A roadmap for urban evolutionary ecology

Insight into the adaptive role of arachnid genome-wide duplication through chromosome-level genome assembly of the Western black widow spider

Although spiders are one of the most diverse groups of arthropods, the genetic architecture of their evolutionary adaptations is largely unknown. Specifically, ancient genome-wide duplication occurring during arachnid evolution ~450 mya resulted in a vast assembly of gene families, yet the extent to which selection has shaped this variation is understudied. To aid in comparative genome sequence analyses, we provide a chromosome-level genome of the Western black widow spider (Latrodectus hesperus)-a focus due to its silk properties, venom applications, and as a model for urban adaptation. We used long-read and Hi-C sequencing data, combined with transcriptomes, to assemble 14 chromosomes in a 1.46 Gb genome, with 38,393 genes annotated, and a BUSCO score of 95.3%. Our analyses identified high repetitive gene content and heterozygosity, consistent with other spider genomes, which has led to challenges in genome characterization. Our comparative evolutionary analyses of eight genomes available for species within the Araneoidea group (orb weavers and their descendants) identified 1,827 single-copy orthologs. Of these, 155 exhibit significant positive selection primarily associated with developmental genes, and with traits linked to sensory perception. These results support the hypothesis that several traits unique to spiders emerged from the adaptive evolution of ohnologs-or retained ancestrally duplicated genes-from ancient genome-wide duplication. These comparative spider genome analyses can serve as a model to understand how positive selection continually shapes ancestral duplications in generating novel traits today within and between diverse taxonomic groups.

The ratting of North America: A 350-year retrospective on Rattus species compositions and competition

While the impacts of black (Rattus rattus) and brown (Rattus norvegicus) rats on human society are well documented-including the spread of disease, broad-scale environmental destruction, and billions spent annually on animal control-little is known about their ecology and behavior in urban areas due to the challenges of studying animals in city environments. We use isotopic and ZooMS analysis of archaeological (1550s-1900 CE) rat remains from eastern North America to provide a large-scale framework for species arrival, interspecific competition, and dietary ecology. Brown rats arrived earlier than expected and rapidly outcompeted black rats in coastal urban areas. This replacement happened despite evidence that the two species occupy different trophic positions. Findings include the earliest molecularly confirmed brown rat in the Americas and show a deep ecological structure to how rats exploit human-structured areas, with implications for understanding urban zoonosis, rat management, and ecosystem planning as well as broader themes of rat dispersal, phylogeny, evolutionary ecology, and climate impacts.

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.

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.

Cities of the Anthropocene: urban sustainability in an eco-evolutionary perspective

Cities across the globe are driving systemic change in social and ecological systems by accelerating the rates of interactions and intensifying the links between human activities and Earth's ecosystems, thereby expanding the scale and influence of human activities on fundamental processes that sustain life. Increasing evidence shows that cities not only alter biodiversity, they change the genetic makeup of many populations, including animals, plants, fungi and microorganisms. Urban-driven rapid evolution in species traits might have significant effects on socially relevant ecosystem functions such as nutrient cycling, pollination, water and air purification and food production. Despite increasing evidence that cities are causing rapid evolutionary change, current urban sustainability strategies often overlook these dynamics. The dominant perspectives that guide these strategies are essentially static, focusing on preserving biodiversity in its present state or restoring it to pre-urban conditions. This paper provides a systemic overview of the socio-eco-evolutionary transition associated with global urbanization. Using examples of observed changes in species traits that play a significant role in maintaining ecosystem function and resilience, I propose that these evolutionary changes significantly impact urban sustainability. Incorporating an eco-evolutionary perspective into urban sustainability science and planning is crucial for effectively reimagining the cities of the Anthropocene. This article is part of the theme issue 'Evolution and sustainability: gathering the strands for an Anthropocene synthesis'.

Independently evolved pollution resistance in four killifish populations is largely explained by few variants of large effect

The genetic architecture of phenotypic traits can affect the mode and tempo of trait evolution. Human-altered environments can impose strong natural selection, where successful evolutionary adaptation requires swift and large phenotypic shifts. In these scenarios, theory predicts that adaptation is due to a few adaptive variants of large effect, but empirical studies that have revealed the genetic architecture of rapidly evolved phenotypes are rare, especially for populations inhabiting polluted environments. Fundulus killifish have repeatedly evolved adaptive resistance to extreme pollution in urban estuaries. Prior studies, including genome scans for signatures of natural selection, have revealed some of the genes and pathways important for evolved pollution resistance, and provide context for the genotype-phenotype association studies reported here. We created multiple quantitative trait locus (QTL) mapping families using progenitors from four different resistant populations, and using RAD-seq genetically mapped variation in sensitivity (developmental perturbations) following embryonic exposure to a model toxicant PCB-126. We found that one to two large-effect QTL loci accounted for resistance to PCB-mediated developmental toxicity. QTLs harbored candidate genes that govern the regulation of aryl hydrocarbon receptor (AHR) signaling. One QTL locus was shared across all populations and another was shared across three populations. One QTL locus showed strong signatures of recent natural selection in the corresponding wild population but another QTL locus did not. Some candidate genes for PCB resistance inferred from genome scans in wild populations were identified as QTL, but some key candidate genes were not. We conclude that rapidly evolved resistance to the developmental defects normally caused by PCB-126 is governed by few genes of large effect. However, other aspects of resistance beyond developmental phenotypes may be governed by additional loci, such that comprehensive resistance to PCB-126, and to the mixtures of chemicals that distinguish urban estuaries more broadly, may be more genetically complex.

Seasonal dynamics in the mammalian microbiome between disparate environments

Host-associated bacterial microbiomes can facilitate host acclimation to seasonal environmental change and are hypothesized to help hosts cope with recent anthropogenic environmental perturbations (e.g., landscape modification). However, it is unclear how recurrent and recent forms of environmental change interact to shape variation in the microbiome. The majority of wildlife microbiome research occurs within a single seasonal context. Meanwhile, the few studies of seasonal variation in the microbiome often restrict focus to a single environmental context. By sampling urban and exurban eastern grey squirrel populations in the spring, summer, autumn, and winter, we explored whether seasonal rhythms in the grey squirrel gut microbiome differed across environments using a 16S amplicon sequencing approach. Differences in the microbiome between urban and exurban squirrels persisted across most of the year, which we hypothesize is linked to anthropogenic food consumption, but we also observed similarities in the urban and exurban grey squirrel microbiome during the autumn, which we attribute to engrained seed caching instincts in preparation for the winter. Host behaviour and diet selection may therefore be capable of maintaining similarities in microbiome structure between disparate environments. However, the depletion of an obligate host mucin glycan specialist (Akkermansia) during the winter in both urban and exurban squirrels was among the strongest differential abundance patterns we observed. In summary, urban grey squirrels showed different seasonal patterns in their microbiome than squirrels from exurban forests; however, in some instances, host behaviour and physiological responses might be capable of maintaining similar microbiome responses across seasons.

From green to red: Urban heat stress drives leaf color evolution

Prevalence of impervious surface and resulting higher temperatures in urban areas, known as urban heat islands, comprises prominent characteristics in global cities. However, it is not known whether and how urban plants adapt to such heat stress. This study focused on Oxalis corniculata, which has intraspecific polymorphism in leaf color (green and red) and examined whether the leaf color variation is associated with urban heat stress. Field observations revealed that green-leaved plants were dominant in green habitats, and red-leaved individuals were dominant in urban habitats, at local (<500 meters), landscape (<50 kilometers), and global scales. Growth and photosynthesis experiments demonstrated that red-leaved individuals performed better under heat stress, while green-leaved individuals performed better under nonstressful conditions. Genome-wide SNP analysis suggests that the red leaf may have evolved multiple times from the ancestral green leaf. Overall, the results suggest that the red leaves of O. corniculata observed in cities worldwide are evidence of plant adaptive evolution due to urban heat islands.

Rural selection drives the evolution of an urban-rural cline in coat color in gray squirrels

Phenotypic differences between urban and rural populations are well-documented, but the evolutionary processes driving trait variation along urbanization gradients are often unclear. We combined spatial data on abundance, trait variation, and measurements of fitness to understand cline structure and test for natural selection on heritable coat color morphs (melanic, gray) of eastern gray squirrels (Sciurus carolinensis) along an urbanization gradient. Population surveys using remote cameras and visual counts at 76 sites along the urbanization gradient revealed a significant cline in melanism, decreasing from 48% in the city center to <5% in rural woodlands. Among 76 squirrels translocated to test for phenotypic selection, survival was lower for the melanic than gray morph in rural woodlands, whereas there was no difference in survival between color morphs in the city. These results suggest the urban-rural cline in melanism is explained by natural selection favoring the gray morph in rural woodlands combined with relaxed selection in the city. Our study illustrates how trait variation between urban and rural populations can emerge from selection primarily in rural populations rather than adaptation to novel features of the urban environment.

Tracing the evolution of green logistics: A latent dirichlet allocation based topic modeling technology and roadmapping

Green logistics (GL) is the main development trend of modern logistics. The analysis of green logistics topics and their evolution is helpful in grasping its development trend and doing research facing the international frontier. Focusing on the hot topics and evolution process of green logistics, this paper analyzes from four aspects: firstly, this study divides the green logistics development progress into three stages based on life cycle theory, which are the emerging stage (1993-2003), slow growth stage (2004-2014) and rapid growth stage (2015-2021). Then, based on latent dirichlet allocation (LDA) topic model, this study summarizes and confirms related words and meaning of each topic in different stages. Furthermore, this study calculates the text similarity in each development stage of green logistics and analyzes the trend of hot topics in green logistics. Finally, this paper visualizes the development roadmap of green logistics and explores the progression among three stages. There are 4, 5, and 7 topics defined respectively in three development stages. The revolution of green logistics is analyzed, and the results show that "model and management on sustainable development of GL", "related issues and potential threats of GL", and "optimization analysis of low-carbon vehicle routing and time" are the primary development trends of green logistics. This study fills the gap in considering the evolution process of green logistics through topic modeling and roadmapping method. It provides a particular theoretical significance for the green and sustainable development of logistics.

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.

Interactive effects of rising temperatures and urbanisation on birds across different climate zones: A mechanistic perspective

Climate change and urbanisation are among the most pervasive and rapidly growing threats to biodiversity worldwide. However, their impacts are usually considered in isolation, and interactions are rarely examined. Predicting species' responses to the combined effects of climate change and urbanisation, therefore, represents a pressing challenge in global change biology. Birds are important model taxa for exploring the impacts of both climate change and urbanisation, and their behaviour and physiology have been well studied in urban and non-urban systems. This understanding should allow interactive effects of rising temperatures and urbanisation to be inferred, yet considerations of these interactions are almost entirely lacking from empirical research. Here, we synthesise our current understanding of the potential mechanisms that could affect how species respond to the combined effects of rising temperatures and urbanisation, with a focus on avian taxa. We discuss potential interactive effects to motivate future in-depth research on this critically important, yet overlooked, aspect of global change biology. Increased temperatures are a pronounced consequence of both urbanisation (through the urban heat island effect) and climate change. The biological impact of this warming in urban and non-urban systems will likely differ in magnitude and direction when interacting with other factors that typically vary between these habitats, such as resource availability (e.g. water, food and microsites) and pollution levels. Furthermore, the nature of such interactions may differ for cities situated in different climate types, for example, tropical, arid, temperate, continental and polar. Within this article, we highlight the potential for interactive effects of climate and urban drivers on the mechanistic responses of birds, identify knowledge gaps and propose promising future research avenues. A deeper understanding of the behavioural and physiological mechanisms mediating species' responses to urbanisation and rising temperatures will provide novel insights into ecology and evolution under global change and may help better predict future population responses.

Independently evolved pollution resistance in four killifish populations is largely explained by few variants of large effect

The genetic architecture of phenotypic traits can affect the mode and tempo of trait evolution. Human-altered environments can impose strong natural selection, where successful evolutionary adaptation requires swift and large phenotypic shifts. In these scenarios, theory predicts the influence of few adaptive variants of large effect, but empirical studies that have revealed the genetic architecture of rapidly evolved phenotypes are rare, especially for populations inhabiting polluted environments. Fundulus killifish have repeatedly evolved adaptive resistance to extreme pollution in urban estuaries. Prior studies, including genome scans for signatures of natural selection, have revealed some of the genes and pathways important for evolved pollution resistance, and provide context for the genotype-phenotype association studies reported here. We created multiple quantitative trait locus (QTL) mapping families using progenitors from four different resistant populations, and genetically mapped variation in sensitivity (developmental perturbations) following embryonic exposure to a model toxicant PCB-126. We found that a few large-effect QTL loci accounted for resistance to PCB-mediated developmental toxicity. QTLs harbored candidate genes that govern the regulation of aryl hydrocarbon receptor (AHR) signaling, where some (but not all) of these QTL loci were shared across all populations, and some (but not all) of these loci showed signatures of recent natural selection in the corresponding wild population. Some strong candidate genes for PCB resistance inferred from genome scans in wild populations were identified as QTL, but some key candidate genes were not. We conclude that rapidly evolved resistance to the developmental defects normally caused by PCB-126 is governed by few genes of large effect. However, other aspects of resistance beyond developmental phenotypes may be governed by additional loci, such that comprehensive resistance to PCB-126, and to the mixtures of chemicals that distinguish urban estuaries more broadly, may be more genetically complex.

Urban evolutionary ecology brings exaptation back into focus

The contribution of pre-existing phenotypic variation to evolution in novel environments has long been appreciated. Nevertheless, evolutionary ecologists have struggled with communicating these aspects of the adaptive process. In 1982, Gould and Vrba proposed terminology to distinguish character states shaped via natural selection for the roles they currently serve ('adaptations') from those shaped under preceding selective regimes ('exaptations'), with the intention of replacing the inaccurate 'preadaptation'. Forty years later, we revisit Gould and Vrba's ideas which, while often controversial, continue to be widely debated and highly cited. We use the recent emergence of urban evolutionary ecology as a timely opportunity to reintroduce the ideas of Gould and Vrba as an integrated framework to understand contemporary evolution in novel environments.

Urban-driven decrease in arthropod richness and diversity associated with group-specific changes in arthropod abundance

Habitat loss and fragmentation caused by land-use changes in urbanised landscapes are main drivers of biodiversity loss and changes in species assemblages. While the effects of urbanisation on arthropods has received increasing attention in the last decade, most of the studies were taxon-specific, limited in time and/or covering only part of the habitats along the rural-urban gradient. To comprehensively assess the effects of urbanisation on arthropod communities, here, we sampled arthropods at 180 sites within an urban mosaic in the city of Innsbruck (Austria) using a systematic grid. At each site, arthropods were collected in three micro-habitats: the canopy, the bush layer and tree bark. They were identified to the family, infra-order or order level, depending on the taxonomic group. Urbanisation level was estimated by five different proxies extracted from land use/land cover data (e.g., impervious surface cover), all of them calculated in a 100, 500, and 1,000 m radius around the sampling points, and three indexes based on distance to settlements. We tested for the effects of different levels of urbanisation on (i) overall arthropod abundance, richness and diversity and (ii) community composition using redundancy analyses. In the canopy and the bush layer, arthropod richness and diversity decreased with increasing urbanisation level, suggesting that urbanisation acts as a filter on taxonomic groups. Our data on arthropod abundance further support this hypothesis and suggest that urbanisation disfavours wingless groups, particularly so on trees. Indeed, urbanisation was correlated to lower abundances of spiders and springtails, but higher abundances of aphids, barklice and flies. Arthropod community composition was better explained by a set of urbanisation proxies, especially impervious surface cover measured in a 100, 500, and 1,000 m radius. Arthropods are key elements of food webs and their availability in urban environments is expected to have bottom-up effects, thus shaping foraging behaviour, distribution, and/or success of species at higher trophic levels. Studying ecological networks in urban ecosystems is the next step that will allow to understand how urbanisation alters biodiversity.

Urbanization and maternal hormone transfer: Endocrine and morphological phenotypes across ontogenetic stages

The phenotypes observed in urban and rural environments are often distinct; however, it remains unclear how these novel urban phenotypes arise. Hormone-mediated maternal effects likely play a key role in shaping developmental trajectories of offspring in different environments. Thus, we measured corticosterone (Cort) and testosterone (T) concentrations in eggs across the laying sequence in addition to Cort concentrations in nestling and adult female house wrens (Troglodytes aedon) at one urban and one rural site. We found that egg T concentrations were not different between birds from urban and rural sites. However, across all life stages (egg, nestling, and adult female), Cort concentrations were higher at the urban site. Additionally, urban nestling Cort concentrations, but not rural, correlated with fine-scale urban density scores. Furthermore, rural egg volume increased over the laying sequence, but urban egg volume leveled off mid-sequence, suggesting either that urban mothers are resource limited or that they are employing a different brood development strategy than rural mothers. Our study is one of the first to show that egg hormone concentrations differ in an urban environment with differences persisting in chick development and adult life stages. We suggest that maternal endocrine programing may shape offspring phenotypes in urban environments and are an overlooked yet important aspect underlying mechanisms of urban evolution.

Genome-wide parallelism underlies contemporary adaptation in urban lizards

Urbanization drastically transforms landscapes, resulting in fragmentation, degradation, and the loss of local biodiversity. Yet, urban environments also offer opportunities to observe rapid evolutionary change in wild populations that survive and even thrive in these novel habitats. In many ways, cities represent replicated "natural experiments" in which geographically separated populations adaptively respond to similar selection pressures over rapid evolutionary timescales. Little is known, however, about the genetic basis of adaptive phenotypic differentiation in urban populations nor the extent to which phenotypic parallelism is reflected at the genomic level with signatures of parallel selection. Here, we analyzed the genomic underpinnings of parallel urban-associated phenotypic change in Anolis cristatellus, a small-bodied neotropical lizard found abundantly in both urbanized and forested environments. We show that phenotypic parallelism in response to parallel urban environmental change is underlain by genomic parallelism and identify candidate loci across the Anolis genome associated with this adaptive morphological divergence. Our findings point to polygenic selection on standing genetic variation as a key process to effectuate rapid morphological adaptation. Identified candidate loci represent several functions associated with skeletomuscular development, morphology, and human disease. Taken together, these results shed light on the genomic basis of complex morphological adaptations, provide insight into the role of contingency and determinism in adaptation to novel environments, and underscore the value of urban environments to address fundamental evolutionary questions.

Moving past the challenges and misconceptions in urban adaptation research

Although the field of urban evolutionary ecology has recently expanded, much progress has been made in identifying adaptations that arise as a result of selective pressures within these unique environments. However, as studies within urban environments have rapidly increased, researchers have recognized that there are challenges and opportunities in characterizing urban adaptation. Some of these challenges are a consequence of increased direct and indirect human influence, which compounds long-recognized issues with research on adaptive evolution more generally. In this perspective, we discuss several common research challenges to urban adaptation related to (1) methodological approaches, (2) trait-environment relationships and the natural history of organisms, (3) agents and targets of selection, and (4) habitat heterogeneity. Ignoring these challenges may lead to misconceptions and further impede our ability to draw conclusions regarding evolutionary and ecological processes in urban environments. Our goal is to first shed light on the conceptual challenges of conducting urban adaptation research to help avoid the propagation of these misconceptions. We further summarize potential strategies to move forward productively to construct a more comprehensive picture of urban adaptation, and discuss how urban environments also offer unique opportunities and applications for adaptation research.

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.

Using fish to understand how cities affect sexual selection before and after mating

Urbanization transforms natural and agricultural areas into built landscapes. Such profound habitat alteration imposes strong pressure on phenotypic trait changes through processes related to natural and/or sexual selection. Evidence of how natural selection drives changes to traits in urban biota is increasing, but little is known about the role of sexual selection. In this study, we assessed the effect of urbanization on the expression and interaction of males' pre-mating traits (body size and color) and a post-mating trait (sperm load). We used a widespread invasive species, the guppy (Poecilia reticulata), which is a wellknown model for studying sexual selection, but have never been studied in urban systems for this purpose. We found that urbanization did not affect mean body size or condition, but it resulted in size-dependent reductions in the expression of orange and iridescent colors, as well as sperm load. The orange color was reduced in small urban guppies, while the iridescent colors were reduced in large urban guppies compared to non-urban guppies. The difference in sperm load was only found in large males, with lower sperm load in urban guppies. The relationship between orange color and sperm load was positive in urban guppies but negative in non-urban guppies, while the association between iridescent color and sperm load followed the opposite pattern. Our findings suggest that sexual selection on pre- and post-mating traits is weaker in urban than in non-urban systems and that interactions between such traits are context dependent. These responses can be related to the pollution and altered visual environment of urban systems and provide an opportunity to advance our understanding of the mechanisms determining adaptation in cities.

A global horizon scan for urban evolutionary ecology

Research on the evolutionary ecology of urban areas reveals how human-induced evolutionary changes affect biodiversity and essential ecosystem services. In a rapidly urbanizing world imposing many selective pressures, a time-sensitive goal is to identify the emergent issues and research priorities that affect the ecology and evolution of species within cities. Here, we report the results of a horizon scan of research questions in urban evolutionary ecology submitted by 100 interdisciplinary scholars. We identified 30 top questions organized into six themes that highlight priorities for future research. These research questions will require methodological advances and interdisciplinary collaborations, with continued revision as the field of urban evolutionary ecology expands with the rapid growth of cities.

Native Lizards Living in Brazilian Cities: Effects of Developmental Environments on Thermal Sensitivity and Morpho-Functional Associations of Locomotion

Environmental conditions often affect developmental processes and consequently influence the range of phenotypic variation expressed at population level. Expansion of urban sites poses new challenges for native species, as urbanization usually affects the intensity of solar exposure and shade availability, determining the thermal regimes organisms are exposed to. In this study, we evaluate the effects of different developmental conditions in a Tropidurus lizard commonly found in Brazilian urban sites. After incubating embryos of Tropidurus catalanensis in two different thermal regimes (Developmental Environments [DE]: cold 24°C and warm 30°C), we measured morphological traits in the neonates and quantified locomotor performance in horizontal and vertical surfaces at three temperatures [Test Temperatures (TT) = 24°C, 30°C and 36°C]. Results indicate effects of developmental temperatures on morphological features, expressing functional implications that might be decisive for the viability of T. catalanensis in urbanized areas. Lizards ran similarly on horizontal and vertical surfaces, and isolated analyses did not identify significant effects of DE or TT on the sprint speeds measured. Absolute Vmax (i.e., the maximum sprint speed reached among all TTs) positively correlated with body size (SVL), and neonates from the warm DE (30°C) were larger than those from the cold DE (24°C). Morpho-functional associations of absolute Vmax also involved pelvic girdle width and forelimb, hindlimb, trunk, and tail lengths. Emerging discussions aim to understand how animals cope with abrupt environmental shifts, a likely common challenge in urbanized sites. Our findings add a new dimension to the topic, providing evidence that temperature, an environmental parameter often affected by urbanization, influences the thermal sensitivity of locomotion and the morphological profile of T. catalanensis neonates. Thermal sensitivity of specific developmental processes may influence the ability of these lizards to remain in habitats that change fast, as those suffering rapid urbanization due to city growth.

Polyploidy in urban environments

Polyploidy is a major driver of evolutionary change in plants, but many aspects of polyploidy in natural systems remain enigmatic. We argue that urban landscapes present an unprecedented opportunity to observe polyploidy in action. Integrating polyploid biology and urban evolutionary ecology, we discuss multiple factors expected to promote polyploid formation, establishment, and persistence in urban systems. We develop a predictive framework for the contemporary ecology and evolution of polyploid plants in cities, and through this novel perspective propose that studying polyploidy in an urban context could lead to breakthroughs in understanding fundamental processes in polyploid evolution. We conclude by highlighting the potential consequences of polyploidy in urban environments, and outline a roadmap for research into this currently unexplored field.

Interactions of Functional Traits With Native Status and Ecosystem Novelty Explain the Establishment of Plant Species Within Urban Ecosystems: Evidence From Berlin, Germany

A key challenge in urban biodiversity conservation is to understand the drivers that govern the population establishment of different groups of species in different urban ecosystems. Here, we ask whether and to what extent vascular plant species establishment (i.e., the ability to establish self-sustaining populations within a certain time span) is driven by interactions of species functional traits, native status, and the type of ecosystem species occur in, with types of ecosystems distinguished by their degree of ecosystem novelty. To answer this question, we use a dataset of 1,178 vascular plant species occurring in Berlin, Germany that originally had been compiled to substantiate the Berlin Red List of endangered plant species. This dataset classifies native and non-native species into casual and established species based on a minimum of 25 years of expert observation. Whether a species is established or casual is distinguished among four broad types of ecosystems: natural remnant, hybrid, novel immature, and novel mature ecosystems. Moreover, we classify species into those native to Berlin and non-native species (split into archaeophytes and neophytes), and link species to selected functional traits and indicator values. By applying ordinal regression within a Bayesian framework, we show that traits are key drivers of these establishment processes and that the traits that drive species establishment differ across types of ecosystems. While across traits, more established species are present in natural remnants, low canopy height, annual life span, and late end of flowering specifically promote establishment in novel immature ecosystems. In hybrid ecosystems, low canopy height and reproduction by seeds are beneficial traits, with the latter promoting establishment in novel mature ecosystems, too. Traits were less important in predicting species establishment in native as compared to non-native species. All types of ecosystems add to urban biodiversity, and trait analyses refine our knowledge on how they can be supported in doing so on the long term. This can help in sharpening conservation measures.

Global urban environmental change drives adaptation in white clover

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.

Origin and status of Culex pipiens mosquito ecotypes

The northern house mosquito Culex pipiens sensu stricto is one of the most important disease vector mosquitoes in temperate zones across the northern hemisphere, responsible for the emergence of West Nile Virus over the last two decades. It comprises two ecologically distinct forms - an aboveground form, pipiens, diapauses in winter and primarily bites birds, while a belowground form, molestus, thrives year-round in subways, basements and other human-made, belowground habitats, bites mammals, and can even lay eggs without a blood meal. The two forms hybridize in some but not all places, leading to a complex ecological mosaic that complicates predictions of vectorial capacity. Moreover, the origin of the belowground molestus is contentious, with iconic populations from the London Underground subway system being held up by evolutionary biologists as a preeminent example of rapid, in situ, urban adaptation and speciation. We review the recent and historical literature on the origin and ecology of this important mosquito and its enigmatic forms. A synthesis of genetic and ecological studies spanning 100+ years clarifies a striking latitudinal gradient - behaviorally divergent and reproductively isolated forms in northern Europe gradually break down into what appear to be well-mixed, intermediate populations in North Africa. Moreover, a continuous narrative thread dating back to the original description of form molestus in Egypt in 1775 refutes the popular idea that belowground mosquitoes in London evolved in situ from their aboveground counterparts. These enigmatic mosquitoes are more likely derived from populations in the Middle East, where human-biting and other adaptations to human environments may have evolved on the timescale of millennia rather than centuries. We outline several areas for future work and discuss the implications of these patterns for public health and for our understanding of urban adaptation in the Anthropocene.

A Theory of City Biogeography and the Origin of Urban Species

Many of the choices humans make with regard to infrastructure, urban planning and other phenomena have impacts that will last thousands of years. This can readily be seen in modern cities in which contemporary streets run along street grids that were laid out thousands of years prior or even in which ancient viaducts still play a role. However, rarely do evolutionary biologists explicitly consider the future of life likely to be associated with the decisions we are making today. Here, we consider the evolutionary future of species in cities with a focus on the origin of lineages and species. We do so by adjusting evolutionary predictions from the theory of island biogeography so as to correspond to the unique features of cities as islands. Specifically, the species endemic to cities tend to be associated with the gray habitats in cities. Those habitats tend to be dominated by human bodies, pet bodies and stored food. It is among such species where the origin of new lineages is most likely, although most research on evolution in cities has focused on green habitats. We conclude by considering a range of scenarios for the far future and their implications for the origin of lineages and species.

Ha Long—Cam Pha Cities Evolution Analysis Utilizing Remote Sensing Data

Socio-economic development has promoted the modification of land cover patterns in the coastal area of Ha Long, Cam Pha cities since the 1990s. The urban growth, together with intensive coal mining activities, has improved the life quality of residents. However, it has also caused many environmental problems in this region. Change detection techniques based on post-classification comparison were applied for monitoring the spatial and temporal evolution of land covers. The confusion matrix for 2001 and 2019 showed high overall accuracy (97.99%, 94.95%) and Kappa coefficient (0.97, 0.92), respectively. Statistics from classified images have revealed that man-made features increased by about 15.32%, while natural features, mangrove jungles, and water bodies decreased 10.64%, 1.96%, 2.72%, respectively, and urban evolution presents various dynamics, soft in the first period (1991–2001), but stronger in the second period (2001–2019) with different characteristics. The study also expresses the constraint of topographic and geologic resources, which have prevented the urban development in this coastal area. Such obtained results are very important for understanding interactions and relations between natural and human phenomena and they may help authorities by providing indicators and maps able to highlight necessary actions for sustainable development.

Detecting patterns of vertebrate biodiversity across the multidimensional urban landscape

Explicit characterisation of the complexity of urban landscapes is critical for understanding patterns of biodiversity and for detecting the underlying social and ecological processes that shape them. Urban environments exhibit variable heterogeneity and connectivity, influenced by different historical contingencies, that affect community assembly across scales. The multidimensional nature of urban disturbance and co-occurrence of multiple stressors can cause synergistic effects leading to nonlinear responses in populations and communities. Yet, current research design of urban ecology and evolutionary studies typically relies on simple representation of the parameter space that can be observed. Sampling approaches apply simple urban gradients such as linear transects in space or comparisons of urban sites across the urban mosaic accounting for a few variables. This rarely considers multiple dimensions and scales of biodiversity, and proves to be inadequate to explain observed patterns. We apply a multidimensional approach that integrates distinctive social, ecological and built characteristics of urban landscapes, representing variations along dimensions of heterogeneity, connectivity and historical contingency. Measuring species richness and beta diversity across 100 US metropolitan areas at the city and 1-km scales, we show that distinctive signatures of urban biodiversity can result from interactions between socioecological heterogeneity and connectivity, mediated by historical contingency.

Parallel evolution of urban-rural clines in melanism in a widespread mammal

Urbanization is the dominant trend of global land use change. The replicated nature of environmental change associated with urbanization should drive parallel evolution, yet insight into the repeatability of evolutionary processes in urban areas has been limited by a lack of multi-city studies. Here we leverage community science data on coat color in > 60,000 eastern gray squirrels (Sciurus carolinensis) across 43 North American cities to test for parallel clines in melanism, a genetically based trait associated with thermoregulation and crypsis. We show the prevalence of melanism was positively associated with urbanization as measured by impervious cover. Urban–rural clines in melanism were strongest in the largest cities with extensive forest cover and weakest or absent in cities with warmer winter temperatures, where thermal selection likely limits the prevalence of melanism. Our results suggest that novel traits can evolve in a highly repeatable manner among urban areas, modified by factors intrinsic to individual cities, including their size, land cover, and climate.

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.

Human-wildlife interactions: presence of the ground-nesting Spotted Thick-knee across a South African mosaic urban landscape

Urbanisation has increasingly encroached on numerous bird species' natural habitats, generally negatively affecting their persistence. Furthermore, increased human-wildlife interactions may benefit or be detrimental to the long term persistence of these species. The Spotted Thick-knee (Burhinus capensis), a ground-nesting species, persists in some mosaic urban landscapes in South Africa. We, therefore, assessed the presence of Spotted Thick-knees and their interactions with humans in the fragmented natural and human-modified landscape of Pietermaritzburg, KwaZulu-Natal. We conducted presence-only surveys at 52 locations between July 2019 and December 2020. 'Presence' locations for Spotted Thick-knee were identified via active surveying and public participation. Newspaper articles were distributed in June 2019, requesting information on Spotted Thick-knee sightings. Questionnaires were also sent to respondents to collect qualitative information regarding their perceptions and observations of this species in Pietermaritzburg. We established that the presence of Spotted Thick-knee's at known locations was not random. They were present at 30 out of 52 sites for 75% of this study's duration. Fewer sites had Spotted Thick-knees present during non-breeding months than breeding months. Respondents' feedback highlighted the pressures associated with Spotted Thick-knees persistence in human-modified mosaic landscapes, particularly predation and disturbance by domestic pets. Our study highlights that some ground-nesting birds, such as Spotted Thick-knees, persist in mosaic urban landscapes, despite the anthropogenic pressures. This study highlights the need to address the paucity of studies on ground-nesting birds in mosaic urban landscapes to determine general trends.

Supplementary information

The online version contains supplementary material available at 10.1007/s11252-022-01254-3.

Evolution in Cities

Although research performed in cities will not uncover new evolutionary mechanisms, it could provide unprecedented opportunities to examine the interplay of evolutionary forces in new ways and new avenues to address classic questions. However, while the variation within and among cities affords many opportunities to advance evolutionary biology research, careful alignment between how cities are used and the research questions being asked is necessary to maximize the insights that can be gained. In this review, we develop a framework to help guide alignment between urban evolution research approaches and questions. Using this framework, we highlight what has been accomplished to date in the field of urban evolution and identify several up-and-coming research directions for further expansion. We conclude that urban environments can be used as evolutionary test beds to tackle both new and long-standing questions in evolutionary biology.

Urbanization alters interactions between Darwin's finches and Tribulus cistoides on the Galápagos Islands

Emerging evidence suggests that humans shape the ecology and evolution of species interactions. Islands are particularly susceptible to anthropogenic disturbance due to the fragility of their ecosystems; however, we know little about the susceptibility of species interactions to urbanization on islands. To address this gap, we studied how the earliest stages of urban development affect interactions between Darwin's finches and its key food resource, Tribulus cistoides, in three towns on the Galápagos Islands. We measured variation in mericarp predation rates, mericarp morphology, and finch community composition using population surveys, experimental manipulations, and finch observations conducted in habitats within and outside of each town. We found that both seed and mericarp removal rates were higher in towns than natural habitats. We also found that selection on mericarp size and defense differed between habitats in the survey and experimental populations and that towns supported smaller and less diverse finch communities than natural habitats. Together, our results suggest that even moderate levels of urbanization can alter ecological interactions between Darwin's finches and T. cistoides, leading to modified natural selection on T. cistoides populations. Our study demonstrates that trophic interactions on islands may be susceptible to the anthropogenic disturbance associated with urbanization. Despite containing the highest diversity in the world, studies of urbanization are lacking from the tropics. Our study identified signatures of urbanization on species interactions in a tropical island ecosystem and suggests that changes to the ecology of species interactions has the potential to alter evolution in urban environments.

Bioindicator snake shows genomic signatures of natural and anthropogenic barriers to gene flow

Urbanisation alters landscapes, introduces wildlife to novel stressors, and fragments habitats into remnant 'islands'. Within these islands, isolated wildlife populations can experience genetic drift and subsequently suffer from inbreeding depression and reduced adaptive potential. The Western tiger snake (Notechis scutatus occidentalis) is a predator of wetlands in the Swan Coastal Plain, a unique bioregion that has suffered substantial degradation through the development of the city of Perth, Western Australia. Within the urban matrix, tiger snakes now only persist in a handful of wetlands where they are known to bioaccumulate a suite of contaminants, and have recently been suggested as a relevant bioindicator of ecosystem health. Here, we used genome-wide single nucleotide polymorphism (SNP) data to explore the contemporary population genomics of seven tiger snake populations across the urban matrix. Specifically, we used population genomic structure and diversity, effective population sizes (Ne), and heterozygosity-fitness correlations to assess fitness of each population with respect to urbanisation. We found that population genomic structure was strongest across the northern and southern sides of a major river system, with the northern cluster of populations exhibiting lower heterozygosities than the southern cluster, likely due to a lack of historical gene flow. We also observed an increasing signal of inbreeding and genetic drift with increasing geographic isolation due to urbanisation. Effective population sizes (Ne) at most sites were small (< 100), with Ne appearing to reflect the area of available habitat rather than the degree of adjacent urbanisation. This suggests that ecosystem management and restoration may be the best method to buffer the further loss of genetic diversity in urban wetlands. If tiger snake populations continue to decline in urban areas, our results provide a baseline measure of genomic diversity, as well as highlighting which 'islands' of habitat are most in need of management and protection.

Phenotypic variation in urban environments: mechanisms and implications

In the past decade, numerous studies have explored how urbanisation affects the mean phenotypes of populations, but it remains unknown how urbanisation impacts phenotypic variation, a key target of selection that shapes, and is shaped by, eco-evolutionary processes. Our review suggests that urbanisation may often increase intraspecific phenotypic variation through several processes; a conclusion aligned with results from our illustrative analysis on tit morphology across 13 European city/forest population pairs. Urban-driven changes in phenotypic variation will have immense implications for urban populations and communities, particularly through urbanisation's effects on individual fitness, species interactions, and conservation. We call here for studies that incorporate phenotypic variation in urban eco-evolutionary research alongside advances in theory.

Urbanisation weakens selection on the timing of breeding and clutch size in blue tits but not in great tits

Abstract

Urbanisation is a globally occurring phenomenon and is predicted to continue increasing rapidly. Urban ecosystems present novel environments and challenges which species must acclimate or adapt to. These novel challenges alter existing or create new selection pressures on behaviours which provide an opportunity to investigate eco-evolutionary responses to contemporary environmental change. We used 7 years of breeding data from urban and forest populations of blue and great tits to understand whether selection for timing of breeding or clutch size differed between the two habitats and species. We found that urban great tits laid eggs earlier than their forest counterparts, but there was no evidence of a difference in selection for earlier breeding. Blue tits, however, did not differ in timing of egg laying between the two habitats, but selection for earlier laying was weaker in the urban environment. Both species laid smaller clutches in the urban site and had positive selection for larger clutch sizes which did not differ in strength for the great tits but did for blue tits, with weaker selection in the urban population. Our results suggest that food availability for nestlings may be constraining urban birds, and that the temporal cues females use to time breeding correctly, such as tree budburst and food availability, may be absent or reduced in urban areas due to lower caterpillar availability. These results have implications for our understanding of the adaptation of wild animals to city life.

Significance statement

Urbanisation is expanding rapidly and changing the environment many species live in. A key challenge is to understand how species adapt to the urban environment, why some species can adapt, why others cannot and what we can do to ensure that cities are ecologically sustainable and biodiversity rich. Here we show that the strength of natural selection for early breeding and larger clutch size is weaker in urban than non-urban blue tits, likely due to reduced and irregular availability of natural insect food in urban areas. This effect was not found in great tits. Thus, urbanisation can alter the selection pressures wild animals are exposed to, but this effect may differ between species, even when closely related. This has implications for our understanding of how species adapt to urban life.

Growing up in a new world: trait divergence between rural, urban, and invasive populations of an amphibian urban invader

Cities are focal points of introduction for invasive species. Urban evolution might facilitate the success of invasive species in recipient urban habitats. Here we test this hypothesis by rearing tadpoles of a successful amphibian urban coloniser and invader in a common garden environment. We compared growth rate, morphological traits, swimming performance, and developmental rate of guttural toad tadpoles (Sclerophrys gutturalis) from native rural, native urban, and non-native urban habitats. By measuring these traits across ontogeny, we were also able to compare divergence across different origins as the tadpoles develop. The tadpoles of non-native urban origin showed significantly slower developmental rate (e.g., the proportion of tadpoles reaching Gosner stage 31 or higher was lower at age 40 days) than tadpoles of native urban origin. Yet, tadpoles did not differ in growth rate or any morphological or performance trait examined, and none of these traits showed divergent ontogenetic changes between tadpoles of different origin. These findings suggest that prior adaptation to urban habitats in larval traits likely does not play an important role in facilitating the invasion success of guttural toads into other urban habitats. Instead, we suggest that evolutionary changes in larval traits after colonization (e.g., developmental rate), together with decoupling of other traits and phenotypic plasticity might explain how this species succeeded in colonising extra-limital urban habitats.