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

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.

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

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

The effects of urban life on animal immunity: Adaptations and constraints

Land transformation, including urbanization, is a dominant form of anthropogenic change to the global environment at the dawn of the Anthropocene epoch. More and more species are brought into direct contact with humans, being either required to develop broad-scale adaptations to urban environment or filtered out from urbanized areas. While behavioural or physiological adaptations are at the forefront of urban biology research, there is accumulating evidence for divergent pathogen pressure across urbanization gradients, requiring adjustments in host immune function. At the same time, host immunity may be constrained by unfavourable components of an urban environment, such as poor-quality food resources, disturbance, or pollution. Here, I reviewed existing evidence for adaptations and constrains in the immune system of urban animals, focusing on the recent implementation of metabarcoding, genomic, transcriptomic, and epigenomic approaches in urban biology research. I show that spatial variation in pathogen pressure across urban and non-urban landscapes is highly complex and may be context-dependent, but there is solid evidence for pathogen-driven immunostimulation in urban-dwelling animals. I also show that genes coding for molecules directly involved in interactions with pathogens are the prime candidates for immunogenetic adaptations to urban life. Evidence emerging from landscape genomics and transcriptomics show that immune adaptations to urban life may have a polygenic nature, but immune traits may not be among the key biological functions experiencing broad-scale microevolutionary changes in response to urbanization. Finally, I provided recommendations for future research, including i) a better integration of different 'omic' approaches to obtain a more complete picture of immune adaptations to urban life in non-model animal taxa, ii) quantification of fitness landscapes for immune phenotypes and genotypes across urbanization gradient, and iii) much broader taxonomic coverage (including invertebrates) necessary to draw more robust conclusions on how general (or taxa-specific) are immune responses of animals to urbanization.

Urbanization is associated with non-coding polymorphisms in candidate behavioural genes in the Eurasian coot

Extensive transformation of natural land cover into urbanized areas enhances accumulation of phenotypic differences between animals from urban and nonurban populations, but there is little information on whether these changes, especially in terms of animal behaviour and circadian rhythm, have a genetic basis. The aim of this study was to investigate genetic background of behavioural differences between four pairs of urban and nonurban populations of a common waterbird, the Eurasian coot Fulica atra. For this purpose, we quantified polymorphisms in personality-related candidate genes, previously reported to be associated with avian circadian rhythms and behavioural traits that may be crucial for urban life. We found general associations between landscape urbanization level and polymorphisms in 3'UTR region of CREB1 gene encoding transcriptional factor, which participates in development of cognitive functions and regulation of circadian rhythm. We also found significant differentiation between urban and nonurban populations in the intronic region of CKIɛ gene responsible for regulation of circadian clock. Although we lacked evidence for linkage of this intronic variation with coding polymorphisms, genetic differentiation between urban populations was significantly stronger at CKIɛ intron compared with neutral microsatellite markers, suggesting possible local adaptations of CKIɛ expression regulation to specific urban sites. Our results indicate that behavioural differentiation between urban and nonurban coot populations may be the effect of habitat-specific selective pressure resulting in genetic adaptations to urban environment and supporting the microevolutionary scenario. These adaptations, however, prevailed in non-coding regulatory rather than coding gene regions and showed either general or local patterns, revealing high complexity of associations between behaviour and landscape urbanization in birds.

Snake life history traits and their association with urban habitat use in a tropical city

Urbanisation changes landscapes, often simplifying and homogenising natural ecosystems while introducing novel environments. Although this transformation often adversely impacts native wildlife, generalist species that exhibit broad dietary and habitat requirements can persist and take advantage of urban environments. To understand which life history traits most influence the occurrence of a diverse snake assemblage in an urban environment, we leveraged a dataset of 5102 detection records for 12 snake species in the tropical city of Darwin, Australia. By building ecological niche models, calculating urban niche hypervolume, and compiling life history data, we analysed the diversity of environments occupied by each species and determined which landscape components were most associated with occurrence data. In keeping with our hypothesis that generalist species would be more successful, we found that species with broader habitat and dietary preferences, as well as a penchant for arboreality, were associated with larger urban niche hypervolumes and more frequent human–snake interactions. Additionally, we found that colubrid snakes had significantly larger urban niche hypervolumes than elapid species. These findings contribute to understanding how life history traits aid wildlife persistence in, and adaptation to, urban ecosystems, and have implications for landscape design and conservation management.

Genetic structure in neotropical birds with different tolerance to urbanization

Gene flow in birds can be affected by urbanization depending on natural history traits and adaptability to habitat change. Contrasting results can be expected when comparing species with opposite resilience to urbanization. In this study, we assessed genetic diversity and structure for two bird species, the urban avoider white-eared ground-sparrow, Melozone leucotis, and the urban dweller house wren Troglodytes aedon. We used seven microsatellite loci and sampled five locations with differing levels of urbanization in Costa Rica. We found considerably higher genetic structure in white-eared ground-sparrows than in house wrens. Circuit theory analyses proved a higher isolation from urban resistance for the white-eared ground-sparrow than for house wrens. These results support that urbanization is a significant barrier for gene flow in urban avoiders, in contrast to urban dweller species that showed little to no impact. Differences could be attributed to a higher plasticity in habitat and nesting site preferences in the house wren, and significant dispersal limitation for the white-eared ground-sparrow. These results emphasize the need for conservation strategies towards white-eared ground-sparrows and other urban avoider species whose habitat and connectivity have been reduced by the recent urban expansion.

Epigenetics in Ecology, Evolution, and Conservation

Epigenetic variation is often characterized by modifications to DNA that do not alter the underlying nucleotide sequence, but can influence behavior, morphology, and physiological phenotypes by affecting gene expression and protein synthesis. In this review, we consider how the emerging field of ecological epigenetics (eco-epi) aims to use epigenetic variation to explain ecologically relevant phenotypic variation and predict evolutionary trajectories that are important in conservation. Here, we focus on how epigenetic data have contributed to our understanding of wild populations, including plants, animals, and fungi. First, we identified published eco-epi literature and found that there was limited taxonomic and ecosystem coverage and that, by necessity of available technology, these studies have most often focused on the summarized epigenome rather than locus- or nucleotide-level epigenome characteristics. We also found that while many studies focused on adaptation and heritability of the epigenome, the field has thematically expanded into topics such as disease ecology and epigenome-based ageing of individuals. In the second part of our synthesis, we discuss key insights that have emerged from the epigenetic field broadly and use these to preview the path toward integration of epigenetics into ecology. Specifically, we suggest moving focus to nucleotide-level differences in the epigenome rather than whole-epigenome data and that we incorporate several facets of epigenome characterization (e.g., methylation, chromatin structure). Finally, we also suggest that incorporation of behavior and stress data will be critical to the process of fully integrating eco-epi data into ecology, conservation, and evolutionary biology.

Stress-induced changes in body surface temperature are repeatable, but do not differ between urban and rural birds

Urbanisation can alter local microclimates, thus creating new thermal challenges for resident species. However, urban environments also present residents with frequent, novel stressors (e.g., noise, human interaction) which may demand investment in costly, self-preserving responses (e.g., the fight-or-flight response). One way that urban residents might cope with this combination of demands is by using regional heterothermy to reduce costs of thermoregulation during the stress response. In this study, we used black-capped chickadees (n_urban = 9; n_rural = 10) to test whether known heterothermic responses to stress exposure (here, at the bare skin around the eye): (1) varied consistently among individuals (i.e., were repeatable), and (2) were most pronounced among urban individuals compared with rural individuals. Further, to gather evidence for selection on stress-induced heterothermic responses in urban settings, we tested: (3) whether repeatability of this response was lower among birds sampled from urban environments compared with those sampled from rural environments. For the first time, we show that heterothermic responses to stress exposures (i.e. changes in body surface temperature) were highly repeatable across chronic time periods (R = 0.58) but not acute time periods (R = 0.13). However, we also show that these responses did not differ between urban and rural birds, nor were our repeatability estimates any lower in our urban sample. Thus, while regional heterothermy during stress exposure may provide energetic benefits to some, but not all, individuals, enhanced use of this response to cope with urban pressures appears unlikely in our study species.

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.

Genomic and common garden approaches yield complementary results for quantifying environmental drivers of local adaptation in rubber rabbitbrush, a foundational Great Basin shrub

The spatial structure of genomic and phenotypic variation across populations reflects historical and demographic processes as well as evolution via natural selection. Characterizing such variation can provide an important perspective for understanding the evolutionary consequences of changing climate and for guiding ecological restoration. While evidence for local adaptation has been traditionally evaluated using phenotypic data, modern methods for generating and analyzing landscape genomic data can directly quantify local adaptation by associating allelic variation with environmental variation. Here, we analyze both genomic and phenotypic variation of rubber rabbitbrush (Ericameria nauseosa), a foundational shrub species of western North America. To quantify landscape genomic structure and provide perspective on patterns of local adaptation, we generated reduced representation sequencing data for 17 wild populations (222 individuals; 38,615 loci) spanning a range of environmental conditions. Population genetic analyses illustrated pronounced landscape genomic structure jointly shaped by geography and environment. Genetic-environment association (GEA) analyses using both redundancy analysis (RDA) and a machine-learning approach (Gradient Forest) indicated environmental variables (precipitation seasonality, slope, aspect, elevation, and annual precipitation) influenced spatial genomic structure and were correlated with allele frequency shifts indicative of local adaptation at a consistent set of genomic regions. We compared our GEA-based inference of local adaptation with phenotypic data collected by growing seeds from each population in a greenhouse common garden. Population differentiation in seed weight, emergence, and seedling traits was associated with environmental variables (e.g., precipitation seasonality) that were also implicated in GEA analyses, suggesting complementary conclusions about the drivers of local adaptation across different methods and data sources. Our results provide a baseline understanding of spatial genomic structure for E. nauseosa across the western Great Basin and illustrate the utility of GEA analyses for detecting the environmental causes and genetic signatures of local adaptation in a widely distributed plant species of restoration significance.

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.

Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe

Urbanisation is increasing worldwide, and there is now ample evidence of phenotypic changes in wild organisms in response to this novel environment. Yet, the genetic changes and genomic architecture underlying these adaptations are poorly understood. Here, we genotype 192 great tits (Parus major) from nine European cities, each paired with an adjacent rural site, to address this major knowledge gap in our understanding of wildlife urban adaptation. We find that a combination of polygenic allele frequency shifts and recurrent selective sweeps are associated with the adaptation of great tits to urban environments. While haplotypes under selection are rarely shared across urban populations, selective sweeps occur within the same genes, mostly linked to neural function and development. Collectively, we show that urban adaptation in a widespread songbird occurs through unique and shared selective sweeps in a core-set of behaviour-linked genes.

Genetic structure of urban and non-urban populations differs between two common parid species

Landscape conversions induced by human activities can affect dispersal patterns of various bird species and, as a result, affect genetic structure of their populations. Genetic differentiation of bird populations may be enhanced by habitat variation, especially in urban-non-urban systems. The majority of population genetic studies focus on single species, which inflicts limitations for direct comparisons of genetic responses of avian populations to urbanization. Here, we used a set of microsatellite markers to examine genetic diversity, gene flow and population structure in two common parid species, great tits Parus major and blue tits Cyanistes caeruleus occupying three sites in habitats with contrasting urbanization level in central Poland. We found low but significant divergence of urban park population with both suburban and non-urban forest great tit populations, while no differentiation was found between suburban forest and non-urban forest populations. In contrast, no evidence for genetic differentiation was found between blue tit populations from the urban park, suburban forest and non-urban forest sites. We conclude that great tits and blue tits respond to urbanization-related changes in a different way, which may be a result of different rates of migration and/or dispersal, likely higher in blue tits. Some impact may be also induced by interspecific competition. We suggest that changing the focus of urban genetic research from single to multiple species may provide novel insights into how natural populations respond to the processes of urbanization.

Urban living influences the nesting success of Darwin's finches in the Galápagos Islands

Urbanization is expanding worldwide with major consequences for organisms. Anthropogenic factors can reduce the fitness of animals but may have benefits, such as consistent human food availability. Understanding anthropogenic trade-offs is critical in environments with variable levels of natural food availability, such as the Galápagos Islands, an area of rapid urbanization. For example, during dry years, the reproductive success of bird species, such as Darwin's finches, is low because reduced precipitation impacts food availability. Urban areas provide supplemental human food to finches, which could improve their reproductive success during years with low natural food availability. However, urban finches might face trade-offs, such as the incorporation of anthropogenic debris (e.g., string, plastic) into their nests, which may increase mortality. In our study, we determined the effect of urbanization on the nesting success of small ground finches (Geospiza fuliginosa; a species of Darwin's finch) during a dry year on San Cristóbal Island. We quantified nest building, egg laying and hatching, and fledging in an urban and nonurban area and characterized the anthropogenic debris in nests. We also documented mortalities including nest trash-related deaths and whether anthropogenic materials directly led to entanglement- or ingestion-related nest mortalities. Overall, urban finches built more nests, laid more eggs, and produced more fledglings than nonurban finches. However, every nest in the urban area contained anthropogenic material, which resulted in 18% nestling mortality while nonurban nests had no anthropogenic debris. Our study showed that urban living has trade-offs: urban birds have overall higher nesting success during a dry year than nonurban birds, but urban birds can suffer mortality from anthropogenic-related nest-materials. These results suggest that despite potential costs, finches benefit overall from urban living and urbanization may buffer the effects of limited resource availability in the Galápagos Islands.

Scale-dependent signatures of local adaptation in a foundation tree species

Understanding local adaptation is critical for conservation management under rapidly changing environmental conditions. Local adaptation inferred from genotype-environment associations may show different genomic patterns depending on the spatial scale of sampling, due to differences in the slope of environmental gradients and the level of gene flow. We compared signatures of local adaptation across the genome of mountain ash (Eucalyptus regnans) at two spatial scales: A species-wide data set and a topographically-complex subregional data set. We genotyped 367 individual trees at over 3700 single-nucleotide polymorphisms (SNPs), quantified patterns of spatial genetic structure among populations, and used two analytical methods to identify loci associated with at least one of three environmental variables at each spatial scale. Together, the analyses identified 549 potentially adaptive SNPs at the subregion scale, and 435 SNPs at the range-wide scale. A total of 39 genic or near-genic SNPs, associated with 28 genes, were identified at both spatial scales, although no SNP was identified by both methods at both scales. We observed that nongenic regions had significantly higher homozygote excess than genic regions, possibly due to selective elimination of inbred genotypes during stand development. Our results suggest that strong environmental selection occurs in mountain ash, and that the identification of putatively adaptive loci can differ substantially depending on the spatial scale of analyses. We also highlight the importance of multiple adaptive genetic architectures for understanding patterns of local adaptation across large heterogenous landscapes, with comparison of putatively adaptive loci among spatial scales providing crucial insights into the process of adaptation.

Rapid changes in DNA methylation associated with the initiation of reproduction in a small songbird

Species with a circannual life cycle need to match the timing of their life history events to the environment to maximize fitness. However, our understanding of how circannual traits such as timing of reproduction are regulated on a molecular level remains limited. Recent studies have implicated that epigenetic mechanisms can be an important part in the processes that regulate circannual traits. Here, we explore the role of DNA methylation in mediating reproductive timing in a seasonally breeding bird species, the great tit (Parus major), using genome‐wide DNA methylation data from individual females that were blood sampled repeatedly throughout the breeding season. We demonstrate rapid and directional changes in DNA methylation within the promoter region of several genes, including a key transcription factor (NR5A1) known from earlier studies to be involved in the initiation of timing of reproduction. Interestingly, the observed changes in DNA methylation at NR5A1 identified here are in line with earlier gene expression studies of reproduction in chicken, indicating that the observed shifts in DNA methylation at this gene can have a regulatory role. Our findings provide an important step towards elucidating the genomic mechanism that mediates seasonal timing of a key life history traits and provide support for the idea that epigenetic mechanisms may play an important role in circannual traits.

see also the Perspective by Melanie J. Heckwolf and Britta S. Meyer

Genomic evidence for parallel adaptation to cities

Urban evolutionary biology is the study of rapid evolutionary change in response to humans and our uses of land to support city dwellers. Because cities are relatively modern additions to the natural world, research on urban evolution tends to focus on microevolutionary change that has happened across a few to many hundreds of generations. These questions still fall under the broad purview of evolutionary ecology. However, the severity, rapidity and replication of environmental changes that drive evolution in this context make it worthy of specific attention. Urban evolution provides the opportunity to study the earliest stages of evolution in a context that is scientifically interesting and societally important. The newness of urban populations and their proximity to natural populations also creates challenges when trying to detect population genetic change. In a From the Cover article in this issue of Molecular Ecology, Mueller et al. use whole genome resequencing data to address some of these challenges while exploring genetic changes associated with urbanization in three replicate urban-rural burrowing owl (Athene cunicularia) populations. Combining multiple approaches across these sample sites Mueller et al. find evidence for selection on genes whose function is related to synapses, neuron projections, brain connectivity and cognitive function in general. That selection was parallel suggests that phenotypes related to brain processes were probably particularly important for urban adaptation.

The Complexity of Urban Eco-evolutionary Dynamics

Urbanization is changing Earth's ecosystems by altering the interactions and feedbacks between the fundamental ecological and evolutionary processes that maintain life. Humans in cities alter the eco-evolutionary play by simultaneously changing both the actors and the stage on which the eco-evolutionary play takes place. Urbanization modifies land surfaces, microclimates, habitat connectivity, ecological networks, food webs, species diversity, and species composition. These environmental changes can lead to changes in phenotypic, genetic, and cultural makeup of wild populations that have important consequences for ecosystem function and the essential services that nature provides to human society, such as nutrient cycling, pollination, seed dispersal, food production, and water and air purification. Understanding and monitoring urbanization-induced evolutionary changes is important to inform strategies to achieve sustainability. In the present article, we propose that understanding these dynamics requires rigorous characterization of urbanizing regions as rapidly evolving, tightly coupled human–natural systems. We explore how the emergent properties of urbanization affect eco-evolutionary dynamics across space and time. We identify five key urban drivers of change—habitat modification, connectivity, heterogeneity, novel disturbances, and biotic interactions—and highlight the direct consequences of urbanization-driven eco-evolutionary change for nature's contributions to people. Then, we explore five emerging complexities—landscape complexity, urban discontinuities, socio-ecological heterogeneity, cross-scale interactions, legacies and time lags—that need to be tackled in future research. We propose that the evolving metacommunity concept provides a powerful framework to study urban eco-evolutionary dynamics.

Effects of low-density urbanization on genetic structure in the Song Sparrow

Urbanization fragments landscapes and can impede the movement of organisms through their environment, which can decrease population connectivity. Reduction in connectivity influences gene flow and allele frequencies, and can lead to a reduction in genetic diversity and the fixation of certain alleles, with potential negative effects for populations. Previous studies have detected effects of urbanization on genetic diversity and structure in terrestrial animals living in landscapes that vary in their degree of urbanization, even over very short distances. We investigated the effects of low-intensity urbanization on genetic diversity and genetic structure in Song Sparrows (Melospiza melodia). We captured 208 Song Sparrows at seven sites along a gradient of urbanization in and around Blacksburg, VA, USA, then genotyped them using a panel of fifteen polymorphic microsatellite loci. We found that genetic diversity was comparable among the seven study sites, and there was no evidence of genetic structuring among sites. These findings suggest that over a gradient of urbanization characterized by low density urban development, Song Sparrows likely exist in a single panmictic population.

Urban coyotes are genetically distinct from coyotes in natural habitats

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

Within-Generation Polygenic Selection Shapes Fitness-Related Traits across Environments in Juvenile Sea Bream

Understanding the genetic underpinnings of fitness trade-offs across spatially variable environments remains a major challenge in evolutionary biology. In Mediterranean gilthead sea bream, first-year juveniles use various marine and brackish lagoon nursery habitats characterized by a trade-off between food availability and environmental disturbance. Phenotypic differences among juveniles foraging in different habitats rapidly appear after larval settlement, but the relative role of local selection and plasticity in phenotypic variation remains unclear. Here, we combine phenotypic and genetic data to address this question. We first report correlations of opposite signs between growth and condition depending on juvenile habitat type. Then, we use single nucleotide polymorphism (SNP) data obtained by Restriction Associated DNA (RAD) sequencing to search for allele frequency changes caused by a single generation of spatially varying selection between habitats. We found evidence for moderate selection operating at multiple loci showing subtle allele frequency shifts between groups of marine and brackish juveniles. We identified subsets of candidate outlier SNPs that, in interaction with habitat type, additively explain up to 3.8% of the variance in juvenile growth and 8.7% in juvenile condition; these SNPs also explained significant fraction of growth rate in an independent larval sample. Our results indicate that selective mortality across environments during early-life stages involves complex trade-offs between alternative growth strategies.

Diet contributes to urban-induced alterations in gut microbiota: experimental evidence from a wild passerine

Urban sprawl increasingly affects the ecology of natural populations, including host-microbiota interactions, with observed differences in the gut microbiota between urban and rural hosts. While different mechanisms could explain this pattern, dietary uptake constitutes a likely candidate. To assess the contribution of diet in explaining urban-rural variation in gut microbiota, we performed an aviary experiment in which urban and rural house sparrows were fed with mimics of urban or rural diets. Before the experiment, rural sparrows hosted more diverse gut communities, with a higher relative abundance of Enterococcaceae and Staphylococcaceae and lower abundance of genes involved in xenobiotic degradation and lipid metabolism than their urban counterparts. The experimental diets significantly altered gut microbiota α- and β-diversity and taxonomic composition, with the strongest shifts occurring in individuals exposed to contrasting diets. Overall, diet-induced shifts resembled initial differences between free-ranging urban and rural hosts. Furthermore, rural diet had a positive impact on urban host body mass but only in hosts with the highest initial gut diversity. Overall, our results indicate that diet constitutes an important factor contributing to differences in gut microbiota along the urbanization gradient and provide new insights on possible fitness consequences of a reduced gut diversity in urban settings.

Urbanization without isolation: the absence of genetic structure among cities and forests in the tiny acorn ant Temnothorax nylanderi

Urban alteration of neutral and adaptive evolutionary processes is still underexplored. Using a genome-wide SNP dataset, we investigated (i) urban-induced modifications of population demography, genetic diversity and population structure and (ii) signature of divergent selection between urban and forest populations in the ant species, Temnothorax nylanderi. Our results did not reveal an impact of urbanization on neutral processes since we observed: (i) analogous genetic diversity among paired urban/forest sites and two control populations; (ii) weak population genetic structure explained neither by habitat (urban versus forest) nor by geography; (iii) a remarkably similar demographic history across populations with an ancestral growth followed by a recent decline, regardless of their current habitat or geographical location. The micro-geographical home range of ants may explain their resilience to urbanization. Finally, we detected 19 candidate loci discriminating urban/forest populations and associated with core cellular components, molecular function or biological process. Two of these loci were associated with a gene ontology term that was previously found to belong to a module of co-expressed genes related to caste phenotype. These results call for transcriptomics analyses to identify genes associated with ant social traits and to infer their potential role in urban adaptation.

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

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

A New Framework for Urban Ecology: An Integration of Proximate and Ultimate Responses to Anthropogenic Change

As urban areas continue to grow, understanding how species respond and adapt to urban habitats is becoming increasingly important. Knowledge of the mechanisms behind observed phenotypic changes of urban-dwelling animals will enable us to better evaluate the impact of urbanization on current and future generations of wildlife and predict how animals respond to novel environments. Recently, urban ecology has emerged not only as a means of understanding organismal adaptation but also as a framework for exploring mechanisms mediating evolutionary phenomena. Here, we have identified four important research topics that will advance the field of urban ecology and shed light on the proximate and ultimate causes of the phenotypic differences commonly seen among species and populations that vary in their responses to urbanization. First, we address the ecological and socio-economic factors that characterize cities, how they might interact with each other, and how they affect urban species. Second, we ask which are the proximate mechanisms underlying the emergence over time of novel traits in urban organisms, focusing on developmental effects. Third, we emphasize the importance of understanding the ultimate causations that link phenotypic shifts to function. This question highlights the need to quantify the strength and direction of selection that urban individuals are exposed to, and whether the phenotypic shifts associated with life in the city are adaptive. Lastly, we stress the need to translate how individual-level responses scale up to population dynamics. Understanding the mechanistic underpinnings of variation among populations and species in their responses to urbanization will unravel species resilience to environmental perturbation, which will facilitate predictive models for sustainability and development of green cities that maintain or even increase urban biodiversity and wildlife health and wellbeing.

Evolution of genomic variation in the burrowing owl in response to recent colonization of urban areas

When a species successfully colonizes an urban habitat it can be expected that its population rapidly adapts to the new environment but also experiences demographic perturbations. It is, therefore, essential to gain an understanding of the population structure and the demographic history of the urban and neighbouring rural populations before studying adaptation at the genome level. Here, we investigate populations of the burrowing owl (Athene cunicularia), a species that colonized South American cities just a few decades ago. We assembled a high-quality genome of the burrowing owl and re-sequenced 137 owls from three urban-rural population pairs at 17-fold median sequencing coverage per individual. Our data indicate that each city was independently colonized by a limited number of founders and that restricted gene flow occurred between neighbouring urban and rural populations, but not between urban populations of different cities. Using long-range linkage disequilibrium statistics in an approximate Bayesian computation approach, we estimated consistently lower population sizes in the recent past for the urban populations in comparison to the rural ones. The current urban populations all show reduced standing variation in rare single nucleotide polymorphisms (SNPs), but with different subsets of rare SNPs in different cities. This lowers the potential for local adaptation based on rare variants and makes it harder to detect consistent signals of selection in the genome.

Urban versus forest ecotypes are not explained by divergent reproductive selection

Increasing urbanization offers a unique opportunity to study adaptive responses to rapid environmental change. Numerous studies have demonstrated phenotypic divergence between urban and rural organisms. However, comparing the direction and magnitude of natural selection between these environments has rarely been attempted. Using seven years of monitoring of great tits (Parus major) breeding in nest-boxes across the city of Montpellier and in a nearby oak forest, we find phenotypic divergence in four morphological and two life-history traits between urban and forest birds. We then measure reproductive selection on these traits, and compare selection between the habitats. Urban birds had significantly smaller morphological features than their rural counterparts, with a shorter tarsus, lower body mass, and smaller wing and tail lengths relative to their overall body size. While urban female tarsus length was under stabilizing selection, and forest males show positive selection for tarsus length and negative selection for body mass, selection gradients were significantly divergent between habitats only for body mass. Urban great tits also had earlier laying dates and smaller clutches. Surprisingly, we found selection for earlier laying date in the forest but not in the city. Conversely, we detected no linear selection on clutch size in the forest, but positive selection on clutch size in the urban habitat. Overall, these results do not support the hypothesis that contemporary reproductive selection explains differences in morphology and life history between urban- and forest-breeding great tits. We discuss how further experimental approaches will help confirm whether the observed divergence is maladaptive while identifying the environmental drivers behind it.