The house sparrow in the service of basic and applied biology

Australian vertebrate hosts of Japanese encephalitis virus; a review of the evidence

Japanese Encephalitis Virus (JEV) transmission in temperate Australia has underscored a critical need to characterise transmission pathways and identify probable hosts of infection within the country. This systematic review consolidates existing research on the vertebrate hosts of JEV that are known to exist in Australia. Specifically, we aim to identify probable species for JEV transmission, their potential role as either a spillover or maintenance host and identify critical knowledge gaps. Data were extracted from studies involving experimental infection, seroprevalence, and virus isolation and were available for 22 vertebrate species known to reside in Australia. A host competence score was calculated to assess the potential for a given species to infect JEV vectors and to quantity their possible role in JEV transmission. Based on the host competence score and ecology of each species, we find ardeid birds, feral pigs, and flying foxes have potential as maintenance hosts for JEV in the Australian context. We also note that brushtail possums and domestic pigs have potential as spillover hosts under certain outbreak conditions. However, evidence to confirm these roles in localized transmission or outbreaks is sparse, emphasizing the need for further targeted research. This review provides a foundation for future investigations into JEV transmission in Australia, advocating for enhanced surveillance and standardized research methodologies to better understand and mitigate the virus's impact.

A chromosome-level genome assembly of a free-living white-crowned sparrow (Zonotrichia leucophrys gambelii)

The white-crowned sparrow, Zonotrichia leucophrys, is a passerine bird with a wide distribution and it is extensively adapted to environmental changes. It has historically acted as a model species in studies on avian ecology, physiology and behaviour. Here, we present a high-quality chromosome-level genome of Zonotrichia leucophrys using PacBio and OmniC sequencing data. Gene models were constructed by combining RNA-seq and Iso-seq data from liver, hypothalamus, and ovary. In total a 1,123,996,003 bp genome was generated, including 31 chromosomes assembled in complete scaffolds along with other, unplaced scaffolds. This high-quality genome assembly offers an important genomic resource for the research community using the white-crowned sparrow as a model for understanding avian genome biology and development, and provides a genomic basis for future studies, both fundamental and applied.

Epigenetic modification of the hypothalamic-pituitary-adrenal (HPA) axis during development in the house sparrow (Passer domesticus)

Epigenetic modifications such as DNA methylation are important mechanisms for mediating developmental plasticity, where ontogenetic processes and their phenotypic outcomes are shaped by early environments. In particular, changes in DNA methylation of genes within the hypothalamic-pituitary-adrenal (HPA) axis can impact offspring growth and development. This relationship has been well documented in mammals but is less understood in other taxa. Here, we use target-enriched enzymatic methyl sequencing (TEEM-seq) to assess how DNA methylation in a suite of 25 genes changes over development, how these modifications relate to the early environment, and how they predict differential growth trajectories in the house sparrow (Passer domesticus). We found that DNA methylation changes dynamically over the postnatal developmental period: genes with initially low DNA methylation tended to decline in methylation over development, whereas genes with initially high DNA methylation tended to increase in methylation. However, sex-specific differentially methylated regions (DMRs) were maintained across the developmental period. We also found significant differences in post-hatching DNA methylation in relation to hatch date, with higher levels of DNA methylation in nestlings hatched earlier in the season. Although these differences were largely absent by the end of development, a number of DMRs in HPA-related genes (CRH, MC2R, NR3C1, NR3C2, POMC)-and to a lesser degree HPG-related genes (GNRHR2)-predicted nestling growth trajectories over development. These findings provide insight into the mechanisms by which the early environment shapes DNA methylation in the HPA axis, and how these changes subsequently influence growth and potentially mediate developmental plasticity.

Spatial Variation in the Inflammatory Response of House Sparrows in their Native Range

Characterizing spatial differences in wildlife immunity is the first step to identify environmental drivers of host defense and disease risks. The house sparrow (Passer domesticus) is a model system for ecoimmunology, but spatial differences in immunity have been largely restricted to the invasive range of this global species. We provide an initial test of spatial variation in immune response to phytohemagglutinin in the native range, finding that birds from Romania have greater inflammatory responses than birds from Egypt. Future broad surveys across the house sparrow native range could contextualize these differences and determine underlying drivers.

Brief exposure to captivity in a songbird is associated with reduced diversity and altered composition of the gut microbiome

The gut microbiome is important for host fitness and is influenced by many factors including the host's environment. Captive environments could potentially influence the richness and composition of the microbiome and understanding these effects could be useful information for the care and study of millions of animals in captivity. While previous studies have found that the microbiome often changes due to captivity, they have not examined how quickly these changes can occur. We predicted that the richness of the gut microbiome of wild-caught birds would decrease with brief exposure to captivity and that their microbiome communities would become more homogeneous. To test these predictions, we captured wild house sparrows (Passer domesticus) and collected fecal samples to measure their gut microbiomes immediately after capture ("wild sample") and again 5-10 days after capture ("captive sample"). There were significant differences in beta diversity between the wild and captive samples, and captive microbiome communities were more homogenous but only when using nonphylogenetic measures. Alpha diversity of the birds' microbiomes also decreased in captivity. The functional profiles of the microbiome changed, possibly reflecting differences in stress or the birds' diets before and during captivity. Overall, we found significant changes in the richness and composition of the microbiome after only a short exposure to captivity. These findings highlight the necessity of considering microbiome changes in captive animals for research and conservation purposes.

Varying intensities of chronic stress induce inconsistent responses in weight and plasma metabolites in house sparrows (Passer domesticus)

One of the biggest unanswered questions in the field of stress physiology is whether variation in chronic stress intensity will produce proportional (a gradient or graded) physiological response. We were specifically interested in the timing of the entrance into homeostatic overload, or the start of chronic stress symptoms. To attempt to fill this knowledge gap we split 40 captive house sparrows (Passer domesticus) into four groups (high stress, medium stress, low stress, and a captivity-only control) and subjected them to six bouts of chronic stress over a 6-month period. We varied the number of stressors/day and the length of each individual bout with the goal of producing groups that would experience different magnitudes of wear-and-tear. To evaluate the impact of chronic stress, at the start and end of each stress bout we measured body weight and three plasma metabolites (glucose, ketones, and uric acid) in both a fasted and fed state. All metrics showed significant differences across treatment groups, with the high stress group most frequently showing the greatest changes. However, the changes did not produce a consistent profile that matched the different chronic stress intensities. We also took samples after a prolonged recovery period of 6 weeks after the chronic stressors ended. The only group difference that persisted after 6 weeks was weight-all differences across groups in metabolites recovered. The results indicate that common blood metabolites are sensitive to stressors and may show signs of wear-and-tear, but are not reliable indicators of the intensity of long-term chronic stress. Furthermore, regulatory mechanisms are robust enough to recover within 6 weeks post-stress.

Mediterranean songbirds show pronounced seasonal variation in thermoregulatory traits

Addressing the patterns of variation in thermal traits is crucial to better predict the potential effects of climate change on organisms. Here, we assessed seasonal (winter vs summer) adjustments in key thermoregulatory traits in eight Mediterranean-resident songbirds. Overall, songbirds increased whole-animal (by 8%) and mass-adjusted (by 9%) basal metabolic rate and decreased (by 56%) thermal conductance below the thermoneutral zone during winter. The magnitude of these changes was within the lower values found in songbirds from northern temperate areas. Moreover, songbirds increased (by 11%) evaporative water loss within the thermoneutral zone during summer, while its rate of increase above the inflection point of evaporative water loss (i.e., the slope of evaporative water loss versus temperature) decreased by 35% during summer - a value well above that reported for other temperate and tropical songbirds. Finally, body mass increased by 5% during winter, a pattern similar to that found in many northern temperate species. Our findings support the idea that physiological adjustments might enhance the resilience of Mediterranean songbirds to environmental changes, with short-term benefits by saving energy and water under thermally stressful conditions. Nevertheless, not all species showed the same patterns, suggesting different strategies in their thermoregulatory adaptations to seasonal environments.

Global invasion history and native decline of the common starling: insights through genetics

Few invasive birds are as globally successful as the Common or European Starling (Sturnus vulgaris). Native to the Palearctic, the starling has been intentionally introduced to North and South America, South Africa, Australia, and the Pacific Islands, enabling us to explore species traits that may contribute to its invasion success. Coupling the rich studies of life history and more recent explorations of genomic variation among invasions, we illustrate how eco-evolutionary dynamics shape the invasion success of this long-studied and widely distributed species. Especially informative is the comparison between Australian and North American invasions, because these populations colonized novel ranges concurrently and exhibit shared signals of selection despite distinct population histories. In this review, we describe population dynamics across the native and invasive ranges, identify putatively selected traits that may influence the starling’s spread, and suggest possible determinants of starling success world-wide. We also identify future opportunities to utilize this species as a model for avian invasion research, which will inform our understanding of species’ rapid evolution in response to environmental change.

Avian behaviour changes in response to human activity during the COVID-19 lockdown in the United Kingdom

Human activities may impact animal habitat and resource use, potentially influencing contemporary evolution in animals. In the United Kingdom, COVID-19 lockdown restrictions resulted in sudden, drastic alterations to human activity. We hypothesized that short-term daily and long-term seasonal changes in human mobility might result in changes in bird habitat use, depending on the mobility type (home, parks and grocery) and extent of change. Using Google human mobility data and 872 850 bird observations, we determined that during lockdown, human mobility changes resulted in altered habitat use in 80% (20/25) of our focal bird species. When humans spent more time at home, over half of affected species had lower counts, perhaps resulting from the disturbance of birds in garden habitats. Bird counts of some species (e.g. rooks and gulls) increased over the short term as humans spent more time at parks, possibly due to human-sourced food resources (e.g. picnic refuse), while counts of other species (e.g. tits and sparrows) decreased. All affected species increased counts when humans spent less time at grocery services. Avian species rapidly adjusted to the novel environmental conditions and demonstrated behavioural plasticity, but with diverse responses, reflecting the different interactions and pressures caused by human activity.

Dopamine receptor activation elicits a possible stress-related coping behavior in a wild-caught songbird

Animals experience stress throughout their lives and exhibit both physiological and behavioral responses to cope with it. The stress response can become harmful when prolonged and increasing evidence suggests that dopamine plays a critical role in extinguishing the stress response. In particular, activation of the D2 dopamine receptor reduces glucocorticoids and increases coping behavior, i.e., behavioral responses to adverse stimuli that reduce the harmful effects of stress. However, few studies have examined the effects of dopamine on the stress responses of wild species. We therefore tested the hypothesis that activation of the D2 dopamine receptor influences coping-like behavior in a wild-caught species. We recorded behavior of house sparrows (Passer domesticus) before and after they received injections of D2 dopamine agonists, D2 dopamine antagonists, or saline. House sparrows are common in urban environments and understanding how they cope with stress may help us better understand how animals cope with urban stressors. We found that the birds significantly increased biting of inanimate objects after the agonist but there was no change following the antagonist or saline. The biting of inanimate objects may be a mechanism of behavioral coping. This change in biting behavior was not correlated with general movement. This study supports the hypothesis that D2 dopamine receptor activation is involved in the regulation of the stress response in a wild bird.

West Nile Virus Occurrence and Ecological Niche Modeling in Wild Bird Species and Mosquito Vectors: An Active Surveillance Program in the Peloponnese Region of Greece

West Nile Virus (WNV) is maintained in nature in a bird-mosquito cycle and human infections follow a seasonal pattern, favored by climatic conditions. Peloponnese Region, located in Southern Greece, initiated an active WNV surveillance program to protect public health during 2019–2020. The project included monitoring of avian hosts and mosquito vectors, while sampling locations were prioritized after consideration of WNV circulation in birds, mosquitos and humans during previous seasons. Biological materials were collected from 493 wild birds of 25 species and 678 mosquito pools, which were molecularly screened for WNV presence. In this case, 14 environmental variables were associated with WNV detection in wild birds and mosquitos by using two separate MaxEnt models. Viral RNA was not detected in the target species during 2019, although in 2020, it was reported on 46 wild birds of ten species and 22 mosquito pools (Culex pipiens and Aedes albopictus). Altitude and land uses were significant predictors for both models and in fact, suitable conditions for virus occurrence were identified in low altitude zones. Bird- and mosquito-based surveillance systems yielded similar results and allowed for targeted vector control applications in cases of increased virus activity. Human cases were not reported on Peloponnese in 2020.

Inbreeding is associated with shorter early-life telomere length in a wild passerine

Inbreeding can have negative effects on survival and reproduction, which may be of conservation concern in small and isolated populations. However, the physiological mechanisms underlying inbreeding depression are not well-known. The length of telomeres, the DNA sequences protecting chromosome ends, has been associated with health or fitness in several species. We investigated effects of inbreeding on early-life telomere length in two small island populations of wild house sparrows (Passer domesticus) known to be affected by inbreeding depression. Using genomic measures of inbreeding we found that inbred nestling house sparrows (n = 371) have significantly shorter telomeres. Using pedigree-based estimates of inbreeding we found a tendency for inbred nestling house sparrows to have shorter telomeres (n = 1195). This negative effect of inbreeding on telomere length may have been complemented by a heterosis effect resulting in longer telomeres in individuals that were less inbred than the population average. Furthermore, we found some evidence of stronger effects of inbreeding on telomere length in males than females. Thus, telomere length may reveal subtle costs of inbreeding in the wild and demonstrate a route by which inbreeding negatively impacts the physiological state of an organism already at early life-history stages.

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.

The Effect of a Combined Fast and Chronic Stress on Body Mass, Blood Metabolites, Corticosterone, and Behavior in House Sparrows (Passer domesticus)

One aspect of the Reactive Scope Model is wear-and-tear, which describes a decrease in an animal's ability to cope with a stressor, typically because of a period of chronic or repeated stressors. We investigated whether wear-and-tear due to chronic stress would accelerate a transition from phase II to phase III of fasting. We exposed house sparrows (Passer domesticus) to three weeks of daily fasts combined with daily intermittent repeated acute stressors to create chronic stress, followed by two weeks of daily fasts without stressors. We measured circulating glucose, β-hydroxybutyrate (a ketone), and uric acid in both fasted and fed states. We expected birds to be in phase II (high fat breakdown) in a fasted state, but if wear-and-tear accumulated sufficiently, we hypothesized a shift to phase III (high protein breakdown). Throughout the experiment, the birds exhibited elevated β-hydroxybutyrate when fasting but no changes in circulating uric acid, indicating that a transition to phase III did not occur. In both a fasted and fed state, the birds increased glucose mobilization throughout the experiment, suggesting wear-and-tear occurred, but was not sufficient to induce a shift to phase III. Additionally, the birds exhibited a significant decrease in weight, no change in corticosterone, and a transient decrease in neophobia with chronic stress. In conclusion, the birds appear to have experienced wear-and-tear, but our protocol did not accelerate the transition from phase II to phase III of fasting.

Natural History of Model Organisms: The big potential of the small frog Eleutherodactylus coqui

The Puerto Rican coquí frog Eleutherodactylus coqui is both a cultural icon and a species with an unusual natural history that has attracted attention from researchers in a number of different fields within biology. Unlike most frogs, the coquí frog skips the tadpole stage, which makes it of interest to developmental biologists. The frog is best known in Puerto Rico for its notoriously loud mating call, which has allowed researchers to study aspects of social behavior such as vocal communication and courtship, while the ability of coquí to colonize new habitats has been used to explore the biology of invasive species. This article reviews existing studies on the natural history of E. coqui and discusses opportunities for future research.

Urbanization effects on temporal variations of avian haemosporidian infections

Urbanization is an important human-driven process that leads to biodiversity loss and alters the interactions between organisms, including disease transmission. Although urbanization affects both host and vector communities, the effects on vector-borne pathogens are still poorly understood. Here, we monitored variation in prevalence and richness of three common blood parasites in birds (Plasmodium, Haemoproteus and Leucocytozoon) from localities with different land uses (urban, rural and natural) during two consecutive years (2013 and 2014). Overall, 1400 juvenile house sparrows (Passer domesticus) from 15 localities in southern Spain were included in this study. Haemoproteus and Leucocytozoon prevalence was higher in 2013 than in 2014, particularly in urban and natural habitats for the case of Leucocytozoon. Prevalence was correlated between years for Haemoproteus and Leucocytozoon, independently of the habitat. Additionally, rural habitats harboured significantly higher Haemoproteus lineage richness compared to urban and natural habitats during 2014. Leucocytozoon lineage richness was negatively correlated between years in rural habitats but positively correlated in urban and natural habitats in comparison. Parasite lineages found in birds were homogeneously distributed along habitats and years and the common lineages prevalence were not influenced by them. Our results highlight different patterns of infection depending on the parasite genera probably related to the composition and density of vector communities. The specific reproductive environmental requirements of the different groups of vectors involved in the transmission may be affected by climatic conditions and landscape features.

Avian haemosporidia in native and invasive sparrows at an Afrotropical region

Bio-invasions are a major threat to biodiversity and ecosystems globally and may contribute to the proliferation of emerging infectious diseases. We examined the prevalence and phylogenetic diversity of avian haemosporidian parasites infecting the non-native house sparrows (Passer domesticus) and the native southern grey-headed sparrows (Passer diffusus). Blood samples from 104 sparrows (74 house sparrows and 30 southern grey-headed sparrows) mist-netted inside and around the Kruger National Park were used. Genomic DNA was extracted from each blood sample and subjected to nested PCR analyses, Sanger sequencing and phylogenetic analyses. Overall, 35.57% (37/104) of the birds sampled were infected with at least one haemosporidian parasites. Southern grey-headed sparrows had a higher parasite prevalence (60%) than house sparrows (24.3%). A total of 16 parasite lineages were identified, of which eight were novel lineages. Whereas Haemoproteus spp. showed the highest lineage diversity, Leucocytozoon spp. were the most prevalent parasites, albeit with significant differences between sparrow species. A single Plasmodium sp. infection was recorded in a southern grey-headed sparrow. In support of the enemy release hypothesis, we found that prevalence on non-native house sparrows was lower than prevalence recorded in their region of origin and also that they were infected only by indigenous parasites lineages.

Epigenetic potential affects immune gene expression in house sparrows

Epigenetic mechanisms may play a central role in mediating phenotypic plasticity, especially during range expansions, when populations face a suite of novel environmental conditions. Individuals may differ in their epigenetic potential (EP; their capacity for epigenetic modifications of gene expression), which may affect their ability to colonize new areas. One form of EP, the number of CpG sites, is higher in introduced house sparrows (Passer domesticus) than in native birds in the promoter region of a microbial surveillance gene, Toll-like Receptor 4 (TLR4), which may allow invading birds to fine-tune their immune responses to unfamiliar parasites. Here, we compared TLR4 gene expression from whole blood, liver and spleen in house sparrows with different EP, first challenging some birds with lipopolysaccharide (LPS), to increase gene expression by simulating a natural infection. We expected that high EP would predict high inducibility and reversibility of TLR4 expression in the blood of birds treated with LPS, but we did not make directional predictions regarding organs, as we could not repeatedly sample these tissues. We found that EP was predictive of TLR4 expression in all tissues. Birds with high EP expressed more TLR4 in the blood than individuals with low EP, regardless of treatment with LPS. Only females with high EP exhibited reversibility in gene expression. Further, the effect of EP varied between sexes and among tissues. Together, these data support EP as one regulator of TLR4 expression.

Social groups with diverse personalities mitigate physiological stress in a songbird

Social groups often consist of diverse phenotypes, including personality types, and this diversity is known to affect the functioning of the group as a whole. Social selection theory proposes that group composition (i.e. social environment) also influences the performance of individual group members. However, the effect of group behavioural composition on group members remains largely unexplored, and it is still contentious whether individuals benefit more in a social environment with homogeneous or diverse behavioural composition. We experimentally formed groups of house sparrows Passer domesticus with high and low diversity of personality (exploratory behaviour), and found that their physiological state (body condition, physiological stress and oxidative damage) improved with increasing group-level diversity of personality. These findings demonstrate that group personality composition affects the condition of group members and individuals benefit from social heterosis (i.e. associating with a diverse set of behavioural types). This aspect of the social life can play a key role in affiliation rules of social animals and might explain the evolutionary coexistence of different personalities in nature.

Birds and plastic pollution: recent advances

Plastic waste and debris have caused substantial environmental pollution globally in the past decades, and they have been accumulated in hundreds of terrestrial and aquatic avian species. Birds are susceptible and vulnerable to external environments; therefore, they could be used to estimate the negative effects of environmental pollution. In this review, we summarize the effects of macroplastics, microplastics, and plastic-derived additives and plastic-absorbed chemicals on birds. First, macroplastics and microplastics accumulate in different tissues of various aquatic and terrestrial birds, suggesting that birds could suffer from the macroplastics and microplastics-associated contaminants in the aquatic and terrestrial environments. Second, the detrimental effects of macroplastics and microplastics, and their derived additives and absorbed chemicals on the individual survival, growth and development, reproductive output, and physiology, are summarized in different birds, as well as the known toxicological mechanisms of plastics in laboratory model mammals. Finally, we identify that human commensal birds, long-life-span birds, and model bird species could be utilized to different research objectives to evaluate plastic pollution burden and toxicological effects of chronic plastic exposure.