Candidate gene polymorphisms for behavioural adaptations during urbanization in blackbirds

Transcriptome analysis of avian livers reveals different molecular changes to three urban pollutants: Soot, artificial light at night and noise

Identifying key molecular pathways and genes involved in the response to urban pollutants is an important step in furthering our understanding of the impact of urbanisation on wildlife. The expansion of urban habitats and the associated human-introduced environmental changes are considered a global threat to the health and persistence of humans and wildlife. The present study experimentally investigates how short-term exposure to three urban-related pollutants -soot, artificial light at night (ALAN) and traffic noise-affects transcriptome-wide gene expression in livers from captive female zebra finches (Taeniopygia guttata). Compared to unexposed controls, 17, 52, and 28 genes were differentially expressed in soot, ALAN and noise-exposed birds, respectively. In soot-exposed birds, the enriched gene ontology (GO) terms were associated with a suppressed immune system such as interferon regulating genes (IRGs) and responses to external stimuli. For ALAN-exposed birds, enriched GO terms were instead based on downregulated genes associated with detoxification, redox, hormonal-, and metabolic processes. Noise exposure resulted in downregulation of genes associated with the GO terms: cellular responses to substances, catabolic and cytokine responses. Among the individually differentially expressed genes (DEGs), soot led to an increased expression of genes related to tumour progression. Likewise, ALAN revealed an upregulation of multiple genes linked to different cancer types. Both sensory pollutants (ALAN and noise) led to increased expression of genes linked to neuronal function. Interestingly, noise caused upregulation of genes associated with serotonin regulation and function (SLC6A4 and HTR7), which previous studies have shown to be under selection in urban birds. These outcomes indicate that short-term exposure to the three urban pollutants perturbate the liver transcriptome, but most often in different ways, which highlights future studies of multiple-stress exposure and their interactive effects, along with their long-term impacts for urban-dwelling wildlife.

Approach/Avoidance Behavior to Novel Objects is Correlated with the Serotonergic and Dopaminergic Systems in the Brown Rat (Rattus norvegicus)

The brown rat (Rattus norvegicus) is known to show three types of behavioral responses to novel objects. Whereas some rats are indifferent to novel objects, neophobic and neophilic rats show avoidance and approach behavior, respectively. Here, we compared the dopaminergic, serotonergic, and noradrenergic systems immunohistochemically among these rats. Trapped wild rats and laboratory rats were first individually exposed to the novel objects in their home cage. Wild rats were divided into neophobic and indifferent rats depending on their behavioral responses. Similarly, laboratory rats were divided into neophilic and indifferent rats. Consistent with the behavioral differences, in the paraventricular nucleus of the hypothalamus, Fos expression in corticotropin-releasing hormone-containing neurons was higher in the neophobic rats than in the indifferent rats. In the anterior basal amygdala, the neophobic rats showed higher Fos expression than the indifferent rats. In the posterior basal amygdala, the neophobic and neophilic rats showed lower and higher Fos expressions than the indifferent rats, respectively. When we compared the neuromodulatory systems, in the dorsal raphe, the number of serotonergic neurons and Fos expression in serotonergic neurons increased linearly from neophobic to indifferent to neophilic rats. In the ventral tegmental area, Fos expression in dopaminergic neurons was higher in the neophilic rats than in the indifferent rats. These results demonstrate that approach/avoidance behavior to novel objects is correlated with the serotonergic and dopaminergic systems in the brown rat. We propose that the serotonergic system suppresses avoidance behavior while the dopaminergic system enhances approach behavior to novel objects.

Urbanization correlates with the prevalence and richness of blood parasites in Eurasian Blackbirds (Turdus merula)

Urbanization is increasing worldwide, producing severe environmental impacts. Biodiversity is affected by the expansion of cities, with many species being unable to cope with the different human-induced stressors present in these landscapes. However, this knowledge is mainly based on research from taxa such as plants or vertebrates, while other organisms like protozoa have been less studied in this context. The impact of urbanization on the transmission of vector-borne pathogens in wildlife is still unclear despite its relevance for animal and human health. Here, we investigated whether cities are associated with changes in the prevalence and richness of lineages of three vector-borne protozoans (Plasmodium, Haemoproteus and Leucocytozoon) in Eurasian blackbirds (Turdus merula) from multiple urban and forest areas in Europe. Our results show important species-specific differences between these two habitat types. We found a significant lower prevalence of Leucocytozoon in urban birds compared to forest birds, but no differences for Plasmodium and Haemoproteus. Furthermore, the richness of parasite lineages in European cities was higher for Plasmodium but lower for Leucocytozoon than in forests. We also found one Plasmodium lineage exclusively from cities while another of Leucocytozoon was only found in forests suggesting a certain level of habitat specialization for these protozoan vectors. Overall, our findings show that cities provide contrasting opportunities for the transmission of different vector-borne pathogens and generate new scenarios for the interactions between hosts, vectors and parasites.

Birds of a feather flock together: a dataset for Clock and Adcyap1 genes from migration genetics studies

Birds in seasonal habitats rely on intricate strategies for optimal timing of migrations. This is governed by environmental cues, including photoperiod. Genetic factors affecting intrinsic timekeeping mechanisms, such as circadian clock genes, have been explored, yielding inconsistent findings with potential lineage-dependency. To clarify this evidence, a systematic review and phylogenetic reanalysis was done. This descriptor outlines the methodology for sourcing, screening, and processing relevant literature and data. PRISMA guidelines were followed, ultimately including 66 studies, with 34 focusing on candidate genes at the genotype-phenotype interface. Studies were clustered using bibliographic coupling and citation network analysis, alongside scientometric analyses by publication year and location. Data was retrieved for allele data from databases, article supplements, and direct author communications. The dataset, version 1.0.2, encompasses data from 52 species, with 46 species for the Clock gene and 43 for the Adcyap1 gene. This dataset, featuring data from over 8000 birds, constitutes the most extensive cross-species collection for these candidate genes, used in studies investigating gene polymorphisms and seasonal bird migration.

Investigating the role of genetic variation in vgll3 and six6 in the domestication of gilthead seabream (Sparus aurata Linnaeus) and European seabass (Dicentrarchus labrax Linnaeus)

Gene function conservation is crucial in molecular ecology, especially for key traits like growth and maturation in teleost fish. The vgll3 and six6 genes are known to influence age-at-maturity in Atlantic salmon, but their impact on other fish species is poorly understood. Here, we investigated the association of vgll3 and six6 in the domestication of gilthead seabream and European seabass, both undergoing selective breeding for growth-related traits in the Mediterranean. We analysed two different sets of samples using two different genotyping approaches. The first dataset comprised farmed and wild populations from Greece, genotyped for SNPs within the two genes ('gene-level genotyping'). The second dataset examined 300-600 k SNPs located in the chromosomes of the two genes, derived from a meta-analysis of a Pool-Seq experiment involving farmed and wild populations distributed widely across the Mediterranean ('chromosome-level genotyping'). The gene-level analysis revealed a statistically significant allele frequency differences between farmed and wild populations on both genes in each species. This finding was partially supported by the chromosome-level analysis, identifying highly differentiated regions may be involved in the domestication process at varying distances from the candidate genes. Noteworthy genomic features were found, such as a CpG island in gilthead seabream and novel candidate genes in European seabass, warranting further investigation. These findings support a putative role of vgll3 and six6 in the maturation and growth of gilthead seabream and European seabass, emphasizing the need for further research on their conserved function.

Urban and rural male song sparrows (Melospiza melodia) differ in territorial aggression and activation of vasotocin neurons in response to song challenge

When living in urban habitats, 'urban adapter' species often show greater aggression toward conspecifics, yet we do not understand the mechanisms underlying this behavioral shift. The neuroendocrine system regulates socio-sexual behaviors including aggression and thus could mediate behavioral responses to urbanization. Indeed, urban male song sparrows (Melospiza melodia), which are more territorially aggressive, also have greater abundance of the neuropeptide arginine vasotocin (AVT) in nodes of the brain social behavior network. Higher abundance of AVT could reflect long-term synthesis that underlies baseline territoriality or short-term changes that regulate aggression in response to social challenge. To begin to resolve the timeframe over which the AVT system contributes to habitat differences in aggression we used immediate early gene co-expression as a measure of the activation of AVT neurons. We compared Fos induction in AVT-immunoreactive neurons of the bed nucleus of the stria terminalis (BSTm) and paraventricular nucleus of the hypothalamus (PVN) between urban and rural male song sparrows in response to a short (< 5 min.) or long (> 30 min.) song playback to simulate territorial intrusion by another male. We found that urban males had a higher proportion of Fos-positive AVT neurons in both brain regions compared to rural males, regardless of the duration of song playback. Our results suggest that AVT neurons remain activated in urban males, independently of the duration of social challenge. These findings that Fos induction in AVT neurons differs between rural and urban male song sparrows further implicate this system in regulating behavioral responses to urbanization.

The genomic response to urbanization in the damselfly Ischnura elegans

The complex and rapid environmental changes brought about by urbanization pose significant challenges to organisms. The multifaceted effects of urbanization often make it difficult to define and pinpoint the very nature of adaptive urban phenotypes. In such situations, scanning genomes for regions differentiated between urban and non-urban populations may be an attractive approach. Here, we investigated the genomic signatures of adaptation to urbanization in the damselfly Ischnura elegans sampled from 31 rural and urban localities in three geographic regions: southern and northern Poland, and southern Sweden. Genome-wide variation was assessed using more than 370,000 single nucleotide polymorphisms (SNPs) genotyped by ddRADseq. Associations between SNPs and the level of urbanization were tested using two genetic environment association methods: Latent Factors Mixed Models and BayPass. While we found numerous candidate SNPs and a highly significant overlap between candidates identified by the two methods within the geographic regions, there was a distinctive lack of repeatability between the geographic regions both at the level of individual SNPs and of genomic regions. However, we found "synapse organization" at the top of the functional categories enriched among the genes located in the proximity of the candidate urbanization SNPs. Interestingly, the overall significance of "synapse organization" was built up by the accretion of different genes associated with candidate SNPs in different geographic regions. This finding is consistent with the highly polygenic nature of adaptation, where the response may be achieved through a subtle adjustment of allele frequencies in different genes that contribute to adaptive phenotypes. Taken together, our results point to a polygenic adaptive response in the nervous system, specifically implicating genes involved in synapse organization, which mirrors the findings from several genomic and behavioral studies of adaptation to urbanization in other taxa.

Urbanization drives adaptive evolution in a Neotropical bird

Urbanization has dramatic impacts on natural habitats and such changes may potentially drive local adaptation of urban populations. Behavioral change has been specifically shown to facilitate the fast adaptation of birds to changing environments, but few studies have investigated the genetic mechanisms of this process. Such investigations could provide insights into questions about both evolutionary theory and management of urban populations. In this study, we investigated whether local adaptation has occurred in urban populations of a Neotropical bird species, Coereba flaveola, specifically addressing whether observed behavioral adaptations are correlated to genetic signatures of natural selection. To answer this question, we sampled 24 individuals in urban and rural environments, and searched for selected loci through a genome-scan approach based on RADseq genomic data, generated and assembled using a reference genome for the species. We recovered 46 loci as putative selection outliers, and 30 of them were identified as associated with biological processes possibly related to urban adaptation, such as the regulation of energetic metabolism, regulation of genetic expression, and changes in the immunological system. Moreover, genes involved in the development of the nervous system showed signatures of selection, suggesting a link between behavioral and genetic adaptations. Our findings, in conjunction with similar results in previous studies, support the idea that cities provide a similar selective pressure on urban populations and that behavioral plasticity may be enhanced through genetic changes in urban populations.

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.

Time trees and clock genes: a systematic review and comparative analysis of contemporary avian migration genetics

Timing is a crucial aspect for survival and reproduction in seasonal environments leading to carefully scheduled annual programs of migration in many species. But what are the exact mechanisms through which birds (class: Aves) can keep track of time, anticipate seasonal changes, and adapt their behaviour? One proposed mechanism regulating annual behaviour is the circadian clock, controlled by a highly conserved set of genes, collectively called 'clock genes' which are well established in controlling the daily rhythmicity of physiology and behaviour. Due to diverse migration patterns observed within and among species, in a seemingly endogenously programmed manner, the field of migration genetics has sought and tested several candidate genes within the clock circuitry that may underlie the observed differences in breeding and migration behaviour. Among others, length polymorphisms within genes such as Clock and Adcyap1 have been hypothesised to play a putative role, although association and fitness studies in various species have yielded mixed results. To contextualise the existing body of data, here we conducted a systematic review of all published studies relating polymorphisms in clock genes to seasonality in a phylogenetically and taxonomically informed manner. This was complemented by a standardised comparative re-analysis of candidate gene polymorphisms of 76 bird species, of which 58 are migrants and 18 are residents, along with population genetics analyses for 40 species with available allele data. We tested genetic diversity estimates, used Mantel tests for spatial genetic analyses, and evaluated relationships between candidate gene allele length and population averages for geographic range (breeding- and non-breeding latitude), migration distance, timing of migration, taxonomic relationships, and divergence times. Our combined analysis provided evidence (i) of a putative association between Clock gene variation and autumn migration as well as a putative association between Adcyap1 gene variation and spring migration in migratory species; (ii) that these candidate genes are not diagnostic markers to distinguish migratory from sedentary birds; and (iii) of correlated variability in both genes with divergence time, potentially reflecting ancestrally inherited genotypes rather than contemporary changes driven by selection. These findings highlight a tentative association between these candidate genes and migration attributes as well as genetic constraints on evolutionary adaptation.

Molecular biology of serotonergic systems in avian brains

Serotonin (5-hydroxytryptamine, 5-HT) is a phylogenetically conserved neurotransmitter and modulator. Neurons utilizing serotonin have been identified in the central nervous systems of all vertebrates. In the central serotonergic system of vertebrate species examined so far, serotonergic neurons have been confirmed to exist in clusters in the brainstem. Although many serotonin-regulated cognitive, behavioral, and emotional functions have been elucidated in mammals, equivalents remain poorly understood in non-mammalian vertebrates. The purpose of this review is to summarize current knowledge of the anatomical organization and molecular features of the avian central serotonergic system. In addition, selected key functions of serotonin are briefly reviewed. Gene association studies between serotonergic system related genes and behaviors in birds have elucidated that the serotonergic system is involved in the regulation of behavior in birds similar to that observed in mammals. The widespread distribution of serotonergic modulation in the central nervous system and the evolutionary conservation of the serotonergic system provide a strong foundation for understanding and comparing the evolutionary continuity of neural circuits controlling corresponding brain functions within vertebrates. The main focus of this review is the chicken brain, with this type of poultry used as a model bird. The chicken is widely used not only as a model for answering questions in developmental biology and as a model for agriculturally useful breeding, but also in research relating to cognitive, behavioral, and emotional processes. In addition to a wealth of prior research on the projection relationships of avian brain regions, detailed subdivision similarities between avian and mammalian brains have recently been identified. Therefore, identifying the neural circuits modulated by the serotonergic system in avian brains may provide an interesting opportunity for detailed comparative studies of the function of serotonergic systems in mammals.

Gut microbiome diversity and composition is associated with exploratory behavior in a wild-caught songbird

BACKGROUND

The gut microbiome influences its host in a myriad of ways, from immune system development to nutrient utilization. However, our understanding of the relationship between the gut microbiome and behavior, especially in wild species, is still poor. One behavior that potentially interacts with the gut microbiome is exploratory behavior, which animals use to acquire new information from the environment. We hypothesized that diversity of the gut microbiome will be correlated with exploratory behavior in a wild-caught bird species. To test this hypothesis, we captured wild house sparrows (Passer domesticus) and collected fecal samples to measure the diversity of their gut microbiomes. We then introduced individuals to a novel environment and measured their exploratory behavior.

RESULTS

We found that birds with higher alpha diversity of the gut microbiome exhibited higher exploratory behavior. These results suggest that high exploratory birds encounter more types of environmental microbes that contribute to their diverse gut microbiome compared with less exploratory birds. Alternatively, increased gut microbiome diversity may contribute to increased exploratory behavior. We also found differences in beta diversity when comparing high and low exploring birds, indicating differences in microbiome community structure. When comparing predicted functional pathways of the birds' microbiomes, we found that the microbiomes of high explorers contained more pathways involved in biofilm formation and xenobiotic degradation than those of low explorers.

CONCLUSIONS

Overall, we found that the alpha and beta diversity of the gut microbiome is correlated with exploratory behavior of house sparrows. The predicted functions of the gut microbiome from high explorers differs from that of low explorers. Our study highlights the importance of considering the gut microbiome when investigating animal behavior.

Past and future: Urbanization and the avian endocrine system

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

Towards evolutionary predictions: Current promises and challenges

Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions.

Responses in thermal tolerance and daily activity rhythm to urban stress in Drosophila suzukii

Cities experience changes in abiotic factors, such as warming, increases in noise and light. These changes can lead to phenotypic changes. Several studies have revealed that altered environments change phenotypes in plants and animals in cities. However, limited studies have isolated evolutionary from nongenetic changes. Here, we analyzed the evolution of thermal tolerance and diurnal activity patterns in the urban population of the fruit pest, Drosophila suzukii. Urban and rural isofemale lines were reared under constant conditions. We compared the lower and upper thermal limits (CT_min and CT_max, respectively), and effects of temperature exposure on the thermal limits of urban and rural populations. Common garden experiments showed that urban populations exhibit a lower CT_min than rural populations, suggesting genetic difference in CT_min among populations. On the other hand, the difference in CT_max between urban and rural populations was not significant. Exposure to cold temperature did not affect CT_min in both urban and rural populations. In contrast, exposure to hot temperature increased CT_max especially in urban population, suggesting that urban populations evolved in response to urban heat. We also investigated the daily activity patterns of urban and rural populations and the effect of lifelong artificial light at night on daily activity. We found that night‐time light (dim light) reduced the total amount of activity compared to dark night condition. In addition, dim light at night altered the daily rhythm of activity and increased the activity rate at night. The effect of night light on total activity was less in urban than that in rural populations, suggesting that populations in cities evolved to mitigate decreased activity under night light. Our results showed that environmental temperature and artificial light at night evolutionarily and plastically influence ecologically important traits, such as temperature tolerance and diurnal activity.

Constitutive gene expression differs in three brain regions important for cognition in neophobic and non-neophobic house sparrows (Passer domesticus)

Neophobia (aversion to new objects, food, and environments) is a personality trait that affects the ability of wildlife to adapt to new challenges and opportunities. Despite the ubiquity and importance of this trait, the molecular mechanisms underlying repeatable individual differences in neophobia in wild animals are poorly understood. We evaluated wild-caught house sparrows (Passer domesticus) for neophobia in the lab using novel object tests. We then selected a subset of neophobic and non-neophobic individuals (n = 3 of each, all females) and extracted RNA from four brain regions involved in learning, memory, threat perception, and executive function: striatum, caudal dorsomedial hippocampus, medial ventral arcopallium, and caudolateral nidopallium (NCL). Our analysis of differentially expressed genes (DEGs) used 11,889 gene regions annotated in the house sparrow reference genome for which we had an average of 25.7 million mapped reads/sample. PERMANOVA identified significant effects of brain region, phenotype (neophobic vs. non-neophobic), and a brain region by phenotype interaction. Comparing neophobic and non-neophobic birds revealed constitutive differences in DEGs in three of the four brain regions examined: hippocampus (12% of the transcriptome significantly differentially expressed), striatum (4%) and NCL (3%). DEGs included important known neuroendocrine mediators of learning, memory, executive function, and anxiety behavior, including serotonin receptor 5A, dopamine receptors 1, 2 and 5 (downregulated in neophobic birds), and estrogen receptor beta (upregulated in neophobic birds). These results suggest that some of the behavioral differences between phenotypes may be due to underlying gene expression differences in the brain. The large number of DEGs in neophobic and non-neophobic birds also implies that there are major differences in neural function between the two phenotypes that could affect a wide variety of behavioral traits beyond neophobia.

The Behavioral Responses of the Chiguanco Thrush to Urbanization in a Neotropical City Comes From Preadapted Behavioral Traits

Several animal species can survive within cities by changing their behavior; such changes could be the result of evolutionary adaptation, epigenetic effects, or come from preadapted traits through phenotypic plasticity or non-random dispersal. Exploring whether behavioral preadapted traits are present in non-urbanized populations could improve our understanding of the processes that allow animals to cope with urbanization. We compared the boldness, neophobia, and solving-test skills of adult individuals of the Chiguanco Thrush (Turdus chiguanco) between urban and extra-urban habitats in La Paz (Bolivia), a high-altitude Neotropical city. The urban Chiguanco Thrushes were bolder, less neophobic, and performed better in problem-solving tests. Extra-urban individuals varied significantly more among them in boldness and neophobia, and although a smaller proportion of individuals were able to solve the simplest problem-solving test, they did so in the same way as the urban ones. This evidence suggests that the behavioral responses of the Chiguanco Thrush to urbanization in La Paz come from preadapted traits.

Local selection signals in the genome of Blue tits emphasize regulatory and neuronal evolution

Understanding the genomic landscape of adaptation is central to the understanding of microevolution in wild populations. Genomic targets of selection and the underlying genomic mechanisms of adaptation can be elucidated by genome-wide scans for past selective sweeps or by scans for direct fitness associations. We sequenced and assembled 150 haplotypes of 75 Blue tits (Cyanistes caeruleus) of a single central-European population by a linked-read technology. We used these genome data in combination with coalescent simulations (1) to estimate an historical effective population size of ~250,000, which recently declined to ~10,000, and (2) to identify genome-wide distributed selective sweeps of beneficial variants most likely originating from standing genetic variation (soft sweeps). The genes linked to these soft sweeps, but also the ones linked to hard sweeps based on new beneficial mutants, showed a significant enrichment for functions associated with gene expression and transcription regulation. This emphasizes the importance of regulatory evolution in the population's adaptive history. Soft sweeps were further enriched for genes related to axon and synapse development, indicating the significance of neuronal connectivity changes in the brain potentially linked to behavioural adaptations. A previous scan of heterozygosity-fitness correlations revealed a consistent negative effect on arrival date at the breeding site for a single microsatellite in the MDGA2 gene. Here, we used the haplotype structure around this microsatellite to explain the effect as a local and direct outbreeding effect of a gene involved in synapse development.

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.

Occurrence patterns of crop-foraging sika deer distribution in an agriculture-forest landscape revealed by nitrogen stable isotopes

Conflicts arising from the consumption of anthropogenic foods by wildlife are increasing worldwide. Conventional tools for evaluating the spatial distribution pattern of large terrestrial mammals that consume anthropogenic foods have various limitations, despite their importance in management to mitigate conflicts. In this study, we examined the spatial distribution pattern of crop-foraging sika deer by performing nitrogen stable isotope analyses of bone collagen. We evaluated whether crop-foraging deer lived closer to agricultural crop fields during the winter and spring, when crop production decreases. We found that female deer in proximity to agricultural crop fields during the winter and spring were more likely to be crop-foraging individuals. Furthermore, the likelihood of crop consumption by females decreased by half as the distance to agricultural crop fields increased to 5-10 km. We did not detect a significant trend in the spatial distribution of crop-foraging male deer. The findings of spatial distribution patterns of crop-foraging female deer will be useful for the establishment of management areas, such as zonation, for efficient removal of them.

Early life experience influences dispersal in coyotes (Canis latrans)

Natal dispersal plays an important role in connecting individual animal behavior with ecological processes at all levels of biological organization. As urban environments are rapidly increasing in extent and intensity, understanding how urbanization influences these long distance movements is critical for predicting the persistence of species and communities. There is considerable variation in the movement responses of individuals within a species, some of which is attributed to behavioral plasticity which interacts with experience to produce interindividual differences in behavior. For natal dispersers, much of this experience occurs in the natal home range. Using data collected from VHF collared coyotes (Canis latrans) in the Chicago Metropolitan Area we explored the relationship between early life experience with urbanization and departure, transience, and settlement behavior. Additionally, we looked at how early life experience with urbanization influenced survival to adulthood and the likelihood of experiencing a vehicle related mortality. We found that coyotes with more developed habitat in their natal home range were more likely to disperse and tended to disperse farther than individuals with more natural habitat in their natal home range. Interestingly, our analysis produced mixed results for the relationship between natal habitat and habitat selection during settlement. Finally, we found no evidence that early life experience with urbanization influenced survival to adulthood or the likelihood of experiencing vehicular mortality. Our study provides evidence that early life exposure influences dispersal behavior; however, it remains unclear how these differences ultimately affect fitness.

Genetic association with boldness and maternal performance in a free-ranging population of grey seals (Halichoerus grypus)

Individual variation in quantitative traits clearly influence many ecological and evolutionary processes. Moderate to high heritability estimates of personality and life-history traits suggest some level of genetic control over these traits. Yet, we know very little of the underlying genetic architecture of phenotypic variation in the wild. In this study, we used a candidate gene approach to investigate the association of genetic variants with repeated measures of boldness and maternal performance traits (weaning mass and lactation duration) collected over an 11- and 28-year period, respectively, in a free-ranging population of grey seals on Sable Island National Park Reserve, Canada. We isolated and re-sequenced five genes: dopamine receptor D4 (DRD4), serotonin transporter (SERT), oxytocin receptor (OXTR), and melanocortin receptors 1 (MC1R) and 5 (MC5R). We discovered single nucleotide polymorphisms (SNPs) in each gene; and, after accounting for loci in linkage disequilibrium and filtering due to missing data, we were able to test for genotype-phenotype relationships at seven loci in three genes (DRD4, SERT, and MC1R). We tested for association between these loci and traits of 180 females having extreme shy-bold phenotypes using mixed-effects models. One locus within SERT was significantly associated with boldness (effect size = 0.189) and a second locus within DRD4 with weaning mass (effect size = 0.232). Altogether, genotypes explained 6.52-13.66% of total trait variation. Our study substantiates SERT and DRD4 as important determinants of behaviour, and provides unique insight into the molecular mechanisms underlying maternal performance variation in a marine predator.

Long-term changes of plumage between urban and rural populations of white-crowned sparrows (Zonotrichia leucophrys)

Urbanization is one of the most extreme forms of land transformation and results in changes to ecosystems and species compositions. As a result, there are strong directional selection pressures compared to nearby rural areas. Despite a surge in research on the different selection pressures on acoustic communication in urban and rural areas, there has been comparatively little investigation into traits involved with visual communication. We measured the plumage of museum specimens of white-crowned sparrows (Zonotrichia leucophrys) from urban and adjacent rural habitats in San Francisco, CA, to assess the effects of divergent habitats on plumage. We found significant differences in dorsal plumage, but not crown plumage, between urban and rural populations that have been diverging over the past 100 years. Urban birds have increasingly darker and duller dorsal plumage, whereas rural birds in adjacent areas have plumage with richer hues and more color complexity. Our findings suggest a newly observed adaptation to urban environments by native species and suggest that many traits, in addition to acoustic signals, may be changing in response to urban selection pressures. Additional collections in urban areas are needed to explore likely divergences in plumage coloration between urban and rural environments.

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.

The serotonin transporter gene and female personality variation in a free-living passerine

Quantifying variation in behaviour-related genes provides insight into the evolutionary potential of repeatable among-individual variation in behaviour (i.e. personality). Yet, individuals typically also plastically adjust their behaviour in response to environmental conditions and/or age, thereby complicating the detection of genotype-phenotype associations. Here, using a population of free-living great tits (Parus major), we assessed the association between single nucleotide polymorphisms (SNPs) in the serotonin transporter gene (SERT) and two repeatable behavioural traits, i.e. female-female aggression and female hissing behaviour. For female-female aggression, a trait showing age-related plasticity, we found no evidence for associations with SERT SNPs, even when assessing potential age-dependent effects of SERT genotype on aggression. We also found no strong support for associations between SERT SNPs and hissing behaviour, yet we identified two synonymous polymorphisms (exon 13 SNP66 and exon 12 SNP144) of particular interest, each explaining about 1.3% of the total variation in hissing behaviour. Overall, our results contribute to the general understanding of the biological underpinning of complex behavioural traits and will facilitate further (meta-analytic) research on behaviour-related genes. Moreover, we emphasize that future molecular genetic studies should consider age-dependent genotype-phenotype associations for behavioural trait (co)variation, as this will vastly improve our understanding of the proximate causes and ultimate consequences of personality variation in natural populations.

Animal cognition in an urbanised world

Explaining how animals respond to an increasingly urbanised world is a major challenge for evolutionary biologists. Urban environments often present animals with novel problems that differ from those encountered in their evolutionary past. To navigate these rapidly changing habitats successfully, animals may need to adjust their behaviour flexibly over relatively short timescales. These behavioural changes, in turn, may be facilitated by an ability to acquire, store and process information from the environment. The question of how cognitive abilities allow animals to avoid threats and exploit resources (or constrain their ability to do so) is attracting increasing research interest, with a growing number of studies investigating cognitive and behavioural differences between urban-dwelling animals and their non-urban counterparts. In this review we consider why such differences might arise, focusing on the informational challenges faced by animals living in urban environments, and how different cognitive abilities can assist in overcoming these challenges. We focus largely on birds, as avian taxa have been the subject of most research to date, but discuss work in other species where relevant. We also address the potential consequences of cognitive variation at the individual and species level. For instance, do urban environments select for, or influence the development of, particular cognitive abilities? Are individuals or species with particular cognitive phenotypes more likely to become established in urban habitats? How do other factors, such as social behaviour and individual personality, interact with cognition to influence behaviour in urban environments? The aim of this review is to synthesise current knowledge and identify key avenues for future research, in order to improve our understanding of the ecological and evolutionary consequences of urbanisation.

An urban–rural spotlight: evolution at small spatial scales among urban and rural populations of common ragweed

Urbanization produces similar environmental changes across cities relative to their neighboring rural environments. However, there may be high environmental heterogeneity across an urban–rural gradient. Previous research in Minneapolis, MN, USA, found mixed evidence that urban and rural plant populations of common ragweed have locally adapted and that urban populations exhibit greater among-population divergence in ecologically-important traits. To investigate whether there are parallel patterns of urban–rural trait divergence across different urban areas, we examined trait variation across an urban–rural gradient in a second city, St. Louis, MO, USA. We used growth chamber and greenhouse common environments to investigate variation in six traits within and among 16 populations of common ragweed (eight from each urban and rural area). Urban and rural plants diverged significantly in three of five traits, with rural plants having lower percent germination, greater height and lower leaf dissection index. We also found greater variance in plant height among urban compared to rural populations, potentially driven by heterogeneity in human management practices on urban populations. Patterns of urban-rural trait divergence (e.g. in flowering time) differ substantially from those found previously in the reciprocal transplant experiment in Minneapolis, contradicting the hypothesis of parallel evolution across different metropolitan areas. The results of this study suggest that there is considerable population variation in ecologically-important traits, but that urban populations do not consistently differ from neighboring rural populations.

Which Traits Influence Bird Survival in the City? A Review

Urbanization poses a major threat to biodiversity worldwide. We focused on birds as a well-studied taxon of interest, in order to review literature on traits that influence responses to urbanization. We review 226 papers that were published between 1979 and 2020, and aggregate information on five major groups of traits that have been widely studied: ecological traits, life history, physiology, behavior and genetic traits. Some robust findings on trait changes in individual species as well as bird communities emerge. A lack of specific food and shelter resources has led to the urban bird community being dominated by generalist species, while specialist species show decline. Urbanized birds differ in the behavioral traits, showing an increase in song frequency and amplitude, and bolder behavior, as compared to rural populations of the same species. Differential food resources and predatory pressure results in changes in life history traits, including prolonged breeding duration, and increases in clutch and brood size to compensate for lower survival. Other species-specific changes include changes in hormonal state, body state, and genetic differences from rural populations. We identify gaps in research, with a paucity of studies in tropical cities and a need for greater examination of traits that influence persistence and success in native vs. introduced populations.

Consistent choice of landscape urbanization level across the annual cycle in a migratory waterbird species

Rapid urbanization has a great impact on avian distribution, ecology, habitat selection, and behavior. Recent avian studies indicated that individuals remain consistent in their behavioral responses to human disturbance across short periods of time. However, there is still little information about keeping consistent behaviors in distinct locations across different stages of the annual cycle. In this study, we aimed to test for long-term consistency in habitat selection with respect to urbanization in a migratory waterbird species, the Eurasian coot Fulica atra. For this purpose, we individually marked ca. 300 coots from four populations that varied in urbanization level and tracked their habitat preferences during the non-breeding season. We found that individuals from urban breeding populations selected habitats with a higher share of artificial areas during the non-breeding season, when compared to non-urban individuals. Also, a comparison of non-breeding sites selected by birds from our study populations with random sites showed that urban birds selected sites with higher urbanization level than resulting from random availability. Finally, we found a seasonal variation in habitat preferences in coots—individuals from all study populations selected more urbanized areas as the non-breeding season progressed. The results indicate that birds are able to remain consistent in habitat preferences not only at a large geographical scale, but also across different seasons. Marked between-population variation in habitat selection across the annual cycle may reflect personality differences of coots from urban and non-urban populations, and it stays in line with the personality-matching habitat choice hypothesis.

Adaptive Evolution in Cities: Progress and Misconceptions

Current narratives suggest that urban adaptation - the adaptive evolution of organisms to cities - is pervasive across taxa and cities. However, in reviewing hundreds of studies, we find only six comprehensive examples of species adaptively evolving to urbanization. We discuss the utility and shortcomings of methods for studying urban adaptation. We then review diverse systems offering preliminary evidence for urban adaptation and outline a research program for advancing its study. Urban environments constitute diverse, interacting selective agents that test the limits of adaptation. Understanding urban adaptation therefore offers unique opportunities for addressing fundamental questions in evolutionary biology and for better conserving biodiversity in cities. However, capitalizing on these opportunities requires appropriate research methods and dissemination of accurate narratives.

Foraging in Urban Environments Increases Bactericidal Capacity in Plasma and Decreases Corticosterone Concentrations in White Ibises

As humans continue to infringe on natural habitats, more animals are exposed to urbanization and its associated challenges. It is still unclear, however, whether the movement of animals into urban habitats negatively influences the health and/or survival of those animals, however those animals often experience shifts in resource availability, diet composition, and exposure to stimuli that are new and potentially stressful. Recently, white ibises (Eudocimus albus) have become increasingly common in urban habitats where they forage in close proximity to humans and even interact with them, collecting food handouts. We hypothesized that foraging in urban habitats would negatively impact measures of health, impair innate immunity, trigger elevated concentrations of corticosterone, and depress physiological responses to stressors in white ibises. We found that plasma from birds captured from urban sites had higher bactericidal capacity against Escherichia coli than those captured in natural sites. Additionally, adults captured in urban habitats had a significantly lower baseline corticosterone concentrations during the post-breeding season, and corticosterone responses to a handling challenge were lower for birds captured from urban sites during year 2 of the study. These results indicate that exposure to urban habitats impacts ibis health, though in the opposite direction of what was predicted.

Genetic Adaptation in New York City Rats

Brown rats (Rattus norvegicus) thrive in urban environments by navigating the anthropocentric environment and taking advantage of human resources and by-products. From the human perspective, rats are a chronic problem that causes billions of dollars in damage to agriculture, health, and infrastructure. Did genetic adaptation play a role in the spread of rats in cities? To approach this question, we collected whole-genome sequences from 29 brown rats from New York City (NYC) and scanned for genetic signatures of adaptation. We tested for 1) high-frequency, extended haplotypes that could indicate selective sweeps and 2) loci of extreme genetic differentiation between the NYC sample and a sample from the presumed ancestral range of brown rats in northeast China. We found candidate selective sweeps near or inside genes associated with metabolism, diet, the nervous system, and locomotory behavior. Patterns of differentiation between NYC and Chinese rats at putative sweep loci suggest that many sweeps began after the split from the ancestral population. Together, our results suggest several hypotheses on adaptation in rats living in proximity to humans.

Paternal exposure to a common herbicide alters the behavior and serotonergic system of zebrafish offspring

Increasingly, studies are revealing that endocrine disrupting chemicals (EDCs) can alter animal behavior. Early life exposure to EDCs may permanently alter phenotypes through to adulthood. In addition, the effects of EDCs may not be isolated to a single generation − offspring may indirectly be impacted, via non-genetic processes. Here, we analyzed the effects of paternal atrazine exposure on behavioral traits (distance moved, exploration, bottom-dwelling time, latency to enter the top zone, and interaction with a mirror) and whole-brain mRNA of genes involved in the serotonergic system regulation (slc6a4a, slc6a4b, htr1Aa, htr1B, htr2B) of zebrafish (Danio rerio). F0 male zebraFIsh were exposed to atrazine at 0.3, 3 or 30 part per billion (ppb) during early juvenile development, the behavior of F1 progeny was tested at adulthood, and the effect of 0.3 ppb atrazine treatment on mRNA transcription was quantified. Paternal exposure to atrazine significantly reduced interactions with a mirror (a proxy for aggression) and altered the latency to enter the top zone of a tank in unexposed F1 offspring. Bottom-dwelling time (a proxy for anxiety) also appeared to be somewhat affected, and activity (distance moved) was reduced in the context of aggression. slc6a4a and htr1Aa mRNA transcript levels were found to correlate positively with anxiety levels in controls, but we found that this relationship was disrupted in the 0.3 ppb atrazine treatment group. Overall, paternal atrazine exposure resulted in alterations across a variety of behavioral traits and showed signs of serotonergic system dysregulation, demonstrating intergenerational effects. Further research is needed to explore transgenerational effects on behavior and possible mechanisms underpinning behavioral effects.

Biologia Futura: adaptive changes in urban populations

Cities represent novel environments where altered ecological conditions can generate strong selection pressures leading to the evolution of specific urban phenotypes. Is there evidence for such adaptive changes in urban populations which have colonized their new environments relatively recently? A growing number of studies suggest that rapid adaptations may be widespread in wild urban populations, including increased tolerance to various anthropogenic stressors, and physiological, morphological and behavioural changes in response to the altered resources and predation risk. Some of these adaptive changes are based on genetic differentiation, although other mechanisms, such as phenotypic plasticity and epigenetic effects, are also frequently involved.

Multisensory pollution: Artificial light at night and anthropogenic noise have interactive effects on activity patterns of great tits (Parus major)

Urbanisation is increasing globally at a rapid pace. Consequently, wild species face novel environmental stressors associated with urban sprawl, such as artificial light at night and noise. These stressors have pervasive effects on the behaviour and physiology of many species. Most studies have singled out the impact of just one of these stressors, while in the real world they are likely to co-occur both temporally and spatially, and we thus lack a clear understanding of the combined effect of anthropogenic stressors on wild species. Here, we experimentally exposed captive male great tits (Parus major) to artificial light at night and 24 h noise in a fully factorial experiment. We then measured the effect of both these stressors on their own and their combination on the amount and timing of activity patterns. We found that both light and noise affected activity patterns when presented alone, but in opposite ways: light increased activity, particularly at night, while noise reduced it, particularly during the day. When the two stressors were combined, we found a synergistic effect on the total activity and the nighttime activity, but an antagonistic effect on daytime activity. The significant interaction between noise and light treatment also differed among forest and city birds. Indeed, we detected a significant interactive effect on light and noise on daytime, nighttime, dusktime and offset of activity of urban birds, but not of forest birds. These results suggest that both artificial light at night and anthropogenic noise can drive changes in activity patterns, but that the specific impacts depend on the habitat of origin. Furthermore, our results demonstrate that co-occurring exposure to noise and light can lead to a stronger impact at night than predicted from the additive effects and thus that multisensory pollution may be a considerable threat for wildlife.

No evidence for an association between Clock gene allelic variation and migration timing in a long-distance migratory shorebird (Limosa lapponica baueri)

The gene Clock is a key part of the Core Circadian Oscillator, and the length of the polyglutamine (poly-Q) repeat sequence in Clock (ClkpolyQcds) has been proposed to be associated with the timing of annual cycle events in birds. We tested whether variation in ClkpolyQcds corresponds to variation in migration timing in the bar-tailed godwit (Limosa lapponica baueri), a species in which individuals show strong annual consistency in their migration timing despite the New Zealand population migrating across a 5-week period. We describe allelic variation of the ClkpolyQcds in 135 godwits over-wintering in New Zealand (N.Z.) and investigate whether polymorphism in this region is associated with northward migration timing (chronophenotype) from N.Z. or (for 32 birds tracked by geolocator) after the primary stopover in Asia. Six Clock alleles were detected (Q₇‒Q₁₂) and there was substantial variation between individuals (heterozygosity of 0.79). There was no association between ClkpolyQcds polymorphism and migration timing from N.Z. The length of the shorter Clock allele was related to migration timing from Asia, though this relationship arose largely from just a few northern-breeding birds with longer alleles. Other studies show no consistent associations between ClkpolyQcds and migration timing in birds, although Clock may be associated with breeding latitude in some species (as an adaptation to photoperiodic regime). Apparent relationships with migration timing could reflect latitude-related variation in migration timing, rather than Clock directly affecting migration timing. On current evidence, ClkpolyQcds is not a strong candidate for driving migration timing in migratory birds generally.

Native and introduced Argentine ant populations are characterised by distinct transcriptomic signatures associated with behaviour and immunity

Biological invasions can be influenced by trait variation in the invader, such as behavioural traits and ecological factors, such as variation in pathogen pressure. High-throughput nucleotide sequencing has increased our capacity to investigate the genomic basis of the functional changes associated with biological invasions. Here, we used RNA-sequencing in Argentina and California, Australia and New Zealand to investigate if native and introduced Argentine ant populations were characterised by distinct transcriptomic signatures. We focused our analysis on viral pressure and immunity, as well as genes associated with biogenic amines known to modulate key behaviour in social insects. Using a combination of differential expression analysis, gene co-expression network analysis and candidate gene approach, we show that native and introduced populations have distinct transcriptomic signatures. Genes associated with biogenic amines were overall up-regulated in the native range compared to introduced populations. Although we found no significant variation in overall viral loads amongst regions for viruses known to infect Argentine ants, viral diversity was lower in most of the introduced range which was interestingly associated with down-regulation of the RNAi immune pathway, primarily directed against viruses. Altogether, our data show that Argentine ant populations exhibit range-specific transcriptomic signatures, perhaps reflecting regional adaptations that may contribute to the ecological success of introduced populations.

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.

Urban blackbirds have shorter telomeres

Urbanization, one of the most extreme human-induced environmental changes, represents a major challenge for many organisms. Anthropogenic habitats can have opposing effects on different fitness components, for example, by decreasing starvation risk but also health status. Assessment of the net fitness effect of anthropogenic habitats is therefore difficult. Telomere length is associated with phenotypic quality and mortality rate in many species, and the rate of telomere shortening is considered an integrative measure of the 'life stress' experienced by an individual. This makes telomere length a promising candidate for examining the effects of urbanization on the health status of individuals. We investigated whether telomere length differed between urban and forest-dwelling common blackbirds (Turdus merula). Using the terminal restriction fragment assay, we analysed telomere length in yearlings and older adults from five population dyads (urban versus forest) across Europe. In both age classes, urban blackbirds had significantly shorter telomeres (547 bp) than blackbirds in natural habitats, indicating lower health status in urban blackbirds. We propose several potential hypotheses to explain our results. Our findings show that even successful city dwellers such as blackbirds pay a price for living in these anthropogenic habitats.

Modern spandrels: the roles of genetic drift, gene flow and natural selection in the evolution of parallel clines

Urban environments offer the opportunity to study the role of adaptive and non-adaptive evolutionary processes on an unprecedented scale. While the presence of parallel clines in heritable phenotypic traits is often considered strong evidence for the role of natural selection, non-adaptive evolutionary processes can also generate clines, and this may be more likely when traits have a non-additive genetic basis due to epistasis. In this paper, we use spatially explicit simulations modelled according to the cyanogenesis (hydrogen cyanide, HCN) polymorphism in white clover (Trifolium repens) to examine the formation of phenotypic clines along urbanization gradients under varying levels of drift, gene flow and selection. HCN results from an epistatic interaction between two Mendelian-inherited loci. Our results demonstrate that the genetic architecture of this trait makes natural populations susceptible to decreases in HCN frequencies via drift. Gradients in the strength of drift across a landscape resulted in phenotypic clines with lower frequencies of HCN in strongly drifting populations, giving the misleading appearance of deterministic adaptive changes in the phenotype. Studies of heritable phenotypic change in urban populations should generate null models of phenotypic evolution based on the genetic architecture underlying focal traits prior to invoking selection's role in generating adaptive differentiation.