Phenotypic variation in urban environments: mechanisms and implications

Developmental bias as a cause and consequence of adaptive radiation and divergence

Efforts to reconcile development and evolution have demonstrated that development is biased, with phenotypic variation being more readily produced in certain directions. However, how this "developmental bias" can influence micro- and macroevolution is poorly understood. In this review, we demonstrate that defining features of adaptive radiations suggest a role for developmental bias in driving adaptive divergence. These features are i) common ancestry of developmental systems; ii) rapid evolution along evolutionary "lines of least resistance;" iii) the subsequent repeated and parallel evolution of ecotypes; and iv) evolutionary change "led" by biased phenotypic plasticity upon exposure to novel environments. Drawing on empirical and theoretical data, we highlight the reciprocal relationship between development and selection as a key driver of evolutionary change, with development biasing what variation is exposed to selection, and selection acting to mold these biases to align with the adaptive landscape. Our central thesis is that developmental biases are both the causes and consequences of adaptive radiation and divergence. We argue throughout that incorporating development and developmental bias into our thinking can help to explain the exaggerated rate and scale of evolutionary processes that characterize adaptive radiations, and that this can be best achieved by using an eco-evo-devo framework incorporating evolutionary biology, development, and ecology. Such a research program would demonstrate that development is not merely a force that imposes constraints on evolution, but rather directs and is directed by evolutionary forces. We round out this review by highlighting key gaps in our understanding and suggest further research programs that can help to resolve these issues.

Extra-pair paternity in two passerine birds breeding in a gradient of urbanisation

Urbanisation has been increasing worldwide in recent decades, driving environmental change and exerting novel selective pressures on wildlife. Phenotypic differences between urban and rural individuals have been widely documented in several taxa. However, the extent to which urbanisation impacts mating strategies is less known. Here, we investigated extra-pair paternity variation in great tits (Parus major) and blue tits (Cyanistes caeruleus) breeding in nestboxes set in a gradient of urbanisation in Warsaw, Poland, over three breeding seasons. Urbanisation was quantified as the amount of light pollution, noise pollution, impervious surface area (ISA) and tree cover within a 100-m radius around each nestbox. We obtained genotypes for 1213 great tits at 7344 SNP markers and for 1299 blue tits at 9366 SNP markers with a genotyping-by-sequencing method, and inferred extra-pair paternity by computing a genomewide relatedness matrix. We report higher extra-pair paternity in blue tits breeding in more urbanised areas, for example, with higher light pollution and ISA, and lower tree cover. However, no such trend was found in great tits. Late-stage survival of individual nestlings in both species was not associated with paternity or urbanisation proxies, thus we were not able to detect fitness benefits or drawbacks of being an extra-pair offspring in relation to urbanisation. Our results contribute to the growing body of knowledge reporting on the effects of urbanisation on avian ecology and behaviour, and confirm species-specific and population-specific patterns of extra-pair paternity variation.

Urbanization alters the relative importance of local and landscape factors affecting plant communities in the Tokyo megacity

Plant communities are impacted by local factors (related to environmental filtering) and landscape factors (related to dispersal limitation). While many studies have shown that the relative importance of these factors in understanding plant community dynamics due to urbanization, little is known about how they are altered by urbanization-a significant threat to biodiversity. This study evaluates the relative importance of local environmental (local factors), landscape, and spatial (landscape factors) variables that influence plant communities in 34 urban green spaces comprising two different habitats (forests and grasslands) along the urban-rural gradients in the Tokyo megacity, Japan. To continuously assess the relative importance of each factor along the urban-rural gradients, we extracted 1000 landscapes within a certain range that contained several sites. Subsequently, the relative importance of each factor and urbanization rate (proportion of artificial built-up area) were estimated for each landscape. Our study found that the relative importance of both local and landscape factors decreased, while that of local factor for native species in forest habitats and that of landscape factors for native species in grassland habitats increased. Collectively, these findings suggest that city size and habitat characteristics must be considered when predicting changes in plant communities caused by urbanization.

Morpho-physiological traits and tissue burdens of Ecklonia radiata linked to environmental variation in an urban estuary

Organisms respond to their environment in various ways, including moving, adapting, acclimatising or a combination of responses. Within estuarine habitats, organisms are exposed to naturally variable environmental conditions. In urbanised estuaries, these natural variations can interact with human stressors such as habitat modification and pollution. Here, we investigated trait variation in the golden kelp Ecklonia radiata across an urban estuary - Sydney Harbour, Australia. We found that kelp morphology differed significantly between the more human-modified inner and the less modified outer harbour. Kelp individuals were smaller, had fewer laminae, and lacked spines in the inner harbour where it was warmer, more contaminated and less light was available. Inner harbour populations were characterised by lower tissue nitrogen and higher lead concentrations. These findings provide insights into how environmental variation could affect kelp morphology and physiology, and the high trait variation suggests adaptive capacity in E. radiata.

Blood transcriptome analysis of common kestrel nestlings living in urban and non-urban environments

Urbanisation is one of the main anthropogenic forms of land cover affecting an ever-increasing number of wild animals and their habitats. Physiological plasticity represents an important process through which animals can adjust to the novel conditions of anthropogenic environments. Relying on the analysis of gene expression, it is possible to identify the molecular responses to the habitat conditions and infer possible environmental factors that affect the organismal physiology. We have quantified for the first time the blood transcriptome of common kestrel (Falco tinnunculus) nestlings living in urban sites and compared it to the transcriptome of kestrel nestlings inhabiting rural and natural environments. We found mild differences in the expression of genes among sites, indicating adaptability or acclimation of the birds to the urban habitat. We identified 58 differentially expressed genes between urban and natural kestrels, and 12 differentially expressed genes between urban and rural kestrels. The most striking differences among sites involved inflammatory-immunological, metabolic, apoptosis, DNA repair and development genes. In particular, we found that (i) urban kestrel nestlings had higher expression of genes linked to inflammation, repair of DNA damage, or apoptosis than natural kestrel nestlings, and (ii) natural and rural kestrel nestlings had higher expression of genes linked to the development and activation of immune cells, type I interferon response, or major histocompatibility complex than urban kestrel nestlings. Finally, the KEGG enrichment analysis identified the insulin signalling as the main pathway that differed between natural and urban kestrel nestlings. This is one of a limited number of studies on vertebrates that revealed habitat-associated differences in the transcriptome. It paves the way for further in-depth studies on the links between physiological variation and habitat structure at different spatial and temporal scales.

Free-ranging dogs match a human's preference in a foraging task

Social learning is a mechanism used by many species to efficiently gain information about their environment. Although many animals live in an environment where members of other species are present, little is known about interspecific social learning. Domesticated and urbanized species provide the opportunity to investigate whether nonhuman animals can learn from heterospecifics such as humans, who are integral parts of their social landscape. Although domestic dogs Canis familiaris have been intensively researched for their ability to learn from humans, most studies have focused on dogs living as pets. However, free-ranging dogs represent the majority of the world's dog population, they live alongside humans, scavenge on human refuse, and are subject to natural and sexual selection. Thus, free-ranging dogs with extensive exposure to humans and their artifacts provide the opportunity to investigate interspecific social learning in a naturalistic setting, where learning from humans might be a benefit for them. Here we tested individual free-ranging dogs in a between-subject design: Dogs in the control group could spontaneously choose between two novel and differently patterned food-delivering boxes. In the experimental group, instead, dogs could first observe an unfamiliar human approaching and eating from 1 of the 2 boxes. We provide the first evidence that free-ranging dogs match the choice of an unfamiliar human. These results show that at least simple forms of interspecific social learning might be involved in dogs' success in living alongside humans in a complex urbanized environment.

Exploring the potential effects of forest urbanization on the interplay between small mammal communities and their gut microbiota

Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid changes. These differential adaptative abilities could be mediated by the microbiome, which may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under anthropic perturbations, the microbiota of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness. The links between the impact of urbanization on host communities and their gut microbiota (GM) have only been scarcely explored. In this study, we tested the hypothesis that the bacterial composition of the GM could play a role in host adaptation to urban environments. We described the GM of several species of small terrestrial mammals sampled in forested areas along a gradient of urbanization, using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM, considering the presence and abundance of bacterial taxa and their putative functions. This enabled to decipher the processes underlying these changes. We found potential impacts of urbanization on small mammal communities and their GM. The urban dweller species had a lower bacterial taxonomic diversity but a higher functional diversity and a different composition compared to urban adapter species. Their GM assembly was mostly governed by stochastic effects, potentially indicating dysbiosis. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite dysbiosis. In urban adapter species, the GM functional diversity and composition remained relatively stable along the urbanization gradient. This observation can be explained by functional redundancy, where certain taxa express the same function. This could favor the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedbacks between the gut microbiota and host species within communities, enabling rapid adaptation.

Clinical data mining: challenges, opportunities, and recommendations for translational applications

Clinical data mining of predictive models offers significant advantages for re-evaluating and leveraging large amounts of complex clinical real-world data and experimental comparison data for tasks such as risk stratification, diagnosis, classification, and survival prediction. However, its translational application is still limited. One challenge is that the proposed clinical requirements and data mining are not synchronized. Additionally, the exotic predictions of data mining are difficult to apply directly in local medical institutions. Hence, it is necessary to incisively review the translational application of clinical data mining, providing an analytical workflow for developing and validating prediction models to ensure the scientific validity of analytic workflows in response to clinical questions. This review systematically revisits the purpose, process, and principles of clinical data mining and discusses the key causes contributing to the detachment from practice and the misuse of model verification in developing predictive models for research. Based on this, we propose a niche-targeting framework of four principles: Clinical Contextual, Subgroup-Oriented, Confounder- and False Positive-Controlled (CSCF), to provide guidance for clinical data mining prior to the model's development in clinical settings. Eventually, it is hoped that this review can help guide future research and develop personalized predictive models to achieve the goal of discovering subgroups with varied remedial benefits or risks and ensuring that precision medicine can deliver its full potential.

Habitat diversification associated with urban development has a little effect on genetic structure in the annual native plant Commelina communis in an East Asian megacity

Urban development greatly alters the natural and semi-natural habitats of native plants. Urbanisation results in a range of diverse habitats including remnant agricultural lands, urban parks, and roadside habitats. This habitat diversity often promotes trait divergence within urban areas. However, the mechanisms by which diverse urban habitats influence the population genetic structure of individual plant species remain poorly understood. We investigated the effects of urbanisation on genetic diversity and structure within 24 Commelina communis populations across diverse habitat types (rural agricultural land, urban agricultural land, urban park land, and urban roadsides) within the Kyoto-Osaka-Kobe megacity in Japan. We conducted multiplexed inter-simple sequence repeat genotyping to compare genetic diversity among populations in different habitats. We also examined the correlation between Nei's genetic distance and geographic and environmental distances and performed principal coordinate analysis (PCoA) to evaluate genetic differentiation among urban habitats. There were no significant differences in genetic diversity indices between urban and rural populations and among urban habitat types. Although we detected no isolation-by-distance structure in population pairs of the same habitat type and in those of different habitats, the difference in surrounding landscape facilitated genetic differentiation not only between urban and rural habitats but also between different urban habitats. PCoA revealed no clear genetic differentiation among rural and urban habitat populations. Our findings indicate that the establishment of diverse habitat types through urbanisation has no and little impact on genetic diversity and structure, respectively, in C. communis, likely due to its high selfing rate and ability to adapt to urban conditions.

Trait variation along an urban-rural gradient in Asian dayflower: the contribution of phenotypic plasticity and genetic divergence

Environmental changes associated with urbanisation can exert pressure that facilitates both adaptations and plastic responses in plants. Field surveys or common garden experiments (CGE) alone cannot differentiate between the observed phenotypic traits resulting from plastic responses versus evolutionary adaptations to urban environments. We conducted a field survey of habitat environmental factors and four vegetative traits in 12 Commelina communis populations along an urban-rural gradient in the Osaka-Kobe megacity area. We collected seedlings from six of the 12 populations, transplanted them into a greenhouse, and measured six vegetative traits. We investigated correlations between pairs of measured traits in both the field survey and CGE. Plant height and leaf area increased significantly in increasingly developed land areas (DLA) in the field survey, whereas no such variations were found in the CGE, suggesting that the observed phenotypic variation was due to a plastic response to urban eutrophication. Leaf number and specific leaf area (SLA) significantly decreased with increasing DLA in the CGE, suggesting the adaptation of these traits to urban environments. Positive correlations between plant height and leaf area were only observed in urban populations in both the field survey and CGE, indicating the evolution of this trait correlation in urban environments. It has been suggested that urban environments promote both plastic response and genetic divergence of a set of traits in native plants. Our findings suggest that low leaf number, SLA, and positive plant height-leaf area correlations have evolved. In addition, larger plant size is achieved via phenotypic plasticity in urban environments.

A bioengineer in the city -the Darwinian fitness of fiddler crabs inhabiting plastic pollution hotspots

Mangrove forests have been widely recognized as effective traps for plastic litter, which tends to accumulate in landward areas. In mangrove forests surrounding cities, plastic litter may increase up to two orders of magnitude. Therefore, crabs that process sediments for feeding and burrowing in landward areas are likely to be impacted by marine litter and other disturbances. As counterintuitive as it may seem, crabs are developing dense populations in urban mangroves from different countries, suggesting parallel adaptive processes related to the availability of anthropogenic food sources. To better understand this, we compared the loads of macroplastics within and between mangroves along an urban-rural-wild forest gradient in the Urabá Gulf, Colombian Caribbean. We then assessed if there is directional selection on crab phenotypes likely associated with human-provided food sources in urbanized forests. Finally, we evaluated the hypothesis that crabs in urban areas exhibit increased fecundity and survival - components of the Darwinian fitness - of female crabs in urban (versus wild) populations through three spawning seasons. Crabs in urban areas were larger (males), showed a healthier body condition (both sexes), and females had a larger reproductive lifespan than crabs in wild areas, strongly suggesting responses to the availability of predictable anthropogenic food subsidies in urban forests. Despite this, higher female fecundity was observed only during a spawning season. However, this short-lived increase in fecundity was offset by reduced survival among female crabs in urban forests, likely due to increased predation by birds, which appear to be emerging as dominant consumers in urban mangroves.

Urbanisation impacts plumage colouration in a songbird across Europe: Evidence from a correlational, experimental and meta-analytical approach

Urbanisation is accelerating across the globe, transforming landscapes, presenting organisms with novel challenges, shaping phenotypes and impacting fitness. Urban individuals are claimed to have duller carotenoid-based colouration, compared to their non-urban counterparts, the so-called 'urban dullness' phenomenon. However, at the intraspecific level, this generalisation is surprisingly inconsistent and often based on comparisons of single urban/non-urban populations or studies from a limited geographical area. Here, we combine correlational, experimental and meta-analytical data on a common songbird, the great tit Parus major, to investigate carotenoid-based plumage colouration in urban and forest populations across Europe. We find that, as predicted, urban individuals are paler than forest individuals, although there are large population-specific differences in the magnitude of the urban-forest contrast in colouration. Using one focal region (Malmö, Sweden), we reveal population-specific processes behind plumage colouration differences, which are unlikely to be the result of genetic or early-life conditions, but instead a consequence of environmental factors acting after fledging. Finally, our meta-analysis indicates that the urban dullness phenomenon is well established in the literature, for great tits, with consistent changes in carotenoid-based plumage traits, particularly carotenoid chroma, in response to anthropogenic disturbances. Overall, our results provide evidence for uniformity in the 'urban dullness' phenomenon but also highlight that the magnitude of the effect on colouration depends on local urban characteristics. Future long-term replicated studies, covering a wider range of species and feeding guilds, will be essential to further our understanding of the eco-evolutionary implications of this phenomenon.

What's going to be on the menu with global environmental changes?

Ongoing anthropogenic change is altering the planet at an unprecedented rate, threatening biodiversity, and ecosystem functioning. Species are responding to abiotic pressures at both individual and population levels, with changes affecting trophic interactions through consumptive pathways. Collectively, these impacts alter the goods and services that natural ecosystems will provide to society, as well as the persistence of all species. Here, we describe the physiological and behavioral responses of species to global changes on individual and population levels that result in detectable changes in diet across terrestrial and marine ecosystems. We illustrate shifts in the dynamics of food webs with implications for animal communities. Additionally, we highlight the myriad of tools available for researchers to investigate the dynamics of consumption patterns and trophic interactions, arguing that diet data are a crucial component of ecological studies on global change. We suggest that a holistic approach integrating the complexities of diet choice and trophic interactions with environmental drivers may be more robust at resolving trends in biodiversity, predicting food web responses, and potentially identifying early warning signs of diversity loss. Ultimately, despite the growing body of long-term ecological datasets, there remains a dearth of diet ecology studies across temporal scales, a shortcoming that must be resolved to elucidate vulnerabilities to changing biophysical conditions.

Contemporary changes in phenotypic variation, and the potential consequences for eco-evolutionary dynamics

Most studies assessing rates of phenotypic change focus on population mean trait values, whereas a largely overlooked additional component is changes in population trait variation. Theoretically, eco-evolutionary dynamics mediated by such changes in trait variation could be as important as those mediated by changes in trait means. To date, however, no study has comprehensively summarised how phenotypic variation is changing in contemporary populations. Here, we explore four questions using a large database: How do changes in trait variances compare to changes in trait means? Do different human disturbances have different effects on trait variance? Do different trait types have different effects on changes in trait variance? Do studies that established a genetic basis for trait change show different patterns from those that did not? We find that changes in variation are typically small; yet we also see some very large changes associated with particular disturbances or trait types. We close by interpreting and discussing the implications of our findings in the context of eco-evolutionary studies.

Urbanization shapes phenotypic selection of fruit traits in a seed-dispersal mutualism

Urbanization is currently one of the trademarks of the Anthropocene, accelerating evolutionary processes and reshaping ecological interactions over short time scales. Species interactions represent a fundamental pillar of diversity that is being altered globally by anthropogenic change. Urban environments, despite their potential impact, have seldom been studied in relation to how they shape natural selection of phenotypic traits in multispecies interactions. Using a seed-dispersal mutualism as a study system, we estimated the regime and magnitude of phenotypic selection exerted by frugivores on fruit and seed traits across three plant populations with different degrees of urbanization (urban, semiurban, and rural). Urbanization weakened phenotypic selection via an indirect positive impact on fruit production and fitness and, to a lesser extent, through a direct positive effect on species visitation rates. Our results show that urban ecosystems may affect multifarious selection of traits in the short term and highlight the role of humans in shaping eco-evolutionary dynamics of multispecies interactions.

Variation in Pheidole nodus (Hymenoptera: Formicidae) functional morphology across urban parks

Background

Habitat fragmentation and consequent population isolation in urban areas can impose significant selection pressures on individuals and species confined to urban islands, such as parks. Despite many comparative studies on the diversity and structure of ant community living in urban areas, studies on ants' responses to these highly variable ecosystems are often based on assemblage composition and interspecific mean trait values, which ignore the potential for high intraspecific functional trait variation among individuals.

Methods

Here, we examined differences in functional traits among populations of the generalist ant Pheidole nodus fragmented between urban parks. We used pitfall trapping, which is more random and objective than sampling colonies directly, despite a trade-off against sample size. We then tested whether trait-filtering could explain phenotypic differences among urban park ant populations, and whether ant populations in different parks exhibited different phenotypic optima, leading to positional shifts in anatomical morphospace through the regional ant meta-population.

Results

Intraspecific morphological differentiation was evident across this urban region. Populations had different convex hull volumes, positioned differently over the morphospace.

Conclusions

Fragmentation and habitat degradation reduced phenotypic diversity and, ultimately, changed the morphological optima of populations in this urban landscape. Considering ants' broad taxonomic and functional diversity and their important role in ecosystems, further work over a variety of ant taxa is necessary to ascertain those varied morphological response pathways operating in response to population segregation in urban environments.

A multidimensional framework to quantify the effects of urbanization on avian breeding fitness

Urbanization has dramatically altered Earth's landscapes and changed a multitude of environmental factors. This has resulted in intense land-use change, and adverse consequences such as the urban heat island effect (UHI), noise pollution, and artificial light at night (ALAN). However, there is a lack of research on the combined effects of these environmental factors on life-history traits and fitness, and on how these interactions shape food resources and drive patterns of species persistence. Here, we systematically reviewed the literature and created a comprehensive framework of the mechanistic pathways by which urbanization affects fitness and thus favors certain species. We found that urbanization-induced changes in urban vegetation, habitat quality, spring temperature, resource availability, acoustic environment, nighttime light, and species behaviors (e.g., laying, foraging, and communicating) influence breeding choices, optimal time windows that reduce phenological mismatch, and breeding success. Insectivorous and omnivorous species that are especially sensitive to temperature often experience advanced laying behaviors and smaller clutch sizes in urban areas. By contrast, some granivorous and omnivorous species experience little difference in clutch size and number of fledglings because urban areas make it easier to access anthropogenic food resources and to avoid predation. Furthermore, the interactive effect of land-use change and UHI on species could be synergistic in locations where habitat loss and fragmentation are greatest and when extreme-hot weather events take place in urban areas. However, in some instances, UHI may mitigate the impact of land-use changes at local scales and provide suitable breeding conditions by shifting the environment to be more favorable for species' thermal limits and by extending the time window in which food resources are available in urban areas. As a result, we determined five broad directions for further research to highlight that urbanization provides a great opportunity to study environmental filtering processes and population dynamics.

Frank Beach Award Winner: The centrality of the hypothalamic-pituitary-adrenal axis in dealing with environmental change across temporal scales

Understanding if and how individuals and populations cope with environmental change is an enduring question in evolutionary ecology that has renewed importance given the pace of change in the Anthropocene. Two evolutionary strategies of coping with environmental change may be particularly important in rapidly changing environments: adaptive phenotypic plasticity and/or bet hedging. Adaptive plasticity could enable individuals to match their phenotypes to the expected environment if there is an accurate cue predicting the selective environment. Diversifying bet hedging involves the production of seemingly random phenotypes in an unpredictable environment, some of which may be adaptive. Here, I review the central role of the hypothalamic-pituitary-adrenal (HPA) axis and glucocorticoids (GCs) in enabling vertebrates to cope with environmental change through adaptive plasticity and bet hedging. I first describe how the HPA axis mediates three types of adaptive plasticity to cope with environmental change (evasion, tolerance, recovery) over short timescales (e.g., 1-3 generations) before discussing how the implications of GCs on phenotype integration may depend upon the timescale under consideration. GCs can promote adaptive phenotypic integration, but their effects on phenotypic co-variation could also limit the dimensions of phenotypic space explored by animals over longer timescales. Finally, I discuss how organismal responses to environmental stressors can act as a bet hedging mechanism and therefore enhance evolvability by increasing genetic or phenotypic variability or reducing patterns of genetic and phenotypic co-variance. Together, this emphasizes the crucial role of the HPA axis in understanding fundamental questions in evolutionary ecology.

Increases in intraspecific body size variation are common among North American mammals and birds between 1880 and 2020

Many studies have documented the average body size of animals declining over time. Compared to mean body size, less is known about long-term changes in intraspecific trait variation (ITV), which is also important to understanding species' ability to cope with environmental challenges. On the basis of 393,499 specimen records from 380 species collected in North America between 1880 and 2020, we found that body size ITV increased by 9.59% for mammals (n = 302) and 30.67% for birds (n = 78); human-harvested species had higher probability of ITV increase. The observed increasing ITV in many species suggests possible niche expansion and potential buffering effects against downsizing but it risks increased maladaptation to rapidly changing environments. The results demonstrate that trait mean and variance do not necessarily respond in similar ways to anthropogenic pressures and both should be considered.

Past and future: Urbanization and the avian endocrine system

Urban environments are evolutionarily novel and differ from natural environments in many respects including food and/or water availability, predation, noise, light, air quality, pathogens, biodiversity, and temperature. The success of organisms in urban environments requires physiological plasticity and adjustments that have been described extensively, including in birds residing in geographically and climatically diverse regions. These studies have revealed a few relatively consistent differences between urban and non-urban conspecifics. For example, seasonally breeding urban birds often develop their reproductive system earlier than non-urban birds, perhaps in response to more abundant trophic resources. In most instances, however, analyses of existing data indicate no general pattern distinguishing urban and non-urban birds. It is, for instance, often hypothesized that urban environments are stressful, yet the activity of the hypothalamus-pituitary-adrenal axis does not differ consistently between urban and non-urban birds. A similar conclusion is reached by comparing blood indices of metabolism. The origin of these disparities remains poorly understood, partly because many studies are correlative rather than aiming at establishing causality, which effectively limits our ability to formulate specific hypotheses regarding the impacts of urbanization on wildlife. We suggest that future research will benefit from prioritizing mechanistic approaches to identify environmental factors that shape the phenotypic responses of organisms to urbanization and the neuroendocrine and metabolic bases of these responses. Further, it will be critical to elucidate whether factors affect these responses (a) cumulatively or synergistically; and (b) differentially as a function of age, sex, reproductive status, season, and mobility within the urban environment. Research to date has used various taxa that differ greatly not only phylogenetically, but also with regard to ecological requirements, social systems, propensity to consume anthropogenic food, and behavioral responses to human presence. Researchers may instead benefit from standardizing approaches to examine a small number of representative models with wide geographic distribution and that occupy diverse urban ecosystems.

Behavioral plasticity can facilitate evolution in urban environments

Plasticity-led evolution is central to evolutionary theory. Although challenging to study in nature, this process may be particularly apparent in novel environments such as cities. We document abundant evidence of plastic behavioral changes in urban animals, including learning, contextual, developmental, and transgenerational plasticities. Using behavioral drive as a conceptual framework, our analysis of notable case studies suggests that plastic behaviors, such as altered habitat use, migration, diurnal and seasonal activity, and courtship, can have faciliatory and cascading effects on urban evolution via spatial, temporal, and mate-choice mechanisms. Our findings highlight (i) the need to incorporate behavioral plasticity more formally into urban evolutionary research and (ii) the opportunity provided by urban environments to study behavioral mechanisms of plasticity-led processes.

A global meta-analysis reveals higher variation in breeding phenology in urban birds than in their non-urban neighbours

Cities pose a major ecological challenge for wildlife worldwide. Phenotypic variation, which can result from underlying genetic variation or plasticity, is an important metric to understand eco-evolutionary responses to environmental change. Recent work suggests that urban populations might have higher levels of phenotypic variation than non-urban counterparts. This prediction, however, has never been tested across species nor over a broad geographical range. Here, we conducted a meta-analysis of the avian literature to compare urban versus non-urban means and variation in phenology (i.e. lay date) and reproductive effort (i.e. clutch size, number of fledglings). First, we show that urban populations reproduce earlier and have smaller broods than non-urban conspecifics. Second, we show that urban populations have higher phenotypic variation in laying date than non-urban populations. This result arises from differences between populations within breeding seasons, conceivably due to higher landscape heterogeneity in urban habitats. These findings reveal a novel effect of urbanisation on animal life histories with potential implications for species adaptation to urban environments (which will require further investigation). The higher variation in phenology in birds subjected to urban disturbance could result from plastic responses to a heterogeneous environment, or from higher genetic variation in phenology, possibly linked to higher evolutionary potential.

Selection in the city: Rapid and fine-scale evolution of urban eastern water dragons

Oceanic archipelagos have long been treated as a Petri dish for studies of evolutionary and ecological processes. Like archipelagos, cities exhibit similar patterns and processes, such as the rapid phenotypic divergence of a species between urban and nonurban environments. However, on a local scale, cities can be highly heterogenous, where geographically close populations can experience dramatically different environmental conditions. Nevertheless, we are yet to understand the evolutionary and ecological implications for populations spread across a heterogenous cityscape. To address this, we compared neutral genetic divergence to quantitative trait divergence within three native riparian and four city park populations of an iconic urban adapter, the eastern water dragon. We demonstrated that selection is likely acting to drive divergence of snout-vent length and jaw width across native riparian populations that are geographically isolated and across city park populations that are geographically close yet isolated by urbanization. City park populations as close as 0.9 km exhibited signs of selection-driven divergence to the same extent as native riparian populations isolated by up to 114.5 km. These findings suggest that local adaptation may be occurring over exceptionally small geographic and temporal scales within a single metropolis, demonstrating that city parks can act as archipelagos for the study of rapid evolution.

Are behaviour and stress-related phenotypes in urban birds adaptive?

Urbanisation is a world-wide phenomenon converting natural habitats into new artificial ones. Environmental conditions associated with urbanisation represent great challenges for wildlife. Behaviour and stress tolerance are considered of major importance in the adaptation to novel urban habitats and numerous studies already reported behavioural and stress response phenotypes associated with urbanisation, often suggesting they represented adaptations, while rarely demonstrating it. The main goal of this study was to test the adaptive nature of urban shifts in behavioural and stress-related traits, and by adaptive we mean phenotypic change favouring traits in the same direction as selection. Using 7 years of monitoring of urban and forest great tits, we first tested for differences in exploratory behaviour, aggressiveness and breath rate, between both habitats. Second, we performed habitat-specific analyses of selection on the three former traits using (a) reproductive success and (b) survival estimated via capture-mark-recapture models, as fitness estimates, to determine whether shifts in these behavioural and stress-related traits were aligned with patterns of ongoing selection. We found that urban birds displayed higher exploratory behaviour and aggressiveness, and higher breath rate, compared to forest birds. Selection analyses overall revealed that these shifts were not adaptive and could even be maladaptive. In particular, higher handling aggression and higher breath rate in urban birds was associated with lower fitness. Higher exploration scores were correlated with lower survival in both habitats, but higher reproductive success only in forest males. Overall, differences in patterns of selection between habitats were not consistent with the phenotypic divergence observed. Taken together, these results highlight that phenotypic shifts observed in cities do not necessarily result from new selection pressures and could be maladaptive. We hypothesise that divergences in behavioural traits for urban birds could result from the filtering of individuals settling in cities. We thus encourage urban evolutionary scientists to further explore the adaptive potential of behavioural traits measured in urban habitats (a) by replicating this type of study in multiple cities and species, (b) by implementing studies focusing on immigrant phenotypes and (c) by measuring selection at multiple life stages.

Does Living in Human-Altered Environments Affect Life-History and Personality of Wild Mice?

In urban habitats, animals are faced with different and often challenging environmental conditions compared to their native habitats. Behavior is the fastest response to environmental change and therefore a very important component to adjust to human-altered environments. Behaviors such as novelty responses and innovativeness which allow animals to cope with novel stimuli are often altered in urban populations. The mechanisms producing such adaptations are currently not well understood. In this study, we investigate whether urban living has an impact on the microevolution of mouse behavioral and life-history traits including boldness, stress-coping, growth, longevity, and emphasis on reproduction. We hypothesized that animals living together with humans for longer show increased novelty-seeking and boldness characteristics at the species and subspecies level. We, therefore, compared behavior and life history characteristics among Mus musculus, a commensal rodent, Mus spicilegus as a synanthropic but not commensal, and Apodemus uralensis as a strictly rural species. In addition, we compared three subspecies of M. musculus (in total six populations) that differ in the time living together with humans. Behavioral and life history differences are stronger between populations even of the same subspecies rather than showing a structural trend with the time animals have spent with humans. In addition, species differ in behavior and life history, albeit not in a pattern that suggests an evolutionary adaptation to living in human-altered habitats. We, therefore, suggest that behavioral adaptations of wild mice are geared toward environmental differences such as geographic origin or habitat specifics but not necessarily directly evolve by living together with humans.

Changes to the gut microbiota of a wild juvenile passerine in a multidimensional urban mosaic

Urbanisation is a major anthropogenic perturbation presenting novel ecological and evolutionary challenges to wild populations. Symbiotic microorganisms residing in the gastrointestinal tracts (gut) of vertebrates have mutual connections with host physiology and respond quickly to environmental alterations. However, the impact of anthropogenic changes and urbanisation on the gut microbiota remains poorly understood, especially in early development. To address this knowledge gap, we characterised the gut microbiota of juvenile great tits (Parus major) reared in artificial nestboxes and in natural cavities in an urban mosaic, employing two distinct frameworks characterising the urban space. Microbial diversity was influenced by cavity type. Alpha diversity was affected by the amount of impervious surface surrounding the breeding location, and positively correlated with tree cover density. Community composition differed between urban and rural sites: these alterations covaried with sound pollution and distance to the city centre. Overall, the microbial communities reflect and are possibly influenced by the heterogeneous environmental modifications that are typical of the urban space. Strikingly, the choice of framework and environmental variables characterising the urban space can influence the outcomes of such ecological studies. Our results open new perspectives to investigate the impact of microbial symbionts on the adaptive capacity of their hosts.

Bumble bees exhibit body size clines across an urban gradient despite low genetic differentiation

Environmental heterogeneity resulting from human-modified landscapes can increase intraspecific trait variation. However, less known is whether such phenotypic variation is driven by plastic or adaptive responses to local environments. Here, we study five bumble bee (Apidae: Bombus) species across an urban gradient in the greater Saint Louis, Missouri region in the North American Midwest and ask: (1) Can urban environments induce intraspecific spatial structuring of body size, an ecologically consequential functional trait? And, if so, (2) is this body size structure the result of plasticity or adaptation? We additionally estimate genetic diversity, inbreeding, and colony density of these species—three factors that affect extinction risk. Using ≥ 10 polymorphic microsatellite loci per species and measurements of body size, we find that two of these species (Bombus impatiens, Bombus pensylvanicus) exhibit body size clines across the urban gradient, despite a lack of population genetic structure. We also reaffirm reports of low genetic diversity in B. pensylvanicus and find evidence that Bombus griseocollis, a species thought to be thriving in North America, is inbred in the greater Saint Louis region. Collectively, our results have implications for conservation in urban environments and suggest that plasticity can cause phenotypic clines across human-modified landscapes.

Urban environments have species-specific associations with invasive insect herbivores

Urban forests are critically important for providing ecosystem services to rapidly expanding urban populations, but their health is threatened by invasive insect herbivores. To protect urban forests against invasive insects and support future delivery of ecosystem services, we must first understand the factors that affect insect density across urban landscapes. This study explores how a variety of environmental factors that vary across urban habitats influence density of invasive insects. Specifically, we evaluate how vegetational complexity, distance to buildings, impervious surface, canopy temperature, host availability and density of co-occurring herbivores impact three invasive pests of elm trees: the elm leaf beetle (Xanthogaleruca luteola), the elm flea weevil (Orchestes steppensis) and the elm leafminer (Fenusa ulmi). Insect responses to these factors were species-specific, and all environmental factors were associated with density of at least one pest species except for distance to buildings. Elm leafminer density decreased with higher temperatures and was influenced by an interaction between vegetational complexity and impervious surface. Elm flea weevil density increased with greater host availability, and elm leaf beetle density increased with higher temperatures. Both elm leaf beetle and elm flea weevil density decreased with greater leafminer density, suggesting that insect density is mediated by species interactions. These findings can be used to inform urban pest management and tree care efforts, making urban forests more resilient in an era when globalization and climate change make them particularly vulnerable to attack.

Epigenetics and the city: Non-parallel DNA methylation modifications across pairs of urban-forest Great tit populations

Identifying the molecular mechanisms involved in rapid adaptation to novel environments and determining their predictability are central questions in evolutionary biology and pressing issues due to rapid global changes. Complementary to genetic responses to selection, faster epigenetic variations such as modifications of DNA methylation may play a substantial role in rapid adaptation. In the context of rampant urbanization, joint examinations of genomic and epigenomic mechanisms are still lacking. Here, we investigated genomic (SNP) and epigenomic (CpG methylation) responses to urban life in a passerine bird, the Great tit (Parus major). To test whether urban evolution is predictable (i.e. parallel) or involves mostly nonparallel molecular processes among cities, we analysed both SNP and CpG methylation variations across three distinct pairs of city and forest Great tit populations in Europe. Our analyses reveal a polygenic response to urban life, with both many genes putatively under weak divergent selection and multiple differentially methylated regions (DMRs) between forest and city great tits. DMRs mainly overlapped transcription start sites and promotor regions, suggesting their importance in modulating gene expression. Both genomic and epigenomic outliers were found in genomic regions enriched for genes with biological functions related to the nervous system, immunity, or behavioural, hormonal and stress responses. Interestingly, comparisons across the three pairs of city-forest populations suggested little parallelism in both genetic and epigenetic responses. Our results confirm, at both the genetic and epigenetic levels, hypotheses of polygenic and largely nonparallel mechanisms of rapid adaptation in novel environments such as urbanized areas.