A global horizon scan for urban evolutionary ecology

Were bed bugs the first urban pest insect? Genome-wide patterns of bed bug demography mirror global human expansion

There are calls for research into the historical evolutionary relationships between humans and their commensals, as it would greatly inform models that predict the spread of pests and diseases under urban population expansion. The earliest civilizations emerged approximately 10 000 years ago and created conditions ideal for the establishment and spread of commensal urban pests. Commensal relations between humans and pests likely emerged with these early civilizations; however, for most species (e.g. German cockroach and black rat), these relationships have formed relatively recently-within the last 5000 years-raising the question of whether others could have emerged earlier. Following comparative whole genome analysis of bed bugs, Cimex lectularius, belonging to two genetically distinct lineages, one associated with bats and the other with humans, coupled with demographic modelling, our findings suggests that while their association with humans dates back potentially hundreds of thousands of years, a dramatic change in the effective population size of the human-associated lineage occurred approximately 13 000 years ago; a pattern not found in the bat-associated lineage. The timing and magnitude of the demographic patterns provide compelling evidence that the human-associated lineage closely tracked the demographic history of modern humans and their movement into the first cities. As such, bed bugs may represent the first true urban pest insect species.

Genetic responses of plants to urban environmental challenges

MAIN CONCLUSION

This review aims to describe the main genetic adaptations of plants to abiotic and biotic stressors in urban landscapes through modulation of gene expression and genotypic changes. Urbanization deeply impacts biodiversity through ecosystem alteration and habitat fragmentation, creating novel environmental challenges for plant species. Plants have evolved cellular, molecular, and biochemical strategies to cope with the diverse biotic and abiotic stresses associated with urbanization. However, many of these defense and resistance mechanisms remain poorly understood. Addressing these knowledge gaps is crucial for advancing our understanding of urban biodiversity and elucidating the ecological and evolutionary dynamics of species in urban landscapes. As sessile organisms, plants depend heavily on modifications in gene expression as a rapid and efficient strategy to survive urban stressors. At the same time, the urban environment pressures induced plant species to evolve genotypic adaptations that enhance their survival and growth in these contexts. This review explores the different genetic responses of plants to urbanization. We focus on key abiotic challenges, such as air pollution, elevated CO2 levels, heavy metal contamination, heat and drought stress, salinity, and biotic stresses caused by herbivorous insects. By examining these genetic mechanisms induced by urban stressors, we aim to analyze the molecular pathways and genetic patterns underlying the adaptation of plant species to urban environments. This knowledge is a valuable tool for enhancing the selection and propagation of adaptive traits in plant populations, supporting species conservation efforts, and promoting urban biodiversity.

Data on the diet and nutrition of urban and rural bumblebees

Land-use changes, driven by agricultural intensification and urbanization, are major contributors to biodiversity loss, altering habitats and reducing available resources. These changes impact species' foraging strategies, particularly in human-modified ecosystems. While dietary shifts due to land-use changes have been well-studied in vertebrates, similar research in invertebrates, such as wild bees, remains limited. The present data paper provides a comprehensive dataset on the pollen collected from urban and rural populations of two bumblebee species (Bombus lapidarius and B. pascuorum) in Switzerland, examining pollen composition, nutrient content, and diet breadth. Additionally, by analyzing pollen from both body and leg-baskets, the dataset also offers a comprehensive overview of plant-bumblebee interactions. The data help understand plant-bumblebee interactions, pollination services, nutritional supply to larvae, and the impact of land-use changes on these processes. Furthermore, the dataset can be integrated with existing plant trait data to explore the effects of non-native species and other ecological factors on bumblebee foraging and nutrition in anthropogenically modified landscapes.

Spatio-temporal hotspots of wildlife-vehicle collisions in Poland: How congruent are mammals, birds, reptiles and amphibians?

The Polish Roadkill Observation System (PROS) database, a large dataset of roadkills collected between 2000 and 2022 in Poland, was used. We calculated the total length for each road type and the main type of environment around the wildlife-vehicle collision (WVC) event, in a grid of 10 × 10 km (e.g., spatial unit). We explored the spatial congruence in WVCs among amphibians, reptiles, birds and mammals across the country, using spatially explicit correlation based on the Mantel tests. We used a) Generalized Linear Mixed Models to investigate the association between WVC and the type of dominant environment and animal group, and b) Generalized Boosted Regression Models to investigate, separately for each animal group, the association between WVC and the length and type of road in each spatial unit. A total of 19,846 roadkills were recorded in Poland, involving 28,952 individuals from different animal species: 14 amphibians, 8 reptiles, 133 birds and 52 mammals. The spatial distribution of roadkill events in the country was mainly clustered around the biggest cities. Hotspots were concentrated near cities (Warsaw, Kraków, Rrzeszów) and in areas known for high biodiversity. Coldspots - relatively smaller than hotspots - were areas characterized by a high density of housing infrastructure, with lower naturality and a predominance of single roadkill casualties. A higher spatial congruence in WVC was found between birds and mammals (71 %) than between the other animal groups. Overall, the animal group less congruent with the other groups was amphibians (13 %), while birds were most congruent with all groups. We discussed some advantages and drawbacks when working with non-systematic survey datasets of roadkills. Finally, we recommended including roadkill clusters of multiple animal groups (hotspots) in strategies for mitigating wildlife-vehicle collisions but also considering more specific strategies, which can combine the type of environment and roads, concerning each animal group.

Complex patterns of morphological diversity across multiple populations of an urban bird species

Urbanization presents a natural evolutionary experiment because selection pressures in cities can be strongly mismatched with those found in species' historic habitats. However, some species have managed to adapt and even thrive in these novel conditions. When a species persists across multiple cities, a fundamental question arises: do we see similar traits evolve in similar novel environments? By testing if and how similar phenotypes emerge across multiple urban populations, we can begin to assess the predictability of population response to anthropogenic change. Here, we examine variation within and across multiple populations of a songbird, the dark-eyed junco (Junco hyemalis). We measured morphological variations in juncos across urban and nonurban populations in Southern California. We investigated whether the variations we observed were due to differences in environmental conditions across cities. Bill shape differed across urban populations; Los Angeles and Santa Barbara juncos had shorter, deeper bills than nonurban juncos, but San Diego juncos did not. On the other hand, wing length decreased with the built environment, regardless of the population. Southern Californian urban juncos exhibit both similarities and differences in morphological traits. Studying multiple urban populations can help us determine the predictability of phenotypic evolutionary responses to novel environments.

Neopolyploidy increases stress tolerance and reduces fitness plasticity across multiple urban pollutants: support for the "general-purpose" genotype hypothesis

Whole-genome duplication is a common macromutation with extensive impacts on gene expression, cellular function, and whole-organism phenotype. As a result, it has been proposed that polyploids have "general-purpose" genotypes that perform better than their diploid progenitors under stressful conditions. Here, we test this hypothesis in the context of stresses presented by anthropogenic pollutants. Specifically, we tested how multiple neotetraploid genetic lineages of the mostly asexually reproducing greater duckweed (Spirodela polyrhiza) perform across a favorable control environment and 5 urban pollutants (iron, salt, manganese, copper, and aluminum). By quantifying the population growth rate of asexually reproducing duckweed over multiple generations, we found that across most pollutants, but not all, polyploidy decreased the growth rate of actively growing propagules but increased that of dormant ones. Yet, when considering total propagule production, polyploidy increased tolerance to most pollutants, and polyploids maintained population-level fitness across pollutants better than diploids. Furthermore, broad-sense genetic correlations in growth rate among pollutants were all positive in neopolyploids but not so for diploids. Our results provide a rare test and support for the hypothesis that polyploids are more tolerant of stressful conditions and can maintain fitness better than diploids across heterogeneous stresses. These results may help predict that polyploids may be likely to persist in stressful environments, such as those caused by urbanization and other human activities.

Effects of urban-induced mutations on ecology, evolution and health

Increasing evidence suggests that urbanization is associated with higher mutation rates, which can affect the health and evolution of organisms that inhabit cities. Elevated pollution levels in urban areas can induce DNA damage, leading to de novo mutations. Studies on mutations induced by urban pollution are most prevalent in humans and microorganisms, whereas studies of non-human eukaryotes are rare, even though increased mutation rates have the potential to affect organisms and their populations in contemporary time. Our Perspective explores how higher mutation rates in urban environments could impact the fitness, ecology and evolution of populations. Most mutations will be neutral or deleterious, and higher mutation rates associated with elevated pollution in urban populations can increase the risk of cancer in humans and potentially other species. We highlight the potential for urban-driven increased deleterious mutational loads in some organisms, which could lead to a decline in population growth of a wide diversity of organisms. Although beneficial mutations are expected to be rare, we argue that higher mutation rates in urban areas could influence adaptive evolution, especially in organisms with short generation times. Finally, we explore avenues for future research to better understand the effects of urban-induced mutations on the fitness, ecology and evolution of city-dwelling organisms.

Online toolkits for collaborative and inclusive global research in urban evolutionary ecology

Urban evolutionary ecology is inherently interdisciplinary. Moreover, it is a field with global significance. However, bringing researchers and resources together across fields and countries is challenging. Therefore, an online collaborative research hub, where common methods and best practices are shared among scientists from diverse geographic, ethnic, and career backgrounds would make research focused on urban evolutionary ecology more inclusive. Here, we describe a freely available online research hub for toolkits that facilitate global research in urban evolutionary ecology. We provide rationales and descriptions of toolkits for: (1) decolonizing urban evolutionary ecology; (2) identifying and fostering international collaborative partnerships; (3) common methods and freely-available datasets for trait mapping across cities; (4) common methods and freely-available datasets for cross-city evolutionary ecology experiments; and (5) best practices and freely available resources for public outreach and communication of research findings in urban evolutionary ecology. We outline how the toolkits can be accessed, archived, and modified over time in order to sustain long-term global research that will advance our understanding of 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.

Coping with light pollution in urban environments: Patterns and challenges

Artificial light at night is a growing environmental problem that is especially pronounced in urban environments. Yet, impacts on urban wildlife have received scant attention and patterns and consequences are largely unknown. Here, I present a conceptual framework outlining the challenges species encounter when exposed to urban light pollution and how they may respond through plastic adjustments and genetic adaptation. Light pollution interferes with biological rhythms, influences behaviors, fragments habitats, and alters predation risk and resource abundance, which changes the diversity and spatiotemporal distribution of species and, hence, the structure and function of urban ecosystems. Furthermore, light pollution interacts with other urban disturbances, which can exacerbate negative effects on species. Given the rapid growth of urban areas and light pollution and the importance of healthy urban ecosystems for human wellbeing, more research is needed on the impacts of light pollution on species and the consequences for urban ecosystems.

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'.

Urban living can rescue Darwin's finches from the lethal effects of invasive vampire flies

Human activity changes multiple factors in the environment, which can have positive or negative synergistic effects on organisms. However, few studies have explored the causal effects of multiple anthropogenic factors, such as urbanization and invasive species, on animals and the mechanisms that mediate these interactions. This study examines the influence of urbanization on the detrimental effect of invasive avian vampire flies (Philornis downsi) on endemic Darwin's finches in the Galápagos Islands. We experimentally manipulated nest fly abundance in urban and non-urban locations and then characterized nestling health, fledging success, diet, and gene expression patterns related to host defense. Fledging success of non-parasitized nestlings from urban (79%) and non-urban (75%) nests did not differ significantly. However, parasitized, non-urban nestlings lost more blood, and fewer nestlings survived (8%) compared to urban nestlings (50%). Stable isotopic values (δ15 N) from urban nestling feces were higher than those from non-urban nestlings, suggesting that urban nestlings are consuming more protein. δ15 N values correlated negatively with parasite abundance, which suggests that diet might influence host defenses (e.g., tolerance and resistance). Parasitized, urban nestlings differentially expressed genes within pathways associated with red blood cell production (tolerance) and pro-inflammatory response (innate immunological resistance), compared to parasitized, non-urban nestlings. In contrast, parasitized non-urban nestlings differentially expressed genes within pathways associated with immunoglobulin production (adaptive immunological resistance). Our results suggest that urban nestlings are investing more in pro-inflammatory responses to resist parasites but also recovering more blood cells to tolerate blood loss. Although non-urban nestlings are mounting an adaptive immune response, it is likely a last effort by the immune system rather than an effective defense against avian vampire flies since few nestlings survived.

Maximum temperatures determine the habitat affiliations of North American mammals

Addressing the ongoing biodiversity crisis requires identifying the winners and losers of global change. Species are often categorized based on how they respond to habitat loss; for example, species restricted to natural environments, those that most often occur in anthropogenic habitats, and generalists that do well in both. However, species might switch habitat affiliations across time and space: an organism may venture into human-modified areas in benign regions but retreat into thermally buffered forested habitats in areas with high temperatures. Here, we apply community occupancy models to a large-scale camera trapping dataset with 29 mammal species distributed over 2,485 sites across the continental United States, to ask three questions. First, are species' responses to forest and anthropogenic habitats consistent across continental scales? Second, do macroclimatic conditions explain spatial variation in species responses to land use? Third, can species traits elucidate which taxa are most likely to show climate-dependent habitat associations? We found that all species exhibited significant spatial variation in how they respond to land-use, tending to avoid anthropogenic areas and increasingly use forests in hotter regions. In the hottest regions, species occupancy was 50% higher in forested compared to open habitats, whereas in the coldest regions, the trend reversed. Larger species with larger ranges, herbivores, and primary predators were more likely to change their habitat affiliations than top predators, which consistently affiliated with high forest cover. Our findings suggest that climatic conditions influence species' space-use and that maintaining forest cover can help protect mammals from warming climates.

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.

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.

Brood parasitism risk drives birds to breed near humans

Urbanization is transforming ecosystems at a global scale and at an increasing rate,^1,2 and its profound consequences for wildlife have been well documented.^3,4,5,6 Understanding how animals thrive in the urban environment and how this environment affects (co-)evolutionary processes remains an important challenge.⁷ Urban environments can provide resources such as food or nest sites (e.g., cavities)^10,8,9 and also reduce exposure to predators.^11,12 For some species, urban environments may also affect susceptibility to brood parasitism,^13,14 but this has never been tested experimentally. Here, we use a combination of field observations and experimental manipulations to show that Daurian redstarts, Phoenicurus auroreus, a common host of the common cuckoo, Cuculus canorus, nest in proximity to humans to avoid brood parasitism. First, redstarts were more likely to be parasitized with increasing distance to the nearest building. Second, redstarts adjusted their nesting location in response to a seasonally predictable change in the risk of brood parasitism. Third, experimentally simulating the presence of cuckoos during a period when they are naturally absent increased the likelihood that redstarts nested indoors or closer to human settlements. These findings suggest that redstarts actively choose to place their nest in the vicinity of a human residence as a defense against cuckoos. Our study exemplifies how animals take advantage of the urban environment by using it as a novel line of defense against detrimental interspecific interactions.

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.