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Because genes and phenotypes are embedded within individuals, and individuals within populations, interactions within one level of biological organization are inherently linked to interactors at others. Here, we expand the network paradigm to consider that nodes can be embedded within other nodes, and connections (edges) between nodes at one level of organization form "bridges" for connections between nodes embedded within them. Such hierarchically embedded networks highlight two central properties of biological systems: 1) processes occurring across multiple levels of organization shape connections among biological units at any given level of organization and 2) ecological effects occurring at a given level of organization can propagate up or down to additional levels. Explicitly considering the embedded structure of evolutionary and ecological networks can capture otherwise hidden feedbacks and generate new insights into key biological phenomena, ultimately promoting a broader understanding of interactions in evolutionary theory.

BackgroundRefugia are island-like habitats that are linked to long-term environmental stability and, as a result, high endemism. Conservation of refugia and endemism hotspots should be based on a deep ecological and evolutionary understanding of their functioning, which remains limited. Although functional traits can provide such insights, a corresponding, coherent framework is lacking.Proposed frameworkPlant communities in refugia and endemism hotspots should, due to long-term environmental stability, display unique functional characteristics linked to distinct phylogenetic patterns. Therefore, such communities should be characterized by a functional signature that exhibits: (1) distinct values and combinations of traits, (2) higher functional diversity and (3) a prevalence of similar traits belonging to more distantly related lineages inside, compared to outside, of endemism hotspots and refugia. While the limited functional trait data available from refugia and endemism hotspots do not allow these predictions to be tested rigorously, three potential applications of the functional signature in biogeography and conservation planning are highlighted. Firstly, it allows the functional characteristics of endemism hotspots and refugia to be identified. Secondly, the strength of the functional signature can be compared among these entities, and with the surrounding landscape, to provide an estimate of the capacity of endemism hotspots and refugia to buffer environmental changes. Finally, the pattern of the functional signature can reveal ecological and evolutionary processes driving community assembly and functioning, which can assist in predicting the effect of environmental changes (e.g. climate, land-use) on communities in endemism hotspots and refugia.ConclusionThe proposed functional signature concept allows the systematic integration of plant functional traits and phylogeny into the study of endemism hotspots and refugia, but more data on functional traits in these entities are urgently needed. Overcoming this limitation would facilitate rigorous testing of the proposed predictions for the functional signature, advancing the eco-evolutionary understanding of endemism hotspots and refugia.

• We released a python library (MetaIBM) for individual-based modelling on GitHub. • The MetaIBM is suitable for a wide range of scenarios in metacommunity ecology. • The library is optimised and is adapted to high-performance computing devices. • The library can simulate a community with up to millions of unique individuals. • Four modelling examples were demonstrated to guide potential users. Individual-based modelling (IBM) is a powerful tool for simulating complex biological communities. By defining a population as comprising individuals that differ from one another, IBM can simulate the assembly and organisation of complex communities under various eco-evolutionary processes in a large spatial scale, with tremendous variables or parameters considered simultaneously. IBM disentangles a complex system into various sub-systems interacting with each other, allowing us to develop a unified library with a modular design for a wide range of complex scenarios in community assembly. In such a library, a number of parameters-controlled processes can be primitively coded as the sub-systems (or sub-models). Here, we released a Python-coded library as a framework for Metacommunity Individual-based Modelling (MetaIBM). As an open-source library, the MetaIBM has several merits, including: (a) it can be used to simulate a wide range of ecological problems of metacommunities. The metacommunity landscape and its environment gradients can be designed flexibly by users. Users can selectively turn off or on and set up parameters-controlled ecological processes according to their needs. (b) It adopts optimised algorithms and adapts to the high-performance computing devices, so that the users can explore a wide range of parameters space synchronously within a reasonable time. (c) It can be used to simulate a group of communities with up to millions of unique individuals, which is an originally plain portrayal of natural communities. To guide potential users, we provided the source codes of the library and a user manual. In the present article, we gave four examples to demonstrate how to design and model a metacommunity using the MetaIBM, simulating the community assembly in an islands-mainland model under the metacommunity framework with (a) neutral assumptions, (b) niche assumptions, (c) slow evolution scenarios, (d) rapid evolution scenarios. The examples showed that the MetaIBM can efficiently fit the community assembly, and reveal several intrigued species diversity patterns under the interaction of evolutionary processes and dispersal processes at multiple scales. The MetaIBM will be continuously maintained and updated to provide more functions in the future. [ABSTRACT FROM AUTHOR]

Over the past few decades, it has become clear that ecological and evolutionary dynamics are influenced by processes operating across spatial and temporal scales. Processes that operate on small spatial scales have the potential to influence dynamics at much larger scales; for example, a change in the physiology of a primary producer can alter primary productivity in an ecosystem. Similarly, evolution—a process that historically was thought of as occurring at longer timescales—can influence ecological dynamics and vice versa. The importance of considering multiple scales is broadly true in ecology and evolution, and it is especially important for studies of disease ecology and evolution. Yet characterizing the scales at which individual studies operate is surprisingly challenging, as we (re)discovered while trying to characterize articles published in this journal over the past three decades. However, while it is difficult to determine where one scale ends and another begins, it is also clear that work that spans across a spectrum can yield insights that could not be gleaned from a narrower focus. To demonstrate this, we highlight studies previously published in this journal that show the value of working across scales. We then introduce the six articles that comprise this Focused Topic section. Together, these articles present systems, theory, and methods that provide important insights that could not have been obtained from studying a single scale in isolation. [ABSTRACT FROM AUTHOR]

• Feral wildlife are eclipsing native wildlife in biomass, restructuring contemporary ecosystems. • Political and biological asymmetries in feral species ensure their persistence in ecosystems. • Ideological opposition to basic feral wildlife research ignores socio-political realities. • Feral species offer unique and unparalleled opportunities to study eco-evolutionary processes. • Current approaches to research are insufficient to understand nor manage feral wildlife. The biomass of feral wildlife is eclipsing that of native wildlife in many parts of the world. Consequently, feral species are playing an increasingly important role in ecological community dynamics. Artificially selected life-history traits of wild but once domesticated species can elicit population dynamics that differ substantially from that of native species. Yet, we continue to lag in our understanding of the ecology and evolution of feral species with direct consequences to resource management and biodiversity conservation. In part, this is because basic and applied research into the ecology of feral wildlife is fraught with social and political challenges unique to science. Feral populations of companion animals or livestock, especially, can evoke strong emotional reactions among advocacy groups, particularly around issues of animal welfare and management policy. Managers tasked with controlling feral populations are often bound by social license, including legislative restrictions, incomparable to that of other wildlife, and harassment or litigation of researchers and managers is not uncommon. Further, research and management of feral species is often delegated to agricultural instead of wildlife government agencies with clear differences in mandate, staff education, and training. Using examples primarily from feral horses in North America, we show how scientists conducting research independent of the management process can find themselves placed between managers, advocates, and opponents of feral species, implicitly tasked with satisfying multiple and often contradictory interests of stakeholders, sometimes with direct and litigious interference. These barriers are exacerbated by inter-disciplinary tendencies to dismiss the importance of basic and applied ecological research into feral species, despite its relevance to sound decision-making. Feral species therefore possess politically and biologically facilitated asymmetries that favor persistence, growth, and expansion relative to native wildlife, while the timely study of these characteristics in nature continues to suffer from ideological opposition. [ABSTRACT FROM AUTHOR]

Species that have sex determined by environmental conditions during development (i.e., environmental sex determination [ESD]) are especially vulnerable to environmental change, including altered stress levels, habitat loss, and species translocations. These factors can produce multigenerational trends in population size and eco‐evolutionary dynamics not captured by existing theory based on lifetime reproductive success (R0). Here, we extend ESD theory to use per capita growth rate r as a more appropriate measure of evolutionary success (fitness), and we demonstrate the importance of this change when males and females can differ in maturation times and when maturation times vary with local conditions (plasticity). In these cases, we show that primary and secondary sex ratios may be strongly biased; that optimal maturation times, when locally plastic, depend on the balance between mortality and growth effects; and that plasticity of maturation times can ameliorate fitness costs of increasing environmental stress. [ABSTRACT FROM AUTHOR]

Many ecological and evolutionary processes are affected by urbanization, but cities vary by orders of magnitude in their human population size and areal extent. To quantify and manage urban biodiversity, one must understand both how biodiversity scales with city size, and how ecological, evolutionary, and socioeconomic drivers of biodiversity scale with city size. We show how environmental abiotic and biotic drivers, as well as human cultural and socioeconomic drivers, may act through ecological and evolutionary processes differently, at different scales, to influence patterns in urban biodiversity. Because relationships likely take linear and nonlinear forms, the need to describe the specific scaling relationships is highlighted, including deviations and potential inflection points, where different management strategies may successfully conserve urban biodiversity. Ecological and evolutionary (hereafter 'eco-evolutionary') processes are influenced by urbanization and therefore influence biodiversity in cities. Cities vary in population and geographic size by many orders of magnitude, and we therefore expect both eco-evolutionary and human cultural processes to scale nonlinearly with city size. It is not expected that all processes will scale similarly, and correlations among deviations in different attributes (e.g., waterfowl diversity and urban water use) can inform management. A mechanistic framework is developed, to study how scale influences biodiversity through eco-evolutionary and socioeconomic mechanisms, and how these relationships might guide biodiversity management in urban areas. [ABSTRACT FROM AUTHOR]

The study of insular systems has a long history in ecology and biogeography. Island plants often differ remarkably from their noninsular counterparts, constituting excellent models for exploring eco-evolutionary processes. Trait-based approaches can help to answer important questions in island biogeography, yet plant trait patterns on islands remain understudied. We discuss three key hypotheses linking functional ecology to island biogeography: (i) plants in insular systems are characterized by distinct functional trait syndromes (compared with noninsular environments); (ii) these syndromes differ between true islands and terrestrial habitat islands; and (iii) island characteristics influence trait syndromes in a predictable manner. We are convinced that implementing trait-based comparative approaches would considerably further our understanding of plant ecology and evolution in insular systems. Trait-based approaches may provide important insights into the dynamics of insular systems (i.e., true islands and terrestrial habitat islands) and can help to address key questions in island biogeography. However, the study of plant traits on islands is in its infancy and a robust framework tailored to island biogeography is lacking. Plants in insular systems, compared with the mainland, experience unique eco-evolutionary histories and are influenced by specific processes such as those related to isolation. These factors should be reflected in specific patterns of plant traits. [ABSTRACT FROM AUTHOR]

Microbial communities are not the easiest to manipulate experimentally in natural ecosystems. However, leaf litter-topmost layer of surface soil-is uniquely suitable to investigate the complexities of community assembly. Here, we reflect on over a decade of collaborative work to address this topic using leaf litter as a model system in Southern California ecosystems. By leveraging a number of methodological advantages of the system, we have worked to demonstrate how four processes-selection, dispersal, drift, and diversification-contribute to bacterial and fungal community assembly and ultimately impact community functioning. Although many dimensions remain to be investigated, our initial results demonstrate that both ecological and evolutionary processes occur simultaneously to influence microbial community assembly. We propose that the development of additional and experimentally tractable microbial systems will be enormously valuable to test the role of eco-evolutionary processes in natural settings and their implications in the face of rapid global change., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Predicting the ecological and evolutionary trajectories of populations in multispecies communities is one of the fundamental challenges in ecology. Many of these predictions are made by scaling patterns observed from pairwise interactions. Here, we show that the coupling of ecological and evolutionary outcomes is likely to be weaker in increasingly complex communities due to greater chance of life‐history trait correlations. Using model microbial communities comprising a focal bacterial species, Bacillus subtilis, a bacterial competitor, protist predator and phage parasite, we found that increasing the number of enemies in a community had an overall negative effect on B. subtilis population growth. However, only the competitor imposed direct selection for B. subtilis trait evolution in pairwise cultures and this effect was weakened in the presence of other antagonists that had a negative effect on the competitor. In contrast, adaptation to parasites was driven indirectly by correlated selection where competitors had a positive and predators a negative effect. For all measured traits, selection in pairwise communities was a poor predictor of B. subtilis evolution in more complex communities. Together, our results suggest that coupling of ecological and evolutionary outcomes is interaction‐specific and generally less evident in more complex communities where the increasing number of trait correlations could mask weak ecological signals. [ABSTRACT FROM AUTHOR]

Because of light constraints, it is expected that latitude exerts a strong influence on reciprocal exchange of resources between mycorrhizal plants and fungi, and this could have consequences on the responsiveness of plants to mycorrhizal fungi. To assess environmental filtering due to AM fungi with regards to latitude, we synthesized data from a common garden experiment on comparative mycorrhizal responsiveness of North American annual and perennial herbaceous plants (Wilson & Hartnett, [31]) with plant distribution data for the specific plants from USDA ([28]; Notes S3). When we analysed annual and perennial plants separately, we found a significant relationship only for perennials (Kendall tau was -0.32 - P = 0.004, whereas for annuals the Kendall tau was 0.03 - P = 0.87). Negative feedback within a mutualism: host-specific growth of mycorrhizal fungi reduces plant benefit. [Extracted from the article]

Marine natural products (NPs) represent an impressive source of novel bioactive molecules with major biotechnological applications. Nevertheless, the usual chemical and applied perspective leading most of bioprospecting projects come along with various limitations blurring our understanding of the extensive marine chemical diversity. Here, we propose several guidelines: (i) to optimize bioprospecting and (ii) to refine our knowledge on marine chemical ecology focusing on octocorals, one of the most promising sources of marine NPs. We identified a significant phylogenetic bias in the octocoral bioprospecting, which calls for the development of a concerted discovery strategy. Given the gap existing between the number of isolated NPs and the knowledge regarding their functions, we provide an ecologically centered workflow prioritizing biological function ahead of chemical identification. Furthermore, we illustrate how-omictechnologies should rapidly increase our knowledge on solving different aspects of the ecology and evolution of marine NPs. [ABSTRACT FROM PUBLISHER]

The expanding scale and increasing rate of marine biological invasions have been documented since the early 20th century. Besides their global ecological and economic impacts, nonindigenous species (NIS) also have attracted much attention as opportunities to explore important eco-evolutionary processes such as rapid adaptation, long-distance dispersal and range expansion, and secondary contacts between divergent evolutionary lineages. In this context, genetic tools have been extensively used in the past 20 years. Three important issues appear to have emerged from such studies. First, the study of NIS has revealed unexpected cryptic diversity in what had previously been assumed homogeneous entities. Second, there has been surprisingly little evidence of strong founder events accompanying marine introductions, a pattern possibly driven by large propagule loads. Third, the evolutionary processes leading to successful invasion have been difficult to ascertain due to faint genetic signals. Here we explore the potential of novel tools associated with high-throughput sequencing (HTS) to address these still pressing issues. Dramatic increase in the number of loci accessible via HTS has the potential to radically increase the power of analyses aimed at species delineation, exploring the population genomic consequences of range expansions, and examining evolutionary processes such as admixture, introgression, and adaptation. Nevertheless, the value of this new wealth of genomic data will ultimately depend on the ability to couple it with expanded "traditional" efforts, including exhaustive sampling of marine populations over large geographic scales, integrated taxonomic analyses, and population level exploration of quantitative trait differentiation through common-garden and other laboratory experiments. [ABSTRACT FROM AUTHOR]

I test for macroscale intraspecific variation of abundance, mortality, and regeneration of four eastern US tree species ( Tsuga canadensis, Betula lenta, Liriodendron tulipifera, and Quercus prinus) by splitting them into three climatic zones based on plant hardiness zones ( PHZs). The primary goals of the analysis are to assess the differences in environmental heterogeneity and demographic responses among climatic zones, map regional species groups based on decision tree rules, and evaluate univariate and multivariate patterns of species demography with respect to environmental variables. I use the Forest Inventory Analysis ( FIA) data to derive abundance, mortality, and regeneration indices and split the range into three climatic zones based on USDA PHZs: (1) cold adapted, leading region; (2) middle, well-adapted region; and (3) warm adapted, trailing region. I employ decision tree ensemble methods to assess the importance of environmental predictors on the abundance of the species between the cold and warm zones and map zonal variations in species groups. Multivariate regression trees are used to simultaneously explore abundance, mortality, and regeneration in tandem to assess species vulnerability. Analyses point to the relative importance of climate in the warm adapted, trailing zone (especially moisture) compared to the cold adapted, leading zone. Higher mortality and lower regeneration patterns in the warm trailing zone point to its vulnerability to growing season temperature and precipitation changes that could figure more prominently in the future. This study highlights the need to account for intraspecific variation of demography in order to understand environmental heterogeneity and differential adaptation. It provides a methodology for assessing the vulnerability of tree species by delineating climatic zones based on easily available PHZ data, and FIA derived abundance, mortality, and regeneration indices as a proxy for overall growth and fitness. Based on decision tree rules, ecologically meaningful variations in species abundance among the climatic zones can be related to environmental variability and mapped. [ABSTRACT FROM AUTHOR]