Transcriptome analysis of a wild bird reveals physiological responses to the urban environment

Genomic advancements in goat breeding: enhancing productivity, disease resistance, and sustainability in India's rural economy

Goats are vital to the rural economy of India, contributing significantly to livelihoods, nutrition, and agricultural sustainability. With a population of 148.88 million, India holds the world's largest goat population, comprising 41 recognized indigenous breeds. These goats provide milk, meat, and fiber, particularly in marginal environments. The genomic advancements in goat research have revolutionized the understanding of genetic diversity, adaptation, and trait improvement. Whole-genome sequencing (WGS), single nucleotide polymorphism (SNP) arrays and transcriptomics have unveiled genetic markers associated with production, disease resistance, and reproductive traits. Genomic tools such as the Illumina Goat SNP50K BeadChip and high-throughput sequencing technologies have facilitated the identification of selection signatures and quantitative trait loci (QTL), influencing economically important traits like milk yield, meat quality, and prolificacy. Notably, genes such as DGAT1, GHR, BMPR1B, and HSP70 have been linked to production efficiency, reproductive performance, and climate resilience. Genome-wide association studies (GWAS) and genomic selection (GS) have enabled precision breeding, enhancing genetic gains and reducing inbreeding risks. The application of RNA sequencing has provided insights into gene expression patterns governing lactation, growth, and reproductive efficiency. Epigenomic studies, focusing on DNA methylation and histone modifications, have highlighted regulatory mechanisms underpinning prolificacy and muscle development. Conservation genomics has played a pivotal role in safeguarding native breeds by assessing genetic diversity and mitigating inbreeding depression. Indicine goat breeds, such as Jamunapari, Beetal, Barbari, and Black Bengal, exhibit unique genetic adaptations to diverse agro-climatic conditions, emphasizing the need for their conservation. Emerging technologies, including CRISPR-Cas9 gene editing, hold promise for precision breeding to enhance productivity and disease resistance. Integrating genomics with artificial intelligence (AI) and big data analytics is poised to revolutionize goat breeding and management. Future efforts should focus on expanding genomic databases, developing breed-specific reference genomes, and promoting genomic literacy among farmers to ensure sustainable goat production and improve rural livelihoods in India.

Life at new extremes: Integrating stress physiology and the bio-exposome in the Anthropocene

Conventional physiological research has focused on elucidating the endogenous mechanisms that underly the adaptations of species to life in extreme habitats, such as polar regions or deserts. In this review article, we argue that even habitats that are not considered extremes are facing unpredictable, rapid, and strong modifications due to human activities that expose animals to novel extreme conditions. Thus, physiological research on these animals can offer insight on the role of physiological plasticity in driving their resilience and adaptation. To this end, we discuss how stress physiology (with a particular focus on oxidative stress) has a central role in mediating the interaction between the exposome (measure of all the environmental exposures of an individual in a lifetime) and cellular processes (bio-exposome) in the contexts of relevant extreme anthropogenic changes to the habitat conditions. We also provide concrete examples on the relationship between oxidative stress and the bio-exposome in free-living animals, and how this research can be relevant to human health. Finally, we propose future research directions integrating the bio-exposome and the One Health framework to achieve a holistic understanding of the proximate mechanisms underlying individual responses to extreme anthropogenic environmental changes.

Assessment of Oxidative Stress and Associated Biomarkers in Wild Avian Species

Reactive oxygen species (ROS) are natural by-products of cellular metabolism and are also formed in response to environmental stressors such as pollution, extreme temperatures, and ultraviolet radiation exposure. Physiological factors such as intense activity, growth, reproduction, nutrient deficiency, captivity, and disease also contribute to ROS production. While ROS, including free radicals, play a key role in cell physiology, including immune defense, their excessive accumulation can damage cellular components and cause oxidative stress when antioxidant defenses are overwhelmed. To regulate ROS levels, wild birds rely on enzymatic (e.g., catalase, superoxide dismutase, glutathione peroxidase) and non-enzymatic antioxidants (e.g., vitamins C and E, carotenoids). Oxidative stress affects important aspects of wild bird biology, including health, reproduction, and survival, and is closely linked to overall fitness. It is also linked to physiological challenges such as migration and the progression of various diseases affecting wild bird populations. The study of oxidative stress in wild birds requires the use of appropriate biomarkers to assess its role in disease development. A deeper understanding of the balance between ROS production and antioxidant defenses is essential to determine how wild birds cope with environmental and physiological challenges. In this review, we summarize the mechanisms of oxidative stress in wild birds and the role of antioxidants in maintaining health and promoting longevity in wild bird populations.

Impact of urbanization on the house sparrow (Passer domesticus): Serum proteome and pathogen prevalence

The house sparrow (Passer domesticus) is a globally distributed species found in rural, urban and other humanised environments. In Europe, sparrow populations have significantly declined in recent decades, especially in urbanised areas. In the present study, we analysed the impact of urbanization on sparrow body condition, pathogen prevalence, and serum proteome changes. Sparrows were captured in four locations with two different urbanization status (rural/urban). Biometric data, blood samples and oral and cloacal swabs were collected. Rural sparrows exhibited significantly better body condition compared to urban sparrows, with no notable differences between sexes. Haemoparasite prevalence was higher in rural sparrows 70.16 % (87/124) than in urban sparrows 50 % (27/54). No avian influenza virus (AIV) or West Nile virus (WNV) genetic material was found, although one urban sparrow (0.58 %) had antibodies to AIV. Serum proteomics revealed that rural sparrows showed an up-regulation of proteins involved in the metabolism, in contrast to proteins of the immune system and the coagulation system, which were found to be over-represented in urban sparrows. Thus, we documented a worse body condition and immune system activation in urban sparrows in contrast to a more active metabolism and a higher prevalence of avian malaria in rural sparrows, and at least occasional exposure to AIV in urban habitats. This information suggests exposure to urban environments may alter the host-pathogen relationship. Urbanization in combination with exposure to AIV, could modulate their role in viral spread and transmission.

Evidence linking cadmium and/or lead exposure to immunomodulatory effects in mammals based upon an adverse outcome pathways approach, and research perspectives

For decades, studies have shown how exposure to non-essential trace metals such as lead (Pb) and cadmium (Cd) largely impact global wildlife. Ecoimmunotoxicology has emerged in the past two decades and focuses on the effects of pollutants on the immune system of free-ranging organisms. Adverse outcome pathways (AOPs) represent a conceptual approach to explore the mechanistic linkage between a molecular initiating event and adverse outcomes, potentially at all biological levels of organisation. The present paper proposes putative AOPs related to the effects of Cd, Pb, and the mixture Cd-Pb, on the immune system of mammals to address future questions in ecoimmunotoxicology. Molecular Initiating Events for both metals relate to entrance in cells through Ca2+ channels or bond to cell surfaces. Exposure to Cd, Pb and Cd-Pb share several similar Key Events (KEs), primarily an increase of oxidative stress (OS) in immune cells through production of reactive oxygen species. For both metals and the mixture, OS affects mitochondrial membranes, and induces apoptosis, ultimately decreasing immune cell number. Both metals affect innate immune system through nuclear factor kappa B (NF-κB) and mitogen-activated protein kinase (MAPK) inflammatory signalling pathways, leading to an upregulation of inflammatory markers and mediators. Adaptive immune system is also affected by the exposure to both metals though a decrease of CD4+/CD8+ ratio, a decrease of MHCII, an inactivation of TH1 and TH2 response, and an inhibition of the humoral response mediated by various Ig. Mixture effects of Cd-Pb are less documented resulting in a more speculative AOP, but potential synergic and antagonistic effects were identified. According to our AOPs, further research in ecoimmunotoxicology of metals in free-ranging mammals should focus on KEs related to NF-κB/MAPK inflammatory signalling pathways, changes in CD4+/CD8+ ratio and MHCII complexes, and on AOs related to auto-immune disorders and on the effective increase of infection rate, particularly in case of exposure to metal mixtures.

The One Health approach in urban ecosystem rehabilitation: An evidence-based framework for designing sustainable cities

Rapid urbanization has led to negative, and sometimes unintended, consequences on biodiversity and human health. While cities offer numerous advantages in meeting the basic needs of a growing population, they also pose less apparent and longer-term health costs. To address the multifaceted impacts of urbanization, an evidence-based design framework for establishing mitigation and regeneration actions is essential. Via a "One Health" approach, this perspective provides recommendations and strategies for the urban ecosystem rehabilitation of future cities, placing biodiversity and ecosystem services at the core of designing healthy and sustainable urban spaces. The framework we propose is based on a Hub and Spoke model to integrate diverse perspectives from public and private sectors and declined in a six-building-blocks structure. This will ensure that efforts are sustainable, health-centered, socially inclusive, and grounded in high-quality data, reinforcing the essential connection between healthy environments and thriving communities.

Comparative analysis of meningeal transcriptomes in birds: Potential pathways of resilience to repeated impacts

The meninges and associated vasculature (MAV) play a crucial role in maintaining cerebral integrity and homeostasis. Recent advances in transcriptomic analysis have illuminated the significance of the MAV in understanding the complex physiological interactions at the interface between the skull and the brain after exposure to mechanical stress. To investigate how physiological responses may confer resilience against repetitive mechanical stress, we performed the first transcriptomic analysis of avian MAV tissues using the Downy Woodpecker (Dryobates pubescens) and Tufted Titmouse (Baeolophus bicolor) as the comparison species. Our findings reveal divergences in gene expression profiles related to immune response, cellular stress management, and protein translation machinery. The male woodpeckers exhibit a tailored immune modulation strategy that potentially dampens neuroinflammation while preserving protective immunity. Overrepresented genes involved in cellular stress responses suggest enhanced mechanisms for mitigating damage and promoting repair. Additionally, the enrichment of translation-associated pathways hints at increased capacity for protein turnover and cellular remodeling vital for recovery. Our study not only fills a critical gap in avian neurobiology but also lays the groundwork for research in comparative neuroprotection.

Urbanisation-associated shifts in the avian metabolome within the annual cycle

While organisms have evolved to cope with predictable changes in the environment, the rapid rate of current global change presents numerous novel and unpredictable stressors to which organisms have had less time to adapt. To persist in the urban environment, organisms must modify their physiology, morphology and behaviour accordingly. Metabolomics offers great potential for characterising organismal responses to natural and anthropogenic stressors at the systems level and can be applied to any species, even without genomic knowledge. Using metabolomic profiling of blood, we investigated how two closely related species of passerine bird respond to the urban environment. Great tits Parus major and blue tits Cyanistes caeruleus residing in urban and forest habitats were sampled during the breeding (spring) and non-breeding (winter) seasons across replicated sites in southern Sweden. During breeding, differences in the plasma metabolome between urban and forest birds were characterised by higher levels of amino acids in urban-dwelling tits and higher levels of fatty acyls in forest-dwelling tits. The suggested higher rates of fatty acid oxidation in forest tits could be driven by habitat-associated differences in diet and could explain the higher reproductive investment and success of forest tits. High levels of amino acids in breeding urban tits could reflect the lack of lipid-rich caterpillars in the urban environment and a dietary switch to protein-rich spiders, which could be of benefit for tackling inflammation and oxidative stress associated with pollution. In winter, metabolomic profiles indicated lower overall levels of amino acids and fatty acyls in urban tits, which could reflect relaxed energetic demands in the urban environment. Our metabolomic profiling of two urban-adapted species suggests that their metabolism is modified by urban living, though whether these changes represent adaptative or non-adaptive mechanisms to cope with anthropogenic challenges remains to be determined.

Constitutive innate immune defenses in relation to urbanization and population density in an urban bird, the feral pigeon Columba livia domestica

Urbanization processes modulate the immunological challenges faced by animals. Urban habitat transformations reshape pathogen diversity and abundance, while high population density-common in urban exploiter species-promotes disease transmission. Responses to urbanization may include adaptive adjustments of constitutive innate immune defenses (e.g. complement system and natural antibodies [NAbs]), which serve as first-line protection against infections. Here, we investigated associations of habitat urbanization and host population density with complement and NAbs in an urban bird, the feral pigeon Columba livia domestica. To do so, we employed the hemolysis-hemagglutination assay to analyze nearly 200 plasma samples collected across urbanization and pigeon population density gradients in five major cities in Poland. We found a negative association between urbanization score and hemagglutination (i.e. NAbs activity), but not hemolysis (i.e. complement activity), indicating either immunosuppression or adaptive downregulation of this immune defense in highly transformed urban landscape. Population density was not significantly related to either immune parameter, providing no evidence for density-dependent modulation of immune defenses. At the same time, there was a negative association of hemolysis with condition (scaled mass index), suggesting resource allocation trade-offs or contrasting effects of the urban environment on immune defenses and body condition. The results demonstrate that habitat structure can be an important factor shaping the immune defenses of the feral pigeon, although these associations were not mediated by variation in population density. Our study highlights the complexity of the links between immune defenses in wildlife and urbanization and reinforces the need for comprehensive ecoimmunological studies on urban animals.

The impact of urbanization on health depends on the health metric, life stage and level of urbanization: a global meta-analysis on avian species

Stressors associated with urban habitats have been linked to poor wildlife health but whether a general negative relationship between urbanization and animal health can be affirmed is unclear. We conducted a meta-analysis of avian literature to test whether health biomarkers differed on average between urban and non-urban environments, and whether there are systematic differences across species, biomarkers, life stages and species traits. Our dataset included 644 effect sizes derived from 112 articles published between 1989 and 2022, on 51 bird species. First, we showed that there was no clear impact of urbanization on health when we categorized the sampling locations as urban or non-urban. However, we did find a small negative effect of urbanization on health when this dichotomous variable was replaced by a quantitative variable representing the degree of urbanization at each location. Second, we showed that the effect of urbanization on avian health was dependent on the type of health biomarker measured as well as the individual life stage, with young individuals being more negatively affected. Our comprehensive analysis calls for future studies to disentangle specific urban-related drivers of health that might be obscured in categorical urban versus non-urban comparisons.

Response of wild aquatic insect communities to thermal variation through comparative landscape transcriptomics

Fluctuations in temperature are recognized as a potent driver of selection pressure, fostering genomic variations that are crucial for the adaptation and survival of organisms under selection. Notably, water temperature is a pivotal factor influencing aquatic organism persistence. By comprehending how aquatic organisms respond to shifts in water temperature, we can understand their potential physiological adaptations to environmental change in one or multiple species. This, in turn, contributes to the formulation of biologically relevant guidelines for the landscape scale transcriptome profile of organisms in lotic systems. Here, we investigated the distinct responses of seven stream stonefly species, collected from four geographical regions across Japan, to variations in temperature, including atmospheric and water temperatures. We achieved this by assessing the differences in gene expression through RNA-sequencing within individual species and exploring the patterns of community-genes among different species. We identified 735 genes that exhibited differential expressions across the temperature gradient. Remarkably, the community displayed expression levels differences of respiration and metabolic genes. Additionally, the diversity in molecular functions appeared to be linked to spatial variation, with water temperature differences potentially contributing to the overall functional diversity of genes. We found 22 community-genes with consistent expression patterns among species in response to water temperature variations. These genes related to respiration, metabolism and development exhibited a clear gradient providing robust evidence of divergent adaptive responses to water temperature. Our findings underscore the differential adaptation of stonefly species to local environmental conditions, suggesting that shared responses in gene expression may occur across multiple species under similar environmental conditions. This study emphasizes the significance of considering various species when assessing the impacts of environmental changes on aquatic insect communities and understanding potential mechanisms to cope with such changes.

Short-term dietary changes are reflected in the cerebral content of adult ring-billed gulls

Omega-3 long-chain polyunsaturated fatty acids (n3-LCPUFAs) are produced primarily in aquatic ecosystems and are considered essential nutrients for predators given their structural role in vertebrates' cerebral tissues. Alarmingly, with urbanization, many aquatic animals now rely on anthropogenic foods lacking n3-LCPUFAs. In this study undertaken in Newfoundland (Canada), we tested whether recent or longer term diet explains the cerebral fatty acid composition of ring-billed gulls (Larus delawarensis), a seabird that now thrives in cities. During the breeding season, cerebral levels of n3-LCPUFAs were significantly higher for gulls nesting in a natural habitat and foraging on marine food (mean ± s.d.: 32 ± 1% of total identified fatty acids) than for urban nesters exploiting rubbish (27 ± 1%). Stable isotope analysis of blood and feathers showed that urban and natural nesters shared similar diets in autumn and winter, suggesting that the difference in cerebral n3-LCPUFAs during the breeding season was owing to concomitant and transient differences in diet. We also experimentally manipulated gulls' diets throughout incubation by supplementing them with fish oil rich in n3-LCPUFAs, a caloric control lacking n3-LCPUFAs, or nothing, and found evidence that fish oil increased urban nesters' cerebral n3-LCPUFAs. These complementary analyses provide evidence that the brain of this seabird remains plastic during adulthood and responds to short-term dietary changes.

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.

Dietary fatty acids modulate oxidative stress response to air pollution but not to infection

Anthropogenic changes to the environment expose wildlife to many pollutants. Among these, tropospheric ozone is of global concern and a highly potent pro-oxidant. In addition, human activities include several other implications for wildlife, e.g., changed food availability and changed distribution of pathogens in cities. These co-occurring habitat changes may interact, thereby modulating the physiological responses and costs related to anthropogenic change. For instance, many food items associated with humans (e.g., food waste and feeders for wild birds) contain relatively more ω6-than ω3-polyunsaturated fatty acids (PUFAs). Metabolites derived from ω6-PUFAs can enhance inflammation and oxidative stress towards a stimulus, whereas the opposite response is linked to ω3-derived metabolites. Hence, we hypothesized that differential intake of ω6-and ω3-PUFAs modulates the oxidative stress state of birds and thereby affects the responses towards pro-oxidants. To test this, we manipulated dietary ω6:ω3 ratios and ozone levels in a full-factorial experiment using captive zebra finches (Taeniopygia guttata). Additionally, we simulated an infection, thereby also triggering the immune system's adaptive pro-oxidant release (i.e., oxidative burst), by injecting lipopolysaccharide. Under normal air conditions, the ω3-diet birds had a lower antioxidant ratio (GSH/GSSG ratio) compared to the ω6-diet birds. When exposed to ozone, however, the diet effect disappeared. Instead, ozone exposure overall reduced the total concentration of the key antioxidant glutathione (tGSH). Moreover, the birds on the ω6-rich diet had an overall higher antioxidant capacity (OXY) compared to birds fed a ω3-rich diet. Interestingly, only the immune challenge increased oxidative damage, suggesting the oxidative burst of the immune system overrides the other pro-oxidative processes, including diet. Taken together, our results show that ozone, dietary PUFAs, and infection all affect the redox-system, but in different ways, suggesting that the underlying responses are decoupled despite that they all increase pro-oxidant exposure or generation. Despite lack of apparent cumulative effect in the independent biomarkers, the combined single effects could together reduce overall cellular functioning and efficiency over time in wild birds exposed to pathogens, ozone, and anthropogenic food sources.

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

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

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.

Feather corticosterone reveals that urban great tits experience lower corticosterone exposure than forest individuals during dominance-rank establishment

Although the consequences of urbanization for the physiological health of animals are the focus of much active research, an overlooked aspect is how physiology could be indirectly modulated by the urban environment via changes in intraspecific behavioural interactions, particularly among gregarious species. Both urbanization and the establishment, as well as maintenance, of hierarchical rank position are processes that could incur physiological stress. Measurements of glucocorticoids (GCs) in relation to urbanization, however, have yielded inconsistent results. In most cases, GCs have been measured in blood, offering only a 'snapshot' of an animal's current physiological state. Because circulating GCs are incorporated into growing feathers or hair, measurements of feather/hair GCs offer a longer term measure of stress exposure reflecting the whole period of feather/hair growth. During two calendar years, we collected tail feathers from 188 urban and forest great tits (P. major) across multiple sampling sites and analysed corticosterone (CORT-the main GC in birds) levels, reflecting CORT exposure during the extended period in late summer and early autumn when great tits moult and winter flocks are formed. Urban individuals exhibited consistently lower feather CORT (fCORT) levels than forest birds indicating lower overall exposure to CORT during this period. The lower fCORT levels in urban individuals could represent an adaptation to cope with the more challenging urban environment, physiological constraints on stress axis function or a trade-off between the ability to respond to stressors and predation risk during moult. Despite the expectation that CORT responses to urbanization are highly context-dependent, the spatial consistency of our results and agreement with a multi-population study of fCORT in European blackbirds (Turdus merula) suggests a generalization of the effect of urbanization on CORT exposure during post-breeding moult (i.e. not site- or species-specific).

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

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

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.

Multi-omics responses in tree swallow (Tachycineta bicolor) nestlings from the Maumee Area of Concern, Maumee River, Ohio

A multi-omics approach was utilized to identify altered biological responses and functions, and to prioritize contaminants to assess the risks of chemical mixtures in the Maumee Area of Concern (AOC), Maumee River, OH, USA. The Maumee AOC is designated by the United States Environmental Protection Agency as having significant beneficial use impairments, including degradation of fish and wildlife populations, bird or animal deformities or reproduction problems, and loss of fish and wildlife habitat. Tree swallow (Tachycineta bicolor) nestlings were collected at five sites along the Maumee River, which included wastewater treatment plants (WWTPs) and industrial land-use sites. Polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), polycyclic aromatic hydrocarbons (PAHs), polychlorinated dibenzo p dioxins and furans (PCDD/Fs), and chlorinated pesticide concentrations were elevated in Maumee tree swallows, relative to a remote reference site, Star Lake, WI, USA. Liver tissue was utilized for non-targeted transcriptome and targeted metabolome evaluation. A significantly differentially expressed gene cluster related to a downregulation in cell growth and cell cycle regulation was identified when comparing all Maumee River sites with the reference site. There was an upregulation of lipogenesis genes, such as PPAR signaling (HMGCS2, SLC22A5), biosynthesis of unsaturated fatty acids (FASN, SCD, ELOVL2, and FADS2), and higher lipogenesis related metabolites, such as docosapentaenoic acid (DPA), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and arachidonic acid (AA) at two industrial land-use sites, Ironhead and Maumee, relative to WWTP sites (Perrysburg and SideCut), and the reference site. Toledo Water, in the vicinity of the other two industrial sites and also adjacent to a WWTP, showed a mix of signals between industrial land-use and WWTP land-use. PAHs, oxychlordane, and PBDEs were determined to be the most likely causes of the differentiation in biological responses, including de novo lipogenesis and biosynthesis of unsaturated fatty acids.

The role of vital dietary biomolecules in eco-evo-devo dynamics

The physiological dependence of animals on dietary intake of vitamins, amino acids, and fatty acids is ubiquitous. Sharp differences in the availability of these vital dietary biomolecules among different resources mean that consumers must adopt a range of strategies to meet their physiological needs. We review the emerging work on omega-3 long-chain polyunsaturated fatty acids, focusing predominantly on predator-prey interactions, to illustrate that trade-off between capacities to consume resources rich in vital biomolecules and internal synthesis capacity drives differences in phenotype and fitness of consumers. This can then feedback to impact ecosystem functioning. We outline how focus on vital dietary biomolecules in eco-eco-devo dynamics can improve our understanding of anthropogenic changes across multiple levels of biological organization.

Behavioral plasticity can facilitate evolution in urban environments

Plasticity-led evolution is central to evolutionary theory. Although challenging to study in nature, this process may be particularly apparent in novel environments such as cities. We document abundant evidence of plastic behavioral changes in urban animals, including learning, contextual, developmental, and transgenerational plasticities. Using behavioral drive as a conceptual framework, our analysis of notable case studies suggests that plastic behaviors, such as altered habitat use, migration, diurnal and seasonal activity, and courtship, can have faciliatory and cascading effects on urban evolution via spatial, temporal, and mate-choice mechanisms. Our findings highlight (i) the need to incorporate behavioral plasticity more formally into urban evolutionary research and (ii) the opportunity provided by urban environments to study behavioral mechanisms of plasticity-led processes.

Transcriptomic responses of Galápagos finches to avian poxvirus infection

Emerging pathogens can have devastating effects on naïve hosts, but disease outcomes often vary among host species. Comparing the cellular response of different hosts to infection can provide insight into mechanisms of host defence. Here, we used RNA-seq to characterize the transcriptomic response of Darwin's finches to avian poxvirus, a disease of concern in the Galápagos Islands. We tested whether gene expression differs between infected and uninfected birds, and whether transcriptomic differences were related either to known antiviral mechanisms and/or the co-option of the host cellular environment by the virus. We compared two species, the medium ground finch (Geospiza fortis) and the vegetarian finch (Platyspiza crassirostris), to determine whether endemic Galápagos species differ in their response to pox. We found that medium ground finches had a strong transcriptomic response to infection, upregulating genes involved in the innate immune response including interferon production, inflammation, and other immune signalling pathways. In contrast, vegetarian finches had a more limited response, and some changes in this species were consistent with viral manipulation of the host's cellular function and metabolism. Many of the transcriptomic changes mirrored responses documented in model and in vitro studies of poxviruses. Our results thus indicate that many pathways of host defence against poxviruses are conserved among vertebrates and present even in hosts without a long evolutionary history with the virus. At the same time, the differences we observed between closely related species suggests that some endemic species of Galápagos finch could be more susceptible to avian pox than others.

Population density mediates induced immune response, but not physiological condition in a well-adapted urban bird

Thriving under high population density is considered a major feature of urban exploiter species. Nevertheless, population density appears to be a surprisingly overlooked factor in urban ecology studies. High population numbers observed in urban species might promote pathogen transmission and negatively affect health or condition, thus requiring investments in immunocompetence. The feral pigeon Columba livia domestica is an example of a successful city-dweller, found in great abundance in large cities across the globe. We investigated the effects of population density on induced immune response (phytohaemagglutinin skin test) and body condition (blood haemoglobin concentration and size-corrected body mass) in 120 feral pigeons, captured along population density gradient in Łódź (central Poland). We found that stronger immune response was associated with higher population density, but was not related to physiological condition and physiological stress (heterophil/lymphocyte ratio). Moreover, condition indices were not associated with population density. However, since pigeon population density was highly correlated with the level of habitat urbanization, we cannot exclude that any density-dependent effects may be mediated by habitat variation. Our results indicate that urban environment, via population density, might exert different selective pressures on immunocompetence and body condition in this successful urban exploiter.

How thermal challenges change gene regulation in the songbird brain and gonad: implications for sexual selection in our changing world

In a rapidly warming world, exposure to high temperatures may impact fitness, but the gene regulatory mechanisms that link sublethal heat to sexually selected traits are not well understood, particularly in endothermic animals. Our experiment used zebra finches (Taeniopygia guttata), songbirds that experience extreme temperature fluctuations in their native Australia. We exposed captive males to an acute thermal challenge (43°C) compared with thermoneutral (35°C) and lower (27°C) temperatures. We found significantly more heat dissipation behaviors at 43°C, a temperature previously shown to reduce song production and fertility, and more heat retention behaviors at 27°C. Next, we characterized transcriptomic responses in tissues important for mating effort - the posterior telencephalon, for its role in song production, and the testis, for its role in fertility and hormone production. Differential expression of hundreds of genes in the testes, but few in the brain, suggest the brain is less responsive to extreme temperatures. Nevertheless, gene network analyses revealed that expression related to dopaminergic signaling in the brain co-varied with heat dissipation behaviors, providing a mechanism by which temporary thermal challenges may alter motivational circuits for song production. In both brain and testis, we observed correlations between thermally sensitive gene networks and individual differences in thermoregulatory behavior. Although we cannot directly relate these gene regulatory changes to mating success, our results suggest that individual variation in response to thermal challenges could impact sexually selected traits in a warming world.

Recovery of RNA from avian nucleated whole blood stored under field conditions: an evaluation of commercial methods

1. Whole blood can be used to gain insights on several molecular mechanisms involved in animal physiology. However, its use to extract RNA from organisms that carry nucleated red blood cells is limited due to its high nuclease content and instability under field conditions.

2. Here, we evaluate three commercially available RNA preservation and extraction methods applied to avian whole blood samples kept in different storage conditions to identify the most suitable ones for use in field studies.

3. Whole blood starting volume was the most important factor; only samples with a starting volume of 50 µl yielded RNA whereas all 100 µl samples failed to provide any RNA regardless of the method used. RNA concentration decreased with storage time in every method employed. Samples stored at -20 °C yielded higher RNA concentration than the ones stored at 4°C although some possible effects of freeze-thaw cycles were observed.

4. For the two out of three methods it is likely that DNA contamination and/or extensive degradation of RNA could have taken place. Only whole blood stored and extracted using the Quick RNA Whole Blood kit provided high quality RNA in every condition tested.

Differences in fatty acids composition between Plasmodium infected and uninfected house sparrows along an urbanization gradient

Anthropogenic activities such as intensification of agriculture, animal husbandry and expansion of cities can negatively impact wildlife through its influence on the availability of high-quality food resources and pathogen transmission. The house sparrow (Passer domesticus), an urban exploiter, is undergoing a population decline. Nutritional constrains and infectious diseases has been highlighted as potential causes. Fatty acids (FAs) play an important role in modulating certain immune responses needed to combat parasite infections. FAs are highly influenced by dietary availability and have been shown to vary between urban and rural birds. Habitat anthropization also affects avian malaria epidemiology but little attention has been given to the relationship between blood parasite infection, host FAs composition and anthropization. Here, we analysed 165 juvenile birds either infected by Plasmodium or uninfected, captured at 15 localities grouped in triplets containing urban, rural and natural habitats. The total level of FAs was higher in birds from urban than from rural habitats, suggesting a greater availability of fat-rich foods sources. Furthermore, Plasmodium infected birds had higher relative levels of ω-3 polyunsaturated fatty acids (PUFAs) but lower of ω-6 PUFAs than uninfected birds. In concordance, the ω-6/ω-3 ratio was also lower in infected than in uninfected birds, but only from natural habitats, likely driven by the slightly higher ω-3 PUFAs in infected birds from natural habitats. Birds from anthropized environments may metabolize the ω-3 PUFAs to promote anti-inflammatory responses against stressors, which would result in lower ω-3 affecting their response against Plasmodium. Alternatively, lower ω-6 PUFAs may influence birds susceptibility to infection due to a weaker pro-inflammatory response. These descriptive results do not allow us to identify the causality of these associations but highlight the need to further investigate the relevance of FAs for birds to fight infectious diseases in habitats with different degree of urbanization.

Spring colonies of the ant Temnothorax nylanderi tolerate cadmium better than winter colonies, in both a city and a forest habitat

A recent study showed that, in the ant Temnothorax nylanderi, city colonies are more tolerant to cadmium than forest colonies. However, because of annual variation in biological factors (e.g. body size, anti-stress protein production or trace metal accumulation rate), trace metal tolerance may vary over the year. We aimed at testing whether tolerance to cadmium of colonies of T. nylanderi differs between two different seasons within the same year (winter and spring). We also assessed whether the better cadmium tolerance of city colonies was constant over these two different time points. We collected colonies at the end of their hibernation period (winter colonies) and several weeks after (spring colonies) from two different habitats (forest and city) to assess whether response to cadmium was consistent regardless of the environment. We exposed colonies to a cadmium or a control treatment for 61 days. We compared tolerance to cadmium between spring/winter and city/forest colonies by measuring several life history traits. We found that spring colonies tolerates cadmium better than winter colonies, and that city colonies have a higher tolerance to cadmium but only in spring. Although further studies with replicated pairs of city/forest habitats and different years will be necessary to confirm those results, our study suggests that tolerance to trace metals can fluctuate along the yearly cycle.

Historical museum samples enable the examination of divergent and parallel evolution during invasion

During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline and global climate change. Concurrently, greater globalization is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species' ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species' invasion success or persistence informs invasive species management, assists with native species preservation and sheds light on important evolutionary mechanisms that occur in novel environments. This approach can be aided by coupling spatial and temporal investigations of evolutionary processes. Here we use the common starling, Sturnus vulgaris, to identify parallel and divergent evolutionary change between contemporary native and invasive range samples and their common ancestral population. To do this, we use reduced-representation sequencing of native samples collected recently in northwestern Europe and invasive samples from Australia, together with museum specimens sampled in the UK during the mid-19th century. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants. We also identified divergent selection in these populations, which might be related to adaptive changes in response to the novel environment encountered in the introduced Australian range. Interestingly, signatures of selection are equally as common within both invasive and native range contemporary samples. Our results demonstrate the value of including historical samples in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.

Fatty acids composition in yellow-legged (Larus michahellis) and lesser black-backed (Larus fuscus) gulls from natural and urban habitats in relation to the ingestion of anthropogenic materials

Urban habitats offer spatially and temporally predictable anthropogenic food sources for opportunistic species, such as several species of gulls that are known to exploit urban areas and take advantage of accessible and diverse food sources, reducing foraging time and energy expenditure. However, human-derived food may have a poorer nutritional quality than the typical natural food resources and foraging in urban habitats may increase birds' susceptibility of ingesting anthropogenic debris materials, with unknown physiological consequences for urban dwellers. Here we compare the fatty acids (FA) composition of two opportunistic gull species (the yellow-legged gull, Larus michahellis, and the lesser black-backed gull, Larus fuscus) from areas with different levels of urbanization, to assess differences in birds' diet quality among foraging habitats, and we investigate the effects of ingesting anthropogenic materials, a toxicological stressor, on gulls' FA composition. Using GC-MS, 23 FAs were identified in the adipose tissue of both gull species. Significant differences in gulls' FA composition were detected among the three urbanization levels, mainly due to physiologically important highly unsaturated FAs that had lower percentages in gulls from the most urbanized habitats, consistent with a diet based on anthropogenic food resources. The deficiency in omega (ω)-3 FAs and the higher ω-6:ω-3 FAs ratio in gulls from the most urbanized location may indicate a diet-induced susceptibility to inflammation. No significant differences in overall FA composition were detected between gull species. While we were unable to detect any effect of ingested anthropogenic materials on gulls' FA composition, these data constitute a valuable contribution to the limited FA literature in gulls. We encourage studies to explore the long-term physiological effects of the lower nutritional quality diet for urban dwellers, and to detect the sub-lethal impacts of the ingestion of anthropogenic materials.

Variation in Hematological Indices, Oxidative Stress, and Immune Function Among Male Song Sparrows From Rural and Low-Density Urban Habitats

A central theme in the field of ecology is understanding how environmental variables influence a species’ distribution. In the last 20 years, there has been particular attention given to understanding adaptive physiological traits that allow some species to persist in urban environments. However, there is no clear consensus on how urbanization influences physiology, and it is unclear whether physiological differences in urban birds are directly linked to adverse outcomes or are representative of urban birds adaptively responding to novel environmental variables. Moreover, though low-density suburban development is the fastest advancing form of urbanization, most studies have focused on animals inhabiting high intensity urban habitats. In this study, we measured a suite of physiological variables that reflect condition and immune function in male song sparrows (Melospiza melodia) from rural and suburban habitats. Specifically, we measured hematological indices [packed cell volume (PCV), hemoglobin concentration, mean corpuscular hemoglobin concentration (MCHC)], circulating glutathione (total, reduced, and oxidized), oxidative damage (d-ROM concentration), antioxidant capacity, and components of the innate immune system [bacteria killing ability (BKA), white blood cell counts]. We also measured whole-animal indices of health, including body condition (scaled mass index length) and furcular fat. Song sparrows inhabiting suburban environments exhibited lower hemoglobin and MCHC, but higher body condition and furcular fat scores. Additionally, suburban birds had higher heterophil counts and lower lymphocyte counts, but there were no differences in heterophil:lymphocyte ratio or BKA between suburban and rural birds. PCV, glutathione concentrations, and oxidative damage did not differ between suburban and rural sparrows. Overall, suburban birds did not exhibit physiological responses suggestive of adverse outcomes. Rather, there is some evidence that sparrows from rural and suburban habitats exhibit phenotypic differences in energy storage and metabolic demand, which may be related to behavioral differences previously observed in sparrows from these populations. Furthermore, this study highlights the need for measuring multiple markers of physiology across different types of urban development to accurately assess the effects of urbanization on wildlife.

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.

Sex differences in immune gene expression in the brain of a small shorebird

Males and females often exhibit differences in behaviour, life histories, and ecology, many of which are typically reflected in their brains. Neuronal protection and maintenance include complex processes led by the microglia, which also interacts with metabolites such as hormones or immune components. Despite increasing interest in sex-specific brain function in laboratory animals, the significance of sex-specific immune activation in the brain of wild animals along with the variables that could affect it is widely lacking. Here, we use the Kentish plover (Charadrius alexandrinus) to study sex differences in expression of immune genes in the brain of adult males and females, in two wild populations breeding in contrasting habitats: a coastal sea-level population and a high-altitude inland population in China. Our analysis yielded 379 genes associated with immune function. We show a significant male-biased immune gene upregulation. Immune gene expression in the brain did not differ in upregulation between the coastal and inland populations. We discuss the role of dosage compensation in our findings and their evolutionary significance mediated by sex-specific survival and neuronal deterioration. Similar expression profiles in the coastal and inland populations suggest comparable genetic control by the microglia and possible similarities in pathogen pressures between habitats. We call for further studies on gene expression of males and females in wild population to understand the implications of immune function for life-histories and demography in natural systems.

Urbanization processes drive divergence at the major histocompatibility complex in a common waterbird

Urban sprawl is one of the most common landscape alterations occurring worldwide, and there is a growing list of species that are recognised to have adapted to urban life. To be successful, processes of urban colonization by wildlife require a broad spectrum of phenotypic (e.g., behavioural or physiological) adjustments, but evidence for genetic adaptations is much scarcer. One hypothesis proposes that different pathogen-driven selective pressures between urban and non-urban landscapes leads to adaptations in host immune genes. Here, we examined urbanization-related differentiation at the key pathogen-recognition genes of vertebrate adaptive immunity-the major histocompatibility complex (MHC)-in a common waterbird, the Eurasian coot (Fulica atra). Samples were collected from an old urban population (established before the 1950s), a new urban population (established in the 2000s), and two rural populations from central Poland. We found strong significant divergence (as measured with Jost's D) at the MHC class II between the old urban population and the remaining (new urban and rural) populations. Also, there was a moderate, but significant divergence at the MHC between the new urban population and two rural populations, while no divergence was found between the two rural populations. The total number of MHC alleles and the number of private (population-specific) MHC alleles was lower in old urban populations, as compared to the rural ones. These patterns of differentiation at the MHC were not consistent with patterns found for neutral genetic markers (microsatellites), which showed few differences between the populations. Our results indicate that MHC allele composition depended on the level of anthropogenic disturbance and the time which passed since urban colonization, possibly due to the processes of genotype sorting and local adaptation. As such, our study contributes to the understanding of genetic mechanisms associated with urbanization processes in wildlife.

Replicated, urban-driven exposure to metallic trace elements in two passerines

While there are increasing examples of phenotypic and genotypic differences between urban and non-urban populations of plants and animals, few studies identified the mechanisms explaining those dissimilarities. The characterization of the urban landscape, which can only be achieved by measuring variability in relevant environmental factors within and between cities, is a keystone prerequisite to understand the effects of urbanization on wildlife. Here, we measured variation in bird exposure to metal pollution within 8 replicated urbanization gradients and within 2 flagship bird species in urban evolutionary ecology: the blue tit (Cyanistes caeruleus) and the great tit (Parus major). We report on a highly significant, positive linear relationship between the magnitude of urbanization-inferred as either tree cover, impervious surface cover, or an urbanization score computed from several environmental variables, and copper, zinc and lead concentrations in bird feathers. The reverse relationship was measured in the case of mercury, while cadmium and arsenic did not vary in response to the urbanization level. This result, replicated across multiple cities and two passerine species, strongly suggests that copper, zinc, lead and mercury pollution is likely to trigger the emergence of parallel responses at the phenotypic and/or genotypic level between urban environments worldwide.

Telomerase activity can mediate the effects of growth on telomeres during post-natal development in a wild bird

In wild animals, telomere attrition during early development has been linked with several fitness disadvantages throughout life. Telomerase enzyme can elongate telomeres, but it is generally assumed that its activity is suppressed in most somatic tissues upon birth. However, recent evidence suggests that this may not be the case for long-lived bird species. We have therefore investigated whether telomerase activity is maintained during the postnatal growth period in a wild yellow-legged gull (Larus michahellis) population. Our results indicate that telomerase activity is not negligible in the blood cells, but activity levels sharply decline from hatching to fledging following a similar pattern to the reduction observed in telomere length. Our results further suggest that the observed variation in telomere length may be the result of a negative effect of fast growth on telomerase activity, thus providing a new mechanism through which growth rates may affect telomere dynamics and potentially life-history trajectories.

The evolutionary ecology of fatty-acid variation: Implications for consumer adaptation and diversification

The nutritional diversity of resources can affect the adaptive evolution of consumer metabolism and consumer diversification. The omega-3 long-chain polyunsaturated fatty acids eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) have a high potential to affect consumer fitness, through their widespread effects on reproduction, growth and survival. However, few studies consider the evolution of fatty acid metabolism within an ecological context. In this review, we first document the extensive diversity in both primary producer and consumer fatty acid distributions amongst major ecosystems, between habitats and amongst species within habitats. We highlight some of the key nutritional contrasts that can shape behavioural and/or metabolic adaptation in consumers, discussing how consumers can evolve in response to the spatial, seasonal and community-level variation of resource quality. We propose a hierarchical trait-based approach for studying the evolution of consumers' metabolic networks and review the evolutionary genetic mechanisms underpinning consumer adaptation to EPA and DHA distributions. In doing so, we consider how the metabolic traits of consumers are hierarchically structured, from cell membrane function to maternal investment, and have strongly environment-dependent expression. Finally, we conclude with an outlook on how studying the metabolic adaptation of consumers within the context of nutritional landscapes can open up new opportunities for understanding evolutionary diversification.

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.

Exposure to artificial light at night alters innate immune response in wild great tit nestlings

The large-scale impact of urbanization on wildlife is rather well documented; however, the mechanisms underlying the effects of urban environments on animal physiology and behaviour are still poorly understood. Here, we focused on one major urban pollutant - artificial light at night (ALAN) - and its effects on the capacity to mount an innate immune response in wild great tit (Parus major) nestlings. Exposure to ALAN alters circadian rhythms of physiological processes, by disrupting the nocturnal production of the hormone melatonin. Nestlings were exposed to a light source emitting 3 lx for seven consecutive nights. Subsequently, nestlings were immune challenged with a lipopolysaccharide injection, and we measured haptoglobin and nitric oxide levels pre- and post-injection. Both haptoglobin and nitric oxide are important markers for innate immune function. We found that ALAN exposure altered the innate immune response, with nestlings exposed to ALAN having lower haptoglobin and higher nitric oxide levels after the immune challenge compared with dark-night nestlings. Unexpectedly, nitric oxide levels were overall lower after the immune challenge than before. These effects were probably mediated by melatonin, as ALAN-treated birds had on average 49% lower melatonin levels than the dark-night birds. ALAN exposure did not have any clear effects on nestling growth. This study provides a potential physiological mechanism underlying the documented differences in immune function between urban and rural birds observed in other studies. Moreover, it gives evidence that ALAN exposure affects nestling physiology, potentially causing long-term effects on physiology and behaviour, which ultimately can affect their fitness.

Species and population specific gene expression in blood transcriptomes of marine turtles

BACKGROUND

Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms' responses to environmental stressors. However, a lack of genomic resources and challenges associated with collecting high-quality RNA can limit its application for many wild populations. Minimally invasive blood sampling combined with de novo transcriptomic approaches has great potential to alleviate these barriers. Here, we advance these goals for marine turtles by generating high quality de novo blood transcriptome assemblies to characterize functional diversity and compare global transcriptional profiles between tissues, species, and foraging aggregations.

RESULTS

We generated high quality blood transcriptome assemblies for hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), green (Chelonia mydas), and leatherback (Dermochelys coriacea) turtles. The functional diversity in assembled blood transcriptomes was comparable to those from more traditionally sampled tissues. A total of 31.3% of orthogroups identified were present in all four species, representing a core set of conserved genes expressed in blood and shared across marine turtle species. We observed strong species-specific expression of these genes, as well as distinct transcriptomic profiles between green turtle foraging aggregations that inhabit areas of greater or lesser anthropogenic disturbance.

CONCLUSIONS

Obtaining global gene expression data through non-lethal, minimally invasive sampling can greatly expand the applications of RNA-sequencing in protected long-lived species such as marine turtles. The distinct differences in gene expression signatures between species and foraging aggregations provide insight into the functional genomics underlying the diversity in this ancient vertebrate lineage. The transcriptomic resources generated here can be used in further studies examining the evolutionary ecology and anthropogenic impacts on marine turtles.

Hibernation Conditions Contribute to the Differential Resistance to Cadmium between Urban and Forest Ant Colonies

Simple Summary

The resistance of organisms to trace metals can have a genetic or a plastic origin. Indeed, differential environmental conditions experienced before the exposure to trace metals could physiologically condition organisms and plastically enhance their subsequent resistance to trace metals. In this study on the ant Temnothorax nylanderi, we investigated whether the better cadmium resistance of urban colonies relative to forest colonies could originate from the distinct hibernation conditions that they experienced prior to cadmium exposure. We compared the ability of urban and forest colonies to resist cadmium depending on whether they had hibernated in their respective urban or forest habitats or under a laboratory common garden setup. We found that urban colonies resisted cadmium better than forest colonies when they had hibernated under a common garden. Surprisingly, this difference was not observed between urban and forest colonies that had hibernated in the field, in contrast with a previous study. One reason may be that winter was particularly mild on the year of our experiment. Our results therefore support the idea that urban colonies are genetically adapted to resist trace metals, but that this adaptation is only revealed under specific environmental conditions.

Abstract

Trace metals such as cadmium are found in high concentrations in urban environments. Animal and plant populations living in heavily contaminated environments could adapt to trace metals exposure. A recent study shows that urban populations of the acorn ant Temnothorax nylanderi are more resistant to cadmium than their forest counterparts. However, this study was performed using field colonies that had just come out of hibernation. Because urban and forest hibernation environments differ, the differential resistance to trace metals may originate either from differential hibernation conditions or from a different resistance baseline to cadmium. In this study, we tested these two hypotheses using laboratory common garden hibernation conditions. We let urban and forest colonies of the ant T. nylanderi hibernate under the same laboratory conditions for four months. After this hibernation period, we also collected field-hibernating colonies and we compared cadmium resistance between urban and forest colonies depending on the hibernation condition. We found a differential response to cadmium under common garden, with urban colonies displaying less larval mortality and lower size reduction of the produced individuals. This suggests a different resistance baseline of urban colonies to cadmium. However, unexpectedly, we did not detect the differential response between urban and forest colonies in the field, suggesting a more complex scenario involving both genetic and environmental influences.

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.

Urbanization is associated with modifications in DNA methylation in a small passerine bird

Urbanization represents a fierce driver of phenotypic change, yet the molecular mechanisms underlying observed phenotypic patterns are poorly understood. Epigenetic changes are expected to facilitate more rapid adaption to changing or novel environments, such as our towns and cities, compared with slow changes in gene sequence. A comparison of liver and blood tissue from great tits Parus major originating from an urban and a forest site demonstrated that urbanization is associated with variation in genome-wide patterns of DNA methylation. Combining reduced representation bisulphite sequencing with transcriptome data, we revealed habitat differences in DNA methylation patterns that suggest a regulated and coordinated response to the urban environment. In the liver, genomic sites that were differentially methylated between urban- and forest-dwelling birds were over-represented in regulatory regions of the genome and more likely to occur in expressed genes. DNA methylation levels were also inversely correlated with gene expression at transcription start sites. Furthermore, differentially methylated CpG sites, in liver, were over-represented in pathways involved in (i) steroid biosynthesis, (ii) superoxide metabolism, (iii) secondary alcohol metabolism, (iv) chylomicron remodelling, (v) cholesterol transport, (vi) reactive oxygen species (ROS) metabolic process and (vii) epithelial cell proliferation. This corresponds with earlier studies identifying diet and exposure to ROS as two of the main drivers of divergence between organisms in urban and nonurban environments. Conversely, in blood, sites that were differentially methylated between urban- and forest-dwelling birds were under-represented in regulatory regions, more likely to occur in nonexpressed genes and not over-represented in specific biological pathways. It remains to be determined whether diverging patterns of DNA methylation represent adaptive evolutionary responses and whether the conclusions can be more widely attributed to urbanization.

Feather corticosterone does not correlate with environmental stressors or body condition in an endangered waterbird

Physiological metrics are becoming popular tools for assessing individual condition and population health to inform wildlife management and conservation decisions. Corticosterone assays can provide information on how animals cope with individual and habitat-level stressors, and the recent development of feather assays is an exciting innovation that could yield important insights for conservation of wild birds. Due to the widespread enthusiasm for feather corticosterone as a potential bioindicator, studies are needed to assess the ability of this technique to detect meaningful differences in physiological stress across a variety of stressor types and intensities. We examined feather corticosterone from 144 individuals among the 13 known breeding populations of Hawaiian gallinule (Gallinula galeata sandvicensis), an endangered waterbird, on the island of O'ahu. These ecologically independent subpopulations are known to have low genetic connectivity and movement rates and differ largely across a number of important conditions, including level of predator management, human disturbance, proximity to urban development and conspecific population density. This system is well suited for assessing the performance of feather corticosterone as a bioindicator of different known habitat-level threats common to this and many other conservation-reliant species. We found no statistically significant relationship between feather corticosterone and level of predator control, level of human disturbance, gallinule population density, percent urban cover or body condition across all sites despite the substantial difference in stressor magnitude in our dataset. We did find that gallinules in habitats with larger population densities were in worse body condition. These findings suggest that feather corticosterone is not a consistent indicator of anthropogenic impacts on populations. Furthermore, they suggest that feather corticosterone may be a poor bioindicator of known habitat-level threats for Hawaiian gallinules and that it should be used with caution in other avian taxa of conservation concern.

Urban ecophysiology: beyond costs, stress and biomarkers

Natural habitats are rapidly declining due to urbanisation, with a concomitant decline in biodiversity in highly urbanised areas. Yet thousands of different species have colonised urban environments. These organisms are exposed to novel urban conditions, which are sometimes beneficial, but most often challenging, such as increased ambient temperature, chemicals, noise and light pollution, dietary alterations and disturbance by humans. Given the fundamental role of physiological responses in coping with such conditions, certain physiological systems such as the redox system, metabolism and hormones are thought to specifically influence organisms' ability to persist and cope with urbanisation. However, these physiological systems often show mixed responses to urbanisation. Does this mean that some individuals, populations or species are resilient to the urban environmental challenges? Or is something missing from our analyses, leading us to erroneous conclusions regarding the impact of urbanisation? To understand the impact of urbanisation, I argue that a more integrated mechanistic and ecological approach is needed, along with experiments, in order to fully understand the physiological responses; without knowledge of their ecological and evolutionary context, physiological measures alone can be misinterpreted. Furthermore, we need to further investigate the causes of and capacity for individual plasticity in order to understand not only the impact of urbanisation, but also species resilience. I argue that abiotic and biotic urban factors can interact (e.g. pollution with micro- and macronutrients) to either constrain or relax individual physiological responses - and, thereby, plasticity - on a temporal and/or spatial scale, which can lead to erroneous conclusions regarding the impact of urbanisation.