pollination networks by honeybees. As honeybees became integrated as a central species within networks, they increased the contribution of indirect effects on several other species, reducing their fitness. Our study shows how and why indirect effects can govern the adaptive landscape of species-rich mutualistic assemblages.

Modularity in host-parasite mixed networks: interaction configuration shifts based on human perturbation and parasitism form

Parasitism is an association based on host individual traits and environmental factors. The complexity of this type of interaction is often lost when studying species-by-species interaction networks. Here we analyze changes in modularity - a metric describing groups of nodes interacting much more frequently among themselves than they do with nodes of other modules, considering the host individual variation and the different forms of parasitism: ecto- and endo-parasitism. For this, we studied mixed networks: bipartite networks comprising host individuals and parasite species as two sets of nodes interacting with each other. We used a fish-parasite mixed network from a highly perturbed coastal river to understand how an anthropogenic perturbation gradient influences the modular structure of host-parasite networks. In addition, we tested how host individual traits drove module configuration within host-parasite mixed networks. Our results showed that different forms of parasitism respond differently to the environment: modularity in fish-ectoparasite networks increased with human perturbation, but modularity was not related to human perturbation in fish-endoparasite networks. In addition, mixed network modules were intrinsically related to individual variation, with host intensity of infection being the most important trait, regardless of the parasite's life form. The effect of total abundance over network structure indicates signs of changes in community equilibrium, with an increase in species with opportunistic behaviors. Module composition was also related to host fitness and body size, which were most predictive in more preserved and diverse river sections. Overall, our results indicate that host-parasite networks are sensitive to ecological gradients marked by human perturbation and that host individual fitness helps to determine network structure.

High Andean Steppes of Southern Chile Contain Little-Explored Peltigera Lichen Symbionts

Peltigera lichens can colonize extreme habitats, such as high-elevation ecosystems, but their biodiversity is still largely unknown in these environments, especially in the southern hemi- sphere. We assessed the genetic diversity of mycobionts and cyanobionts of 60 Peltigera lichens collected in three high Andean steppes of southern Chile using LSU, β-tubulin, COR3 and ITS loci for mycobionts, and SSU and rbcLX loci for cyanobionts. We obtained 240 sequences for the different mycobiont markers and 118 for the cyanobiont markers, including the first report of β-tubulin sequences of P. patagonica through modifying a previously designed primer. Phylogenetic analyses, ITS scrutiny and variability of haplotypes were used to compare the sequences with those previously reported. We found seven mycobiont species and eleven cyanobiont haplotypes, including considerable novel symbionts. This was reflected by ~30% of mycobionts and ~20% of cyanobionts haplotypes that yielded less than 99% BLASTn sequence identity, 15 new sequences of the ITS1-HR, and a putative new Peltigera species associated with 3 Nostoc haplotypes not previously reported. Our results suggest that high Andean steppe ecosystems are habitats of unknown or little-explored lichen species and thus valuable environments to enhance our understanding of global Peltigera biodiversity.

Mutualistic interactions shape global spatial congruence and climatic niche evolution in Neotropical mimetic butterflies

Understanding the mechanisms underlying species distributions and coexistence is both a priority and a challenge for biodiversity hotspots such as the Neotropics. Here, we highlight that Müllerian mimicry, where defended prey species display similar warning signals, is key to the maintenance of biodiversity in the c. 400 species of the Neotropical butterfly tribe Ithomiini (Nymphalidae: Danainae). We show that mimicry drives large-scale spatial association among phenotypically similar species, providing new empirical evidence for the validity of Müller's model at a macroecological scale. Additionally, we show that mimetic interactions drive the evolutionary convergence of species climatic niche, thereby strengthening the co-occurrence of co-mimetic species. This study provides new insights into the importance of mutualistic interactions in shaping both niche evolution and species assemblages at large spatial scales. Critically, in the context of climate change, our results highlight the vulnerability to extinction cascades of such adaptively assembled communities tied by positive interactions.

The non-random assembly of network motifs in plant-pollinator networks

Ecological processes leave distinct structural imprints on the species interactions that shape the topology of animal-plant mutualistic networks. Detecting how direct and indirect interactions between animals and plants are organised is not trivial since they go beyond pairwise interactions, but may get blurred when considering global network descriptors. Recent work has shown that the meso-scale, the intermediate level of network complexity between the species and the global network, can capture this important information. The meso-scale describes network subgraphs representing patterns of direct and indirect interactions between a small number of species, and when these network subgraphs differ statistically from a benchmark, they are often referred to as 'network motifs'. Although motifs can capture relevant ecological information of species interactions, they remain overlooked in natural plant-pollinator networks. By exploring 60 empirical plant-pollinator networks from 18 different studies with wide geographical coverage, we show that some network subgraphs are consistently under- or over-represented, suggesting the presence of worldwide network motifs in plant-pollinator networks. In addition, we found a higher proportion of densely connected network subgraphs that, based on previous findings, could reflect that species relative abundances are the main driver shaping the structure of the meso-scale on plant-pollinator communities. Moreover, we found that distinct subgraph positions describing species ecological roles (e.g. generalisation and number of indirect interactions) are occupied by different groups of animal and plant species representing their main life-history strategies (i.e. functional groups). For instance, we found that the functional group of 'bees' was over-represented in subgraph positions with a lower number of indirect interactions in contrast to the rest of floral visitors groups. Finally, we show that the observed functional group combinations within a subgraph cannot be retrieved from their expected probabilities (i.e. joint probability distributions), indicating that plant and floral visitor associations within subgraphs are not random either. Our results highlight the presence of common network motifs in plant-pollinator communities that are formed by a non-random association of plants and floral visitors functional groups.

Different influences of phylogenetically conserved and independent floral traits on plant functional specialization and pollination network structure

Plant specialization and pollination network structure play important roles in community assembly. Floral traits can mediate plant-pollinator interactions and thus have important impacts on nestedness and modularity of pollination network. When such traits are phylogenetically conserved, therefore, phylogeny and traits should predict network structure to similar degrees. Moreover, conserved network structures were also found attributed to pollination syndrome or pollination system. However, we still know little about the relation between pollination syndrome and pollination network, especially under a phylogenetic framework. Herein, we established a phylogenetic framework including five floral traits (flower density, floral size, floral shape, floral symmetry, and floral color) and five species-level metrics (species strength, weighted closeness, specialization d', nestedness contribution, and modularity contribution) to test how floral traits could directly or indirectly influence species' specialization and network structure in central China. Phylogenetic signals were found in all floral traits except flower density. Structural equation model and phylogenetic structural equation model results showed that both floral size and floral density affected plant specialization and its contribution to network modularity indirectly. However, compared with phylogenetic independent flower density, phylogenetic conserved floral size had much more complexed influences, having a direct influence both on species' specialization and on modularity contribution. In this nested and modular network, abundant species with larger flowers tend to be more central and had larger values of z. Floral shape, symmetry, and color could act as co-flowering filters in pollination sharing and help to shape network modularity. Our results emphasize that phylogenetically conserved traits partially represent pollination syndrome and are important drivers for modular structure of local pollination network. This study may improve the understanding how the evolutionary history and ecological process drive local network structure and dynamics.

Mutualistic coevolution and community diversity favour persistence in metacommunities under environmental changes

Linking local to regional ecological and evolutionary processes is key to understand the response of Earth's biodiversity to environmental changes. Here we integrate evolution and mutualistic coevolution in a model of metacommunity dynamics and use numerical simulations to understand how coevolution can shape species distribution and persistence in landscapes varying in space and time. Our simulations show that coevolution and species richness can synergistically shape distribution patterns by increasing colonization and reducing extinction of populations in metacommunities. Although conflicting selective pressures emerging from mutualisms may increase mismatches with the local environment and the rate of local extinctions, coevolution increases trait matching among mutualists at the landscape scale, counteracting local maladaptation and favouring colonization and range expansions. Our results show that by facilitating colonization, coevolution can also buffer the effects of environmental changes, preventing species extinctions and the collapse of metacommunities. Our findings reveal the mechanisms whereby coevolution can favour persistence under environmental changes and highlight that these positive effects are greater in more diverse systems that retain landscape connectivity.

Genetic architecture of multiple mutualisms and mating system in Turnera ulmifolia

Plants often associate with multiple arthropod mutualists. These partners provide important services to their hosts, but multiple interactions can constrain a plant's ability to respond to complex, multivariate selection. Here, we quantified patterns of genetic variance and covariance among rewards for pollination, biotic defence and seed dispersal mutualisms in multiple populations of Turnera ulmifolia to better understand how the genetic architecture of multiple mutualisms might influence their evolution. We phenotyped plants cultivated from 17 Jamaican populations for several mutualism and mating system-related traits. We then fit genetic variance-covariance (G) matrices for the island metapopulation and the five largest individual populations. At the metapopulation level, we observed significant positive genetic correlations among stigma-anther separation, floral nectar production and extrafloral nectar production. These correlations have the potential to significantly constrain or facilitate the evolution of multiple mutualisms in T. ulmifolia and suggest that pollination, seed dispersal and defence mutualisms do not evolve independently. In particular, we found that positive genetic correlations between floral and extrafloral nectar production may help explain their stable coexistence in the face of physiological trade-offs and negative interactions between pollinators and ant bodyguards. Locally, we found only small differences in G among our T. ulmifolia populations, suggesting that geographic variation in G may not shape the evolution of multiple mutualisms.

Limited predictability of body length in a fish population

Recent theoretical studies have identified chaotic dynamics in eco-evolutionary models. Yet, empirical evidence for eco-evolutionary chaos in natural ecosystems is lacking. In this study, we combine analyses of empirical data and an eco-evolutionary model to uncover chaotic dynamics of body length in a fish population (northeast Arctic cod: Gadus morhua). Consistent with chaotic attractors, the largest Lyapunov exponent (LE) of empirical data is positive, and approximately matches the LE of the model calculation, thus suggesting the potential for chaotic dynamics in this fish population. We also find that the autocorrelation function (ACF) of both empirical data and eco-evolutionary model shows a similar lag of approximately 7 years. Our combined analyses of natural time series and mathematical models suggest that chaotic dynamics of a phenotypic trait may be driven by trait evolution. This finding supports a growing theory that eco-evolutionary feedbacks can produce chaotic dynamics.

Effects of habitat destruction on coevolving metacommunities

Habitat destruction is a growing threat to biodiversity and ecosystem services. The ecological consequences of habitat loss and fragmentation involve reductions in species abundance and even the extinction of species and their interactions. However, we do not yet understand how habitat loss alters the coevolutionary trajectories of the remaining species or how coevolution, in turn, affects their response to habitat loss. To investigate this, we develop a spatially explicit model which couples metacommunity and coevolutionary dynamics. We show that, by changing the size, composition and structure of local networks, habitat destruction increases the diversity of coevolutionary trajectories of mutualists across the landscape. Conversely, in antagonistic communities, some species increase while others reduce their spatial trait heterogeneity. Furthermore, we show that while coevolution dampens the negative effects of habitat destruction in mutualistic networks, its effects on the persistence of antagonistic communities tend to be smaller and less predictable.

The fundamental benefits of multiplexity in ecological networks

A tipping point presents perhaps the single most significant threat to an ecological system as it can lead to abrupt species extinction on a massive scale. Climate changes leading to the species decay parameter drifts can drive various ecological systems towards a tipping point. We investigate the tipping-point dynamics in multi-layer ecological networks supported by mutualism. We unveil a natural mechanism by which the occurrence of tipping points can be delayed by multiplexity that broadly describes the diversity of the species abundances, the complexity of the interspecific relationships, and the topology of linkages in ecological networks. For a double-layer system of pollinators and plants, coupling between the network layers occurs when there is dispersal of pollinator species. Multiplexity emerges as the dispersing species establish their presence in the destination layer and have a simultaneous presence in both. We demonstrate that the new mutualistic links induced by the dispersing species with the residence species have fundamental benefits to the well-being of the ecosystem in delaying the tipping point and facilitating species recovery. Articulating and implementing control mechanisms to induce multiplexity can thus help sustain certain types of ecosystems that are in danger of extinction as the result of environmental changes.

The Synergy of Patterns vs. Processes at Community Level: A Key Linkage for Subtropical Native Forests along the Urban Riparian Zone

Riparian zones possesses unique ecological position with biota differing from aquatic body and terrestrial lands, and plant–animal coevolution through a propagule-dispersal process may be the main factor for the framework of riparian vegetation was proposed. In the current study, the riparian forests and avifauna along with three subtropical mountainous riparian belts of Chongqing, China, were investigated, and multivariate analysis technique was adopted to examine the associations among the plants’ and birds’ species. The results show that: (1) the forest species’ composition and vertical layers are dominated by native catkins of Moraceae species, which have the reproductive traits with small and numerous propagules facilitating by frugivorous bird species, revealing an evolutionary trend different from the one in the terrestrial plant climax communities in the subtropical evergreen broad-leaved forests. The traits may provide a biological base for the plant–bird coevolution; (2) there are significant associations of plant–bird species clusters, i.e., four plant–bird coevolution groups (PBs) were divided out according to the plant species’ dominance and growth form relating to the fruit-dispersing birds’ abundance; (3) the correlation intensity within a PB ranks as PB I > II > IV > III, indicating the PB I is the leading type of coevolution mainly shaped by the dominant plant species of Moraceae; (4) the PB correlation may be a key node between patterns vs. process of a riparian ecosystem responsible for the riparian native vegetation, or even the ecosystem health. Our results contribute understanding the plant–animal coevolution interpreting the forests’ structures in riparian environments. The results may also be used by urban planner and managers to simulate the patterns for restoring a more stable riparian biota, a better functioning ecosystem in subtropical zone.

The overlooked complexity of avian brood parasite-host relationships

The relationships between avian brood parasites and their hosts are widely recognised as model systems for studying coevolution. However, while most brood parasites are known to parasitise multiple species of host and hosts are often subject to parasitism by multiple brood parasite species, the examination of multispecies interactions remains rare. Here, we compile data on all known brood parasite-host relationships and find that complex brood parasite-host systems, where multiple species of brood parasites and hosts coexist and interact, are globally commonplace. By examining patterns of past research, we outline the disparity between patterns of network complexity and past research emphases and discuss factors that may be associated with these patterns. Drawing on insights gained from other systems that have embraced a multispecies framework, we highlight the potential benefits of considering brood parasite-host interactions as ecological networks and brood parasitism as a model system for studying multispecies interactions. Overall, our results provide new insights into the diversity of these relationships, highlight the stark mismatch between past research efforts and global patterns of network complexity, and draw attention to the opportunities that more complex arrangements offer for examining how species interactions shape global patterns of biodiversity.

Forest degradation limits the complementarity and quality of animal seed dispersal

Forest degradation changes the structural heterogeneity of forests and species communities, with potential consequences for ecosystem functions including seed dispersal by frugivorous animals. While the quantity of seed dispersal may be robust towards forest degradation, changes in the effectiveness of seed dispersal through qualitative changes are poorly understood. Here, we carried out extensive field sampling on the structure of forest microhabitats, seed deposition sites and plant recruitment along three characteristics of forest microhabitats (canopy cover, ground vegetation and deadwood) in Europe's last lowland primeval forest (Białowieża, Poland). We then applied niche modelling to study forest degradation effects on multi-dimensional seed deposition by frugivores and recruitment of fleshy-fruited plants. Forest degradation was shown to (i) reduce the niche volume of forest microhabitat characteristics by half, (ii) homogenize the spatial seed deposition within and among frugivore species, and (iii) limit the regeneration of plants via changes in seed deposition and recruitment. Our study shows that the loss of frugivores in degraded forests is accompanied by a reduction in the complementarity and quality of seed dispersal by remaining frugivores. By contrast, structure-rich habitats, such as old-growth forests, safeguard the diversity of species interactions, forming the basis for high-quality ecosystem functions.

Global structural stability and the role of cooperation in mutualistic systems

Dynamical systems on graphs allow to describe multiple phenomena from different areas of Science. In particular, many complex systems in Ecology are studied by this approach. In this paper we analize the mathematical framework for the study of the structural stability of each stationary point, feasible or not, introducing a generalization for this concept, defined as Global Structural Stability. This approach would fit with the proper mathematical concept of structural stability, in which we find a full description of the complex dynamics on the phase space due to nonlinear dynamics. This fact can be analyzed as an informational field grounded in a global attractor whose structure can be completely characterized. These attractors are stable under perturbation and suppose the minimal structurally stable sets. We also study in detail, mathematically and computationally, the zones characterizing different levels of biodiversity in bipartite graphs describing mutualistic antagonistic systems of population dynamics. In particular, we investigate the dependence of the region of maximal biodiversity of a system on its connectivity matrix. On the other hand, as the network topology does not completely determine the robustness of the dynamics of a complex network, we study the correlation between structural stability and several graph measures. A systematic study on synthetic and biological graphs is presented, including 10 mutualistic networks of plants and seed-dispersal and 1000 random synthetic networks. We compare the role of centrality measures and modularity, concluding the importance of just cooperation strength among nodes when describing areas of maximal biodiversity. Indeed, we show that cooperation parameters are the central role for biodiversity while other measures act as secondary supporting functions.

Phylogenetic structure of specialization: A new approach that integrates partner availability and phylogenetic diversity to quantify biotic specialization in ecological networks

Biotic specialization holds information about the assembly, evolution, and stability of biological communities. Partner availabilities can play an important role in enabling species interactions, where uneven partner availabilities can bias estimates of biotic specialization when using phylogenetic diversity indices. It is therefore important to account for partner availability when characterizing biotic specialization using phylogenies. We developed an index, phylogenetic structure of specialization (PSS), that avoids bias from uneven partner availabilities by uncoupling the null models for interaction frequency and phylogenetic distance. We incorporate the deviation between observed and random interaction frequencies as weights into the calculation of partner phylogenetic α‐diversity. To calculate the PSS index, we then compare observed partner phylogenetic α‐diversity to a null distribution generated by randomizing phylogenetic distances among the same number of partners. PSS quantifies the phylogenetic structure (i.e., clustered, overdispersed, or random) of the partners of a focal species. We show with simulations that the PSS index is not correlated with network properties, which allows comparisons across multiple systems. We also implemented PSS on empirical networks of host–parasite, avian seed‐dispersal, lichenized fungi–cyanobacteria, and hummingbird pollination interactions. Across these systems, a large proportion of taxa interact with phylogenetically random partners according to PSS, sometimes to a larger extent than detected with an existing method that does not account for partner availability. We also found that many taxa interact with phylogenetically clustered partners, while taxa with overdispersed partners were rare. We argue that species with phylogenetically overdispersed partners have often been misinterpreted as generalists when they should be considered specialists. Our results highlight the important role of randomness in shaping interaction networks, even in highly intimate symbioses, and provide a much‐needed quantitative framework to assess the role that evolutionary history and symbiotic specialization play in shaping patterns of biodiversity. PSS is available as an R package at https://github.com/cjpardodelahoz/pss.