Adaptive evolution in urban ecosystems

Urban coyotes are genetically distinct from coyotes in natural habitats

Urbanization is increasing throughout the world, transforming natural habitats. Coyotes (Canis latrans) are found in highly urban, suburban, rural and undeveloped mountainous habitats, making them an exemplary model organism to investigate the effects of urbanization on animals. We hypothesized that coyotes in natural habitats are more genetically related to distant coyotes in similar natural habitats and less related to coyotes in urban areas due to natal habitat-biased dispersal. We also hypothesized that increasing urbanization would result in decreased genetic diversity due to habitat fragmentation, dispersal barriers and genetic drift. We analyzed 10 microsatellite genetic markers from 125 individual coyotes sampled across a spectrum of highly urban to highly natural areas in southern California. Most coyotes clustered into four distinct genetic populations, whereas others appeared to have admixed ancestry. Three genetic populations were associated primarily with urban habitats in Los Angeles and Orange Counties. In contrast, the remaining population was associated with more naturally vegetated land near the surrounding mountains. Coyotes living in natural areas formed a genetically distinct cluster despite long geographic distances separating them. Genetic diversity was negatively associated with urban/suburban land cover and local road density, and positively associated with the relative amount of natural vegetation. These results indicate that genetic differentiation and loss of genetic diversity coincided with the extremely rapid expansion of Greater Los Angeles throughout the 1900s. Thus, urbanization reduces gene flow and erodes genetic diversity even in a habitat generalist thought to be minimally impacted by land development.

Fear and stressing in predator-prey ecology: considering the twin stressors of predators and people on mammals

Predators induce stress in prey and can have beneficial effects in ecosystems, but can also have negative effects on biodiversity if they are overabundant or have been introduced. The growth of human populations is, at the same time, causing degradation of natural habitats and increasing interaction rates of humans with wildlife, such that conservation management routinely considers the effects of human disturbance as tantamount to or surpassing those of predators. The need to simultaneously manage both of these threats is particularly acute in urban areas that are, increasingly, being recognized as global hotspots of wildlife activity. Pressures from altered predator-prey interactions and human activity may each initiate fear responses in prey species above those that are triggered by natural stressors in ecosystems. If fear responses are experienced by prey at elevated levels, on top of responses to multiple environmental stressors, chronic stress impacts may occur. Despite common knowledge of the negative effects of stress, however, it is rare that stress management is considered in conservation, except in intensive ex situ situations such as in captive breeding facilities or zoos. We propose that mitigation of stress impacts on wildlife is crucial for preserving biodiversity, especially as the value of habitats within urban areas increases. As such, we highlight the need for future studies to consider fear and stress in predator-prey ecology to preserve both biodiversity and ecosystem functioning, especially in areas where human disturbance occurs. We suggest, in particular, that non-invasive in situ investigations of endocrinology and ethology be partnered in conservation planning with surveys of habitat resources to incorporate and reduce the effects of fear and stress on wildlife.

The luxury effect beyond cities: bats respond to socioeconomic variation across landscapes

Background

The luxury effect describes the positive relationship between affluence and organism diversity or activity in urban ecosystems. Driven by human activities, the luxury effect can potentially be found at a broader scale across different landscapes. Previously, the luxury effect relationship has been established within a city for two bat species, the red bat (Lasiurus borealis) and the evening bat (Nycticeius humeralis). We examined landscape-scale patterns of bat activity distribution—using empirical data for seven bat species for the luxury effect. We also identified bat-land cover associations for each species. Across North Carolina, USA, we used the mobile transect survey protocol of the North American Monitoring Program to record bat activity at 43 sites from 2015 to 2018. We collected land cover and income data at our transect locations to construct generalized linear mixed models to identify bat-land cover and bat-income relationships.

Results

We found that across landscapes, activity of the red bat and the evening bat was positively correlated to income independent of land cover, consistent with previous single-city results. We found a negative relationship between hoary bat (Lasiurus cinereus) activity and income. All seven species had specific land cover associations. Additionally, we found a positive interaction term between income and evergreen forest for the red bat and a positive interaction term between income and woody wetland for hoary bat.

Conclusions

Our results demonstrated that the luxury effect is an ecological pattern that can be found at a broad spatial scale across different landscapes. We highlight the need for multi-scale ecology studies to identify the mechanism(s) underlying the luxury effect and that the luxury effect could cause inequity in how people receive the ecosystem services provided by bats.

Replicated Landscape Genomics Identifies Evidence of Local Adaptation to Urbanization in Wood Frogs

Native species that persist in urban environments may benefit from local adaptation to novel selection factors. We used double-digest restriction-side associated DNA (RAD) sequencing to evaluate shifts in genome-wide genetic diversity and investigate the presence of parallel evolution associated with urban-specific selection factors in wood frogs (Lithobates sylvaticus). Our replicated paired study design involved 12 individuals from each of 4 rural and urban populations to improve our confidence that detected signals of selection are indeed associated with urbanization. Genetic diversity measures were less for urban populations; however, the effect size was small, suggesting little biological consequence. Using an FST outlier approach, we identified 37 of 8344 genotyped single nucleotide polymorphisms with consistent evidence of directional selection across replicates. A genome-wide association study analysis detected modest support for an association between environment type and 12 of the 37 FST outlier loci. Discriminant analysis of principal components using the 37 FST outlier loci produced correct reassignment for 87.5% of rural samples and 93.8% of urban samples. Eighteen of the 37 FST outlier loci mapped to the American bullfrog (Rana [Lithobates] catesbeiana) genome, although none were in coding regions. This evidence of parallel evolution to urban environments provides a powerful example of the ability of urban landscapes to direct evolutionary processes.

Evolution, not transgenerational plasticity, explains the adaptive divergence of acorn ant thermal tolerance across an urban-rural temperature cline

Although studies increasingly disentangle phenotypic plasticity from evolutionary responses to environmental change, few test for transgenerational plasticity in this context. Here, we evaluate whether phenotypic divergence of acorn ants in response to urbanization is driven by transgenerational plasticity rather than evolution. F2 generation worker ants (offspring of laboratory-born queens) exhibited similar divergence among urban and rural populations as field-born worker ants, suggesting that evolutionary divergence rather than transgenerational plasticity was primarily responsible for shifts toward higher heat tolerance and diminished cold tolerance in urban acorn ants. Hybrid offspring from matings between urban and rural populations also indicated that evolutionary divergence was likely the primary mechanism underlying population differences in thermal tolerance. Specifically, thermal tolerance traits were not inherited either maternally or paternally in the hybrid pairings as would be expected for strong parental or grandparental effects mediated through a single sex. Urban-rural hybrid offspring provided further insight into the genetic architecture of thermal adaptation. Heat tolerance of hybrids more resembled the urban-urban pure type, whereas cold tolerance of hybrids more resembled the rural-rural pure type. As a consequence, thermal tolerance traits in this system appear to be influenced by dominance rather than being purely additive traits, and heat and cold tolerance might be determined by separate genes. Though transgenerational plasticity does not appear to explain divergence of acorn ant thermal tolerance, its role in divergence of other traits and across other urbanization gradients merits further study.

How does urbanization affect the reproductive characteristics and ecological affinities of street plant communities?

Anthropogenic activities in urban ecosystems induce a myriad of environmental changes compared with adjacent rural areas. These environmental changes can be seen as series of abiotic and biotic selection filters affecting the distribution of plant species. What are the attributes of plant species that compose urban communities, compared with rural communities, as related to their ecological affinities (e.g., to temperature, humidity), and reproductive traits (e.g., entomophily, autogamy, floral morphology)? Using a floristic dataset from a citizen science project recording plant species growing spontaneously in the streets, we analyzed the distribution of species according to their ecological requirements and reproductive traits along an urbanization gradient in the Parisian region. We developed an original floral and pollinator typology composed of five floral and four pollinator morphotypes. The proportion of impervious areas, used as a proxy of urbanization, was measured at different spatial scales, to reveal at which spatial scales urbanization is selecting plant traits. We found significant differences in plant communities along the urbanization gradient. As expected with the warmer and drier conditions of urban areas, species with higher affinities to higher temperature, light and nutrient soil content, and lower atmospheric moisture were over-represented in urban plant communities. Interestingly, all of the significant changes in plant abiotical affinities were the most pronounced at the largest scale of analysis (1,000 m buffer radius), probably because the specific urban conditions are more pronounced when they occur on a large surface. The proportion of autogamous, self-compatible, and nonentomophilous species was significantly higher in urban plant communities, strongly suggesting a lower abundance or efficiency of the pollinating fauna in urban environments. Last, among insect-pollinated species, those with relatively long and narrow tubular corollas were disadvantaged in urban areas, possibly resulting from a reduction in pollinator abundance particularly affecting specialized plant-pollinator interactions.

Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians

In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.

Urbanization erodes niche segregation in Darwin's finches

Urbanization is influencing patterns of biological evolution in ways that are only beginning to be explored. One potential effect of urbanization is in modifying ecological resource distributions that underlie niche differences and that thus promote and maintain species diversification. Few studies have assessed such modifications, or their potential evolutionary consequences, in the context of ongoing adaptive radiation. We study this effect in Darwin's finches on the Galápagos Islands, by quantifying feeding preferences and diet niche partitioning across sites with different degrees of urbanization. We found higher finch density in urban sites and that feeding preferences and diets at urban sites skew heavily toward human food items. Furthermore, we show that finches at urban sites appear to be accustomed to the presence of people, compared with birds at sites with few people. In addition, we found that human behavior via the tendency to feed birds at non-urban but tourist sites is likely an important driver of finch preferences for human foods. Site differences in diet and feeding behavior have resulted in larger niche breadth within finch species and wider niche overlap between species at the urban sites. Both factors effectively minimize niche differences that would otherwise facilitate interspecies coexistence. These findings suggest that both human behavior and ongoing urbanization in Galápagos are starting to erode ecological differences that promote and maintain adaptive radiation in Darwin's finches. Smoothing of adaptive landscapes underlying diversification represents a potentially important yet underappreciated consequence of urbanization. Overall, our findings accentuate the fragility of the initial stages of adaptive radiation in Darwin's finches and raise concerns about the fate of the Galápagos ecosystems in the face of increasing urbanization.

Selection at behavioural, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer

What makes a species able to colonize novel environments? This question is key to understand the dynamics of adaptive radiations and ecological niche shifts, but the mechanisms that underlie expansion into novel habitats remain poorly understood at a genomic scale. Lizards from the genus Anolis are typically tropical, and the green anole (Anolis carolinensis) constitutes an exception since it expanded into temperate North America from subtropical Florida. Thus, we used the green anole as a model to investigate signatures of selection associated with colonization of a new environment, namely temperate North America. To this end, we analysed 29 whole-genome sequences, covering the entire native range of the species. We used a combination of recent methods to quantify both positive and balancing selection in northern populations, including F_ST outlier methods, machine learning and ancestral recombination graphs. We naively scanned for genes of interest and assessed the overlap between multiple tests. Strikingly, we identified many genes involved in behaviour, suggesting that the recent successful colonization of northern environments may have been linked to behavioural shifts as well as physiological adaptation. Using a candidate genes strategy, we determined that genes involved in response to cold or behaviour displayed more frequently signals of selection, while controlling for local recombination rate, gene clustering and gene length. In addition, we found signatures of balancing selection at immune genes in all investigated genetic groups, but also at genes involved in neuronal and anatomical development.

Comparison of wormlion behavior under man-made and natural shelters: urban wormlions more strongly prefer shaded, fine-sand microhabitats, construct larger pits and respond faster to prey

Urban habitats differ from their natural surroundings in various aspects, such as a higher temperature and a distinct species composition. It is therefore not surprising that animal behavior too differs between these habitat types. We studied the foraging and habitat selection behavior of a pit-building predator, a wormlion, originating from either an urban or a more natural site. Wormlions occur in nature under structures that provide shelter from sunlight and rain, such as caves, and are also common in cities, occurring under artificial shelters. Wormlions construct pit-traps to hunt arthropods, and the pits constructed by urban wormlions were larger than those constructed by wormlions from caves. Urban wormlions responded faster to prey falling into their pit, probably leading to a higher capture success. We suggest that these 2 findings indicate the higher investment of urban wormlions in foraging, resulting from the higher abundance of potential prey in the city. Urban wormlions were choosier regarding their preferred microhabitat. While both fine sand and shaded microhabitats were preferred by wormlions, urban wormlions demonstrated a greater preference for such conditions. We suggest that relocation is more likely to lead wormlions in cities to find microhabitats of a higher quality compared with wormlions inhabiting caves. This is probably due to the larger areas in the city available for wormlions. Wormlions from the caves possessed more lipids, suggesting that they employ a conservative growth strategy, intended to contend with the uncertainty of prey arrival, in contrast to the city, where potential prey are more abundant.

A roadmap for urban evolutionary ecology

Urban ecosystems are rapidly expanding throughout the world, but how urban growth affects the evolutionary ecology of species living in urban areas remains largely unknown. Urban ecology has advanced our understanding of how the development of cities and towns change environmental conditions and alter ecological processes and patterns. However, despite decades of research in urban ecology, the extent to which urbanization influences evolutionary and eco-evolutionary change has received little attention. The nascent field of urban evolutionary ecology seeks to understand how urbanization affects the evolution of populations, and how those evolutionary changes in turn influence the ecological dynamics of populations, communities, and ecosystems. Following a brief history of this emerging field, this Perspective article provides a research agenda and roadmap for future research aimed at advancing our understanding of the interplay between ecology and evolution of urban-dwelling organisms. We identify six key questions that, if addressed, would significantly increase our understanding of how urbanization influences evolutionary processes. These questions consider how urbanization affects nonadaptive evolution, natural selection, and convergent evolution, in addition to the role of urban environmental heterogeneity on species evolution, and the roles of phenotypic plasticity versus adaptation on species' abundance in cities. Our final question examines the impact of urbanization on evolutionary diversification. For each of these six questions, we suggest avenues for future research that will help advance the field of urban evolutionary ecology. Lastly, we highlight the importance of integrating urban evolutionary ecology into urban planning, conservation practice, pest management, and public engagement.

Urban colonization through multiple genetic lenses: The city-fox phenomenon revisited

Urbanization is driving environmental change on a global scale, creating novel environments for wildlife to colonize. Through a combination of stochastic and selective processes, urbanization is also driving evolutionary change. For instance, difficulty in traversing human-modified landscapes may isolate newly established populations from rural sources, while novel selective pressures, such as altered disease risk, toxicant exposure, and light pollution, may further diverge populations through local adaptation. Assessing the evolutionary consequences of urban colonization and the processes underlying them is a principle aim of urban evolutionary ecology. In the present study, we revisited the genetic effects of urbanization on red foxes (Vulpes vulpes) that colonized Zurich, Switzerland. Through use of genome-wide single nucleotide polymorphisms and microsatellite markers linked to the major histocompatibility complex (MHC), we expanded upon a previous neutral microsatellite study to assess population structure, characterize patterns of genetic diversity, and detect outliers associated with urbanization. Our results indicated the presence of one large evolutionary cluster, with substructure evident between geographic sampling areas. In urban foxes, we observed patterns of neutral and functional diversity consistent with founder events and reported increased differentiation between populations separated by natural and anthropogenic barriers. We additionally reported evidence of selection acting on MHC-linked markers and identified outlier loci with putative gene functions related to energy metabolism, behavior, and immunity. We concluded that demographic processes primarily drove patterns of diversity, with outlier tests providing preliminary evidence of possible urban adaptation. This study contributes to our overall understanding of urban colonization ecology and emphasizes the value of combining datasets when examining evolutionary change in an increasingly urban world.

Urban environment and cancer in wildlife: available evidence and future research avenues

While it is generally known that the risk of several cancers in humans is higher in urban areas compared with rural areas, cancer is often deemed a problem of human societies with modern lifestyles. At the same time, more and more wild animals are affected by urbanization processes and are faced with the need to adapt or acclimate to urban conditions. These include, among other things, increased exposure to an assortment of pollutants (e.g. chemicals, light and noise), novel types of food and new infections. According to the abundant literature available for humans, all of these factors are associated with an increased probability of developing cancerous neoplasias; however, the link between the urban environment and cancer in wildlife has not been discussed in the scientific literature. Here, we describe the available evidence linking environmental changes resulting from urbanization to cancer-related physiological changes in wild animals. We identify the knowledge gaps in this field and suggest future research avenues, with the ultimate aim of understanding how our modern lifestyle affects cancer prevalence in urbanizing wild populations. In addition, we consider the possibilities of using urban wild animal populations as models to study the association between environmental factors and cancer epidemics in humans, as well as to understand the evolution of cancer and defence mechanisms against it.

Eco-Evolutionary Dynamics: The Predator-Prey Adaptive Play and the Ecological Theater

The emerging field of eco-evolutionary dynamics has demonstrated that both ecological and evolutionary processes can occur contemporaneously. Ecological interactions, such as between predator and prey, are important focal areas where an eco-evolutionary perspective can advance understanding about phenotypically plastic and adaptive evolutionary responses. In predator-prey interactions, both species reciprocally respond and adapt to each other in order to simultaneously ensure resource consumption and predation avoidance. Here we sketch out a way to help unify experimental and analytical approaches to both eco-evolutionary dynamics and predator-prey interactions, with a specific focus on terrestrial systems. We discuss the need to view predator-prey eco-evolutionary dynamics as a perpetually adaptive interplay with constantly shifting pressures and feedbacks, rather than viewing it as driving a set evolutionary trajectory. We then outline our perspective on how to understand eco-evolutionary patterns in a predator-prey context. We propose initiating insight by distinguishing phenotypic plasticity against genetic change (i.e., "molecular reductionism") and further applying a landscape-scale perspective (i.e., "landscape holism"). We believe that studying predator-prey interactions under an eco-evolutionary lens can provide insights into how general and, consequently, predictable species' evolutionary responses are to their contemporary environments.

Prey abundance and urbanization influence the establishment of avian predators in a metropolitan landscape

Urbanization causes the simplification of natural habitats, resulting in animal communities dominated by exotic species with few top predators. In recent years, however, many predators such as hawks, and in the US coyotes and cougars, have become increasingly common in urban environments. Hawks in the Accipiter genus, especially, are recovering from widespread population declines and are increasingly common in urbanizing landscapes. Our goal was to identify factors that determine the occupancy, colonization and persistence of Accipiter hawks in a major metropolitan area. Through a novel combination of citizen science and advanced remote sensing, we quantified how urban features facilitate the dynamics and long-term establishment of Accipiter hawks. Based on data from Project FeederWatch, we quantified 21 years (1996-2016) of changes in the spatio-temporal dynamics of Accipiter hawks in Chicago, IL, USA. Using a multi-season occupancy model, we estimated Cooper's (Accipiter cooperii) and sharp-shinned (A. striatus) hawk occupancy dynamics as a function of tree canopy cover, impervious surface cover and prey availability. In the late 1990s, hawks occupied 26% of sites around Chicago, but after two decades, their occupancy fluctuated close to 67% of sites and they colonized increasingly urbanized areas. Once established, hawks persisted in areas with high levels of impervious surfaces as long as those areas supported high abundances of prey birds. Urban areas represent increasingly habitable environments for recovering predators, and understanding the precise urban features that drive colonization and persistence is important for wildlife conservation in an urbanizing world.

Urban Behavioral Ecology: Lessons from Anolis Lizards

Human-driven rapid environmental changes such as urbanization challenge the persistence of animal populations worldwide. A major aim of research in urban ecology is to unravel which traits allow animals to successfully deal with these new selective pressures. Since behavior largely determines how animals interact with the environment, it is expected to be an important factor determining their success in urban environments. However, behavior is a complex trait and fully understanding how it contributes to urban success is not straightforward: different behaviors may help animals deal with urbanization at different levels of biological organization. For instance, at the species level, urban exploiters often share behaviors that allow them to successfully forage and reproduce in urban areas. However, these behaviors are not necessarily the same that differentiate urban populations from populations of the same species in less disturbed environments. In addition, individual-level studies are essential to identify which mechanisms favor survival and reproduction in urbanized settings. Yet, longitudinal, mid-to-long-term studies of animal behavior at the individual level have largely been limited by logistic challenges. Here, I suggest that research programs in urban behavioral ecology should consider studying behavior at species-, population-, and individual-levels to achieve an integrative understanding of how animal behavior governs urban success. I use recent research carried out in Anolis lizards as an example to illustrate recent progress in behavioral urban ecology. Finally, I suggest some avenues of research at the individual level that could bring insight toward an integrative perspective of the role of behavior in urbanization. Integrative research programs in urban behavioral ecology will provide valuable insight to design management measures to maximize biodiversity and preserve ecosystem services.

The evolution of city life

Urbanization represents a dominant and growing form of disturbance to Earth's natural ecosystems, affecting biodiversity and ecosystem services on a global scale. While decades of research have illuminated the effects of urban environmental change on the structure and function of ecological communities in cities, only recently have researchers begun exploring the effects of urbanization on the evolution of urban populations. The 15 articles in this special feature represent the leading edge of urban evolutionary biology and address existing gaps in our knowledge. These gaps include: (i) the absence of theoretical models examining how multiple evolutionary mechanisms interact to affect evolution in urban environments; (ii) a lack of data on how urbanization affects natural selection and local adaptation; (iii) poor understanding of whether urban areas consistently affect non-adaptive and adaptive evolution in similar ways across multiple cities; (iv) insufficient data on the genetic and especially genomic signatures of urban evolutionary change; and (v) limited understanding of the evolutionary processes underlying the origin of new human commensals. Using theory, observations from natural populations, common gardens, genomic data and cutting-edge population genomic and landscape genetic tools, the papers in this special feature address these gaps and highlight the power of urban evolutionary biology as a globally replicated 'experiment' that provides a powerful approach for understanding how human altered environments affect evolution.

Urbanization drives contemporary evolution in stream fish

Human activities reduce biodiversity but may also drive diversification by modifying selection. Urbanization alters stream hydrology by increasing peak water velocities, which should in turn alter selection on the body morphology of aquatic species. Here, we show how urbanization can generate evolutionary divergence in the body morphology of two species of stream fish, western blacknose dace (Rhinichthys obtusus) and creek chub (Semotilus atromaculatus). We predicted that fish should evolve more streamlined body shapes within urbanized streams. We found that in urban streams, dace consistently exhibited more streamlined bodies while chub consistently showed deeper bodies. Comparing modern creek chub populations with historical museum collections spanning 50 years, we found that creek chub (1) rapidly became deeper bodied in streams that experienced increasing urbanization over time, (2) had already achieved deepened bodies 50 years ago in streams that were then already urban (and showed no additional deepening over time), and (3) remained relatively shallow bodied in streams that stayed rural over time. By raising creek chub from five populations under common conditions in the laboratory, we found that morphological differences largely reflected genetically based differences, not velocity-induced phenotypic plasticity. We suggest that urbanization can drive rapid, adaptive evolutionary responses to disturbance, and that these responses may vary unpredictably in different species.

Contrasting the effects of natural selection, genetic drift and gene flow on urban evolution in white clover (Trifolium repens)

Urbanization is a global phenomenon with profound effects on the ecology and evolution of organisms. We examined the relative roles of natural selection, genetic drift and gene flow in influencing the evolution of white clover (Trifolium repens), which thrives in urban and rural areas. Trifolium repens exhibits a Mendelian polymorphism for the production of hydrogen cyanide (HCN), a potent antiherbivore defence. We quantified the relative frequency of HCN in 490 populations sampled along urban-rural transects in 20 cities. We also characterized genetic variation within 120 populations in eight cities using 16 microsatellite loci. HCN frequency increased by 0.6% for every kilometre from an urban centre, and the strength of this relationship did not significantly vary between cities. Populations did not exhibit changes in genetic diversity with increasing urbanization, indicating that genetic drift is unlikely to explain urban-rural clines in HCN frequency. Populations frequently exhibited isolation-by-distance and extensive gene flow along most urban-rural transects, with the exception of a single city that exhibited genetic differentiation between urban and rural populations. Our results show that urbanization repeatedly drives parallel evolution of an ecologically important trait across many cities that vary in size, and this evolution is best explained by urban-rural gradients in natural selection.

Urbanization drives genetic differentiation in physiology and structures the evolution of pace-of-life syndromes in the water flea Daphnia magna

Natural and human-induced stressors elicit changes in energy metabolism and stress physiology in populations of a wide array of species. Cities are stressful environments that may lead to differential selection on stress-coping mechanisms. Given that city ponds are exposed to the urban heat island effect and receive polluted run-off, organisms inhabiting these ecosystems might show genetic differentiation for physiological traits enabling them to better cope with higher overall stress levels. A common garden study with 62 Daphnia magna genotypes from replicated urban and rural populations revealed that urban Daphnia have significantly higher concentrations of total body fat, proteins and sugars. Baseline activity levels of the antioxidant defence enzymes superoxide dismutase (SOD) and glutathione-S-transferase (GST) were higher in rural compared with city populations, yet urban animals were equally well protected against lipid peroxidation. Our results add to the recent evidence of urbanization-driven changes in stress physiology and energy metabolism in terrestrial organisms. Combining our results with data on urban life history evolution in Daphnia revealed that urban genotypes show a structured pace-of-life syndrome involving both life-history and physiological traits, whereas this is absent in rural populations.

Evolution of thermal tolerance and its fitness consequences: parallel and non-parallel responses to urban heat islands across three cities

The question of parallel evolution-what causes it, and how common it is-has long captured the interest of evolutionary biologists. Widespread urban development over the last century has driven rapid evolutionary responses on contemporary time scales, presenting a unique opportunity to test the predictability and parallelism of evolutionary change. Here we examine urban evolution in an acorn-dwelling ant species, focusing on the urban heat island signal and the ant's tolerance of these altered urban temperature regimes. Using a common-garden experimental design with acorn ant colonies collected from urban and rural populations in three cities and reared under five temperature treatments in the laboratory, we assessed plastic and evolutionary shifts in the heat and cold tolerance of F1 offspring worker ants. In two of three cities, we found evolved losses of cold tolerance, and compression of thermal tolerance breadth. Results for heat tolerance were more complex: in one city, we found evidence of simple evolved shifts in heat tolerance in urban populations, though in another, the difference in urban and rural population heat tolerance depended on laboratory rearing temperature, and only became weakly apparent at the warmest rearing temperatures. The shifts in tolerance appeared to be adaptive, as our analysis of the fitness consequences of warming revealed that while urban populations produced more sexual reproductives under warmer laboratory rearing temperatures, rural populations produced fewer. Patterns of natural selection on thermal tolerances supported our findings of fitness trade-offs and local adaptation across urban and rural acorn ant populations, as selection on thermal tolerance acted in opposite directions between the warmest and coldest rearing temperatures. Our study provides mixed support for parallel evolution of thermal tolerance under urban temperature rise, and, importantly, suggests the promising use of cities to examine parallel and non-parallel evolution on contemporary time scales.

Getting ahead of the curve: cities as surrogates for global change

Urbanization represents an unintentional global experiment that can provide insights into how species will respond and interact under future global change scenarios. Cities produce many conditions that are predicted to occur widely in the future, such as warmer temperatures, higher carbon dioxide (CO2) concentrations and exacerbated droughts. In using cities as surrogates for global change, it is challenging to disentangle climate variables-such as temperature-from co-occurring or confounding urban variables-such as impervious surface-and then to understand the interactive effects of multiple climate variables on both individual species and species interactions. However, such interactions are also difficult to replicate experimentally, and thus the challenges of cities are also their unique advantage. Here, we review insights gained from cities, with a focus on plants and arthropods, and how urban findings agree or disagree with experimental predictions and historical data. We discuss the types of hypotheses that can be best tested in cities, caveats to urban research and how to further validate cities as surrogates for global change. Lastly, we summarize how to achieve the goal of using urban species responses to predict broader regional- and ecosystem-level patterns in the future.

Great tits and the city: Distribution of genomic diversity and gene-environment associations along an urbanization gradient

Urbanization is a growing concern challenging the evolutionary potential of wild populations by reducing genetic diversity and imposing new selection regimes affecting many key fitness traits. However, genomic footprints of urbanization have received little attention so far. Using RAD sequencing, we investigated the genomewide effects of urbanization on neutral and adaptive genomic diversity in 140 adult great tits Parus major collected in locations with contrasted urbanization levels (from a natural forest to highly urbanized areas of a city; Montpellier, France). Heterozygosity was slightly lower in the more urbanized sites compared to the more rural ones. Low but significant effect of urbanization on genetic differentiation was found, at the site level but not at the nest level, indicative of the geographic scale of urbanization impact and of the potential for local adaptation despite gene flow. Gene-environment association tests identified numerous SNPs with small association scores to urbanization, distributed across the genome, from which a subset of 97 SNPs explained up to 81% of the variance in urbanization, overall suggesting a polygenic response to selection in the urban environment. These findings open stimulating perspectives for broader applications of high-resolution genomic tools on other cities and larger sample sizes to investigate the consistency of the effects of urbanization on the spatial distribution of genetic diversity and the polygenic nature of gene-urbanization association.

Evolution of life in urban environments

Our planet is an increasingly urbanized landscape, with over half of the human population residing in cities. Despite advances in urban ecology, we do not adequately understand how urbanization affects the evolution of organisms, nor how this evolution may affect ecosystems and human health. Here, we review evidence for the effects of urbanization on the evolution of microbes, plants, and animals that inhabit cities. Urbanization affects adaptive and nonadaptive evolutionary processes that shape the genetic diversity within and between populations. Rapid adaptation has facilitated the success of some native species in urban areas, but it has also allowed human pests and disease to spread more rapidly. The nascent field of urban evolution brings together efforts to understand evolution in response to environmental change while developing new hypotheses concerning adaptation to urban infrastructure and human socioeconomic activity. The next generation of research on urban evolution will provide critical insight into the importance of evolution for sustainable interactions between humans and our city environments.

Urbanization disrupts latitude-size rule in 17-year cicadas

Many ectotherms show a decrease in body size with increasing latitude due to changes in climate, a pattern termed converse Bergmann's rule. Urban conditions-particularly warmer temperatures and fragmented landscapes-may impose stresses on development that could disrupt these body size patterns. To test the impact of urbanization on development and latitudinal trends in body size, we launched a citizen science project to collect periodical cicadas (Magicicada septendecim) from across their latitudinal range during the 2013 emergence of Brood II. Periodical cicadas are long-lived insects whose distribution spans a broad latitudinal range covering both urban and rural habitats. We used a geometric morphometric approach to assess body size and developmental stress based on fluctuating asymmetry in wing shape. Body size of rural cicadas followed converse Bergmann's rule, but this pattern was disrupted in urban habitats. In the north, urban cicadas were larger than their rural counterparts, while southern populations showed little variation in body size between habitats. We detected no evidence of differences in developmental stress due to urbanization. To our knowledge, this is the first evidence that urbanization disrupts biogeographical trends in body size, and this pattern highlights how the effects of urbanization may differ over a species' range.

The heat is on: Genetic adaptation to urbanization mediated by thermal tolerance and body size

Worldwide, urbanization leads to tremendous anthropogenic environmental alterations, causing strong selection pressures on populations of animals and plants. Although a key feature of urban areas is their higher temperature ("urban heat islands"), adaptive thermal evolution in organisms inhabiting urban areas has rarely been studied. We tested for evolution of a higher heat tolerance (CT_MAX ) in urban populations of the water flea Daphnia magna, a keystone grazer in freshwater ecosystems, by carrying out a common garden experiment at two temperatures (20°C and 24°C) with genotypes of 13 natural populations ordered along a well-defined urbanization gradient. We also assessed body size and haemoglobin concentration to identify underlying physiological drivers of responses in CT_MAX . We found a higher CT_MAX in animals isolated from urban compared to rural habitats and in animals reared at higher temperatures. We also observed substantial genetic variation in thermal tolerance within populations. Overall, smaller animals were more heat tolerant. While urban animals mature at smaller size, the effect of urbanization on thermal tolerance is only in part caused by reductions in body size. Although urban Daphnia contained higher concentrations of haemoglobin, this did not contribute to their higher CT_MAX . Our results provide evidence of adaptive thermal evolution to urbanization in the water flea Daphnia. In addition, our results show both evolutionary potential and adaptive plasticity in rural as well as urban Daphnia populations, facilitating responses to warming. Given the important ecological role of Daphnia in ponds and lakes, these adaptive responses likely impact food web dynamics, top-down control of algae, water quality, and the socio-economic value of urban ponds.

Eco-evolutionary dynamics in urbanized landscapes: evolution, species sorting and the change in zooplankton body size along urbanization gradients

Urbanization causes both changes in community composition and evolutionary responses, but most studies focus on these responses in isolation. We performed an integrated analysis assessing the relative contribution of intra- and interspecific trait turnover to the observed change in zooplankton community body size in 83 cladoceran communities along urbanization gradients quantified at seven spatial scales (50-3200 m radii). We also performed a quantitative genetic analysis on 12 Daphnia magna populations along the same urbanization gradient. Body size in zooplankton communities generally declined with increasing urbanization, but the opposite was observed for communities dominated by large species. The contribution of intraspecific trait variation to community body size turnover with urbanization strongly varied with the spatial scale considered, and was highest for communities dominated by large cladoceran species and at intermediate spatial scales. Genotypic size at maturity was smaller for urban than for rural D. magna populations and for animals cultured at 24°C compared with 20°C. While local genetic adaptation likely contributed to the persistence of D. magna in the urban heat islands, buffering for the phenotypic shift to larger body sizes with increasing urbanization, community body size turnover was mainly driven by non-genetic intraspecific trait change.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.

Urban driven phenotypic changes: empirical observations and theoretical implications for eco-evolutionary feedback

Emerging evidence that cities drive micro-evolution raises the question of whether rapid urbanization of Earth might impact ecosystems by causing systemic changes in functional traits that regulate urban ecosystems' productivity and stability. Intraspecific trait variation-variation in organisms' morphological, physiological or behavioural characteristics stemming from genetic variability and phenotypic plasticity-has significant implications for ecological functions such as nutrient cycling and primary productivity. While it is well established that changes in ecological conditions can drive evolutionary change in species' traits that, in turn, can alter ecosystem function, an understanding of the reciprocal and simultaneous processes associated with such interactions is only beginning to emerge. In urban settings, the potential for rapid trait change may be exacerbated by multiple selection pressures operating simultaneously. This paper reviews evidence on mechanisms linking urban development patterns to rapid phenotypic changes, and differentiates phenotypic changes for which there is evidence of micro-evolution versus phenotypic changes which may represent plasticity. Studying how humans mediate phenotypic trait changes through urbanization could shed light on fundamental concepts in ecological and evolutionary theory. It can also contribute to our understanding of eco-evolutionary feedback and provide insights for maintaining ecosystem function over the long term.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.

Divergent habitat use of two urban lizard species

Faunal responses to anthropogenic habitat modification represent an important aspect of global change. In Puerto Rico, two species of arboreal lizard, Anolis cristatellus and A. stratulus, are commonly encountered in urban areas, yet seem to use the urban habitat in different ways. In this study, we quantified differences in habitat use between these two species in an urban setting. For each species, we measured habitat use and preference, and the niche space of each taxon, with respect to manmade features of the urban environment. To measure niche space of these species in an urban environment, we collected data from a total of six urban sites across four different municipalities on the island of Puerto Rico. We quantified relative abundance of both species, their habitat use, and the available habitat in the environment to measure both microhabitat preference in an urban setting, as well as niche partitioning between the two different lizards. Overall, we found that the two species utilize different portions of the urban habitat. Anolis stratulus tends to use more “natural” portions of the urban environment (i.e., trees and other cultivated vegetation), whereas A. cristatellus more frequently uses anthropogenic structures. We also found that aspects of habitat discrimination in urban areas mirror a pattern measured in prior studies for forested sites in which A. stratulus was found to perch higher than A. cristatellus and preferred lower temperatures and greater canopy cover. In our study, we found that the multivariate niche space occupied by A. stratulus did not differ from the available niche space in natural portions of the urban environment and in turn represented a subset of the niche space occupied by A. cristatellus. The unique niche space occupied by A. cristatellus corresponds to manmade aspects of the urban environment generally not utilized by A. stratulus. Our results demonstrate that some species are merely tolerant of urbanization while others utilize urban habitats in novel ways. This finding has implications for long‐term persistence in urban habitats and suggests that loss of natural habitat elements may lead to nonrandom species extirpations as urbanization intensifies.

Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus)

Urbanization significantly alters natural ecosystems and has accelerated globally. Urban wildlife populations are often highly fragmented by human infrastructure, and isolated populations may adapt in response to local urban pressures. However, relatively few studies have identified genomic signatures of adaptation in urban animals. We used a landscape genomic approach to examine signatures of selection in urban populations of white-footed mice (Peromyscus leucopus) in New York City. We analysed 154,770 SNPs identified from transcriptome data from 48 P. leucopus individuals from three urban and three rural populations and used outlier tests to identify evidence of urban adaptation. We accounted for demography by simulating a neutral SNP data set under an inferred demographic history as a null model for outlier analysis. We also tested whether candidate genes were associated with environmental variables related to urbanization. In total, we detected 381 outlier loci and after stringent filtering, identified and annotated 19 candidate loci. Many of the candidate genes were involved in metabolic processes and have well-established roles in metabolizing lipids and carbohydrates. Our results indicate that white-footed mice in New York City are adapting at the biomolecular level to local selective pressures in urban habitats. Annotation of outlier loci suggests selection is acting on metabolic pathways in urban populations, likely related to novel diets in cities that differ from diets in less disturbed areas.

Living in the city: urban environments shape the evolution of a native annual plant

Urban environments are warmer, have higher levels of atmospheric CO₂ and have altered patterns of disturbance and precipitation than nearby rural areas. These differences can be important for plant growth and are likely to create distinct selective environments. We planted a common garden experiment with seeds collected from natural populations of the native annual plant Lepidium virginicum, growing in five urban and nearby rural areas in the northern United States to determine whether and how urban populations differ from those from surrounding rural areas. When grown in a common environment, plants grown from seeds collected from urban areas bolted sooner, grew larger, had fewer leaves, had an extended time between bolting and flowering, and produced more seeds than plants grown from seeds collected from rural areas. Interestingly, the rural populations exhibited larger phenotypic differences from one another than urban populations. Surprisingly, genomic data revealed that the majority of individuals in each of the urban populations were more closely related to individuals from other urban populations than they were to geographically proximate rural areas - the one exception being urban and rural populations from New York which were nearly identical. Taken together, our results suggest that selection in urban environments favors different traits than selection in rural environments and that these differences can drive adaptation and shape population structure.

Urbanization shapes the demographic history of a native rodent (the white-footed mouse, Peromyscus leucopus) in New York City

How urbanization shapes population genomic diversity and evolution of urban wildlife is largely unexplored. We investigated the impact of urbanization on white-footed mice,Peromyscus leucopus,in the New York City (NYC) metropolitan area using coalescent-based simulations to infer demographic history from the site-frequency spectrum. We assigned individuals to evolutionary clusters and then inferred recent divergence times, population size changes and migration using genome-wide single nucleotide polymorphisms genotyped in 23 populations sampled along an urban-to-rural gradient. Both prehistoric climatic events and recent urbanization impacted these populations. Our modelling indicates that post-glacial sea-level rise led to isolation of mainland and Long Island populations. These models also indicate that several urban parks represent recently isolated P. leucopus populations, and the estimated divergence times for these populations are consistent with the history of urbanization in NYC.

Using fine-scale spatial genetics of Norway rats to improve control efforts and reduce leptospirosis risk in urban slum environments

The Norway rat (Rattus norvegicus) is a key pest species globally and responsible for seasonal outbreaks of the zoonotic bacterial disease leptospirosis in the tropics. The city of Salvador, Brazil, has seen recent and dramatic increases in human population residing in slums, where conditions foster high rat density and increasing leptospirosis infection rates. Intervention campaigns have been used to drastically reduce rat numbers. In planning these interventions, it is important to define the eradication units - the spatial scale at which rats constitute continuous populations and from where rats are likely recolonizing, post-intervention. To provide this information, we applied spatial genetic analyses to 706 rats collected across Salvador and genotyped at 16 microsatellite loci. We performed spatially explicit analyses and estimated migration levels to identify distinct genetic units and landscape features associated with genetic divergence at different spatial scales, ranging from valleys within a slum community to city-wide analyses. Clear genetic breaks exist between rats not only across Salvador but also between valleys of slums separated by <100 m-well within the dispersal capacity of rats. The genetic data indicate that valleys may be considered separate units and identified high-traffic roads as strong impediments to rat movement. Migration data suggest that most (71-90%) movement is contained within valleys, with no clear source population contributing to migrant rats. We use these data to recommend eradication units and discuss the importance of carrying out individual-based analyses at different spatial scales in urban landscapes.