Passer Domesticus Research Articles

Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.

Comprehensive characterization of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation, reproducible and high-confidence structural variation callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus). To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of structural variants is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analyzing short-read-discovered structural variation data sets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence structural variation callsets.

ECR Spotlight – Elizabeth Rogers

ECR Spotlight is a series of interviews with early-career authors from a selection of papers published in Journal of Experimental Biology and aims to promote not only the diversity of early-career researchers (ECRs) working in experimental biology but also the huge variety of animals and physiological systems that are essential for the ‘comparative’ approach. Elizabeth (Beth) Rogers is an author on ‘ Water restriction increases oxidation of endogenous amino acids in house sparrows (Passer domesticus)’, published in JEB. Beth is a PhD candidate in the lab of Alex Gerson at University of Massachusetts Amherst, USA, investigating the physiological and metabolic adaptations that allow animals to contend with ecological challenges such as long-distance migration, disease, environmental change and the confluence of all three.

Assessment of Cyclical Spreading and Ecological Extortions to the Avian Species in Distt. Jhang, Punjab, Pakistan

The study was conducted to estimate the bird diversity and the risks they confront at Head Trimmu, Distt. Jhang, Punjab, Pakistan. A number of field surveys were managed over 12-months by employing both direct and indirect means during certain hours of a day. The study found a total of 54 species from 15 orders and 31 families. The bird species were classified as residents (64.4%), breeders (8%), migrants (26%), and passage migrants (1.4%). The most frequent species observed during the study were house sparrow, house crow, domestic rock pigeon, ring-necked dove and common myna. Overall, the study revealed a diversified avian community with Shannon-Wiener diversity index of 3.3367. Only two species found near threatened like the Houbara bustard (Chlamydotis undulata)and Alexandrine parakeet (Psittacula eupatria) but the majority of the species are of least concern. The ecological richness of the area is under threat by urban development due to growing human population. So, the major threats to avian species in the study area are habitat degradation, Illegal hunting and lack of awareness. It is suggested to preserve avian diversity by the involvement of government agencies, private groups (WWF, IUCN, BirdLife International) and the general public.

Exploring the value of ecosystem services at health clinic gardens in a South African context

Ecosystem services (ESs) valuation is important for advancing biodiversity objectives and investing in green infrastructure (GI) establishment. Little is known about the potential of health clinic gardens (HCGs) to provide ESs and their potential values. This study sought to determine the plant and bird species composition and potential value of ESs provided by 32 HCGs in two South African district municipalities. HCG sizes range from 513.0m2 to 13531.0m2 and each had at least one micro-garden. Among the 312 plant species observed across all HCGs, 60% were exotic. The small HCGs had 31 ± 3.6 different plant species per garden, compared to the medium-sized (32 ± 3.7) and large ones (49 ± 5.2). Provisioning ESs from the observed species were prominent with 17.4 ± 1.16 species potentially used for general well-being, 13.66 ± 1.08 as potential food plants, and 11.91 ± 0.93 potentially raw materials. Trees in HCGs were estimated to sequester up to 163481.87 kg of carbon from trees covering an area of up to 9620.80m2. Approximately 1390.70 ± 427.50m2 of HCG space had the potential to provide a habitat for plants and birds, and 11 bird species were observed across all HCGs. Sixty-three bird nests encountered in 18 HCGs are believed to belong to the Passer domesticus. HCGs resemble other types of gardens like home and domestic gardens, and their rich plant biodiversity positions them as ideal ecosystems to benefit even the most vulnerable members of society. They provide an opportune platform for knowledge upscaling in the cultivation and use of plant species as a supplement of primary healthcare and food security issues in the summer months to the rural, urban, and peri-urban poor in the Global South.

Long-term Exposure to Industrial Chemical Contamination Affects the Magnitude of Predator-induced Immunosuppression in a Free-living Passerine.

Industrial chemical contamination is known to have immuno-toxic effects on birds. It may also interfere with natural stressful conditions to further disrupt the immune responses, but these possible interactive effects are still poorly documented in free-living birds. Using the phytohaemagglutinin skin-swelling test, we assessed how the T-cell mediated immune response varied according to the perceived risk of predation in hybrid sparrows, Passer domesticus × Passer hispaniolensis, originating from two sites differentially impacted by industrial chemical contamination, in southern Tunisia. Results showed that T-cell mediated immune response decreased with increasing perceived risk of predation, but the extent of this predator-associated immunosuppression was weaker in birds from the contaminated site compared to those from the control site. The immune response of birds living in the contaminated site was so weak that it could not be further weakened by a predator-related stress. Overall, these results support the idea that chemical contamination interferes with natural environmental stressors, such as predators, thus entailing profound disruption of the immune responses, with possible deleterious repercussions on the ability of birds to cope with diseases.

The genetic basis of dispersal in a vertebrate metapopulation.

Dispersal affects evolutionary processes by changing population size and genetic composition, influencing the viability and persistence of populations. Investigating which mechanisms underlie variation in dispersal phenotypes and whether populations harbour adaptive potential for dispersal is crucial to understanding the eco-evolutionary dynamics of this important trait. Here, we investigate the genetic architecture of dispersal among successfully recruited individuals in an insular metapopulation of house sparrows. We use an extensive long-term individual-based ecological data set and high-density single-nucleotide polymorphism (SNP) genotypes for over 2500 individuals. We conducted a genome-wide association study (GWAS), and found a relationship between dispersal probability and a SNP located near genes known to regulate circadian rhythm, glycogenesis and exercise performance, among other functions. However, this SNP only explained 3.8% of variance, suggesting that dispersal is a polygenic trait. We then used an animal model to estimate heritable genetic variation (σA 2 ), which composes 10% of the total variation in dispersal probability. Finally, we investigated differences in σA 2 across populations occupying ecologically relevant habitat types (farm vs. non-farm) using a genetic groups animal model. We found different adaptive potentials across habitats, with higher mean breeding value, σA 2 , and heritability for the habitat presenting lower dispersal rates, suggesting also different roles of environmental variation. Our results suggest a complex genetic architecture of dispersal and demonstrate that adaptive potential may be environment dependent in key eco-evolutionary traits. The eco-evolutionary implications of such environment dependence and consequent spatial variation are likely to become ever more important with the increased fragmentation and loss of suitable habitats for many natural populations.

Only rare classical MHC-I alleles are highly expressed in the European house sparrow.

The exceptional polymorphism observed within genes of the major histocompatibility complex (MHC), a core component of the vertebrate immune system, has long fascinated biologists. The highly polymorphic classical MHC class-I (MHC-I) genes are maintained by pathogen-mediated balancing selection (PMBS), as shown by many sites subject to positive selection, while the more monomorphic non-classical MHC-I genes show signatures of purifying selection. In line with PMBS, at any point in time, rare classical MHC alleles are more likely than common classical MHC alleles to confer a selective advantage in host-pathogen interactions. Combining genomic and expression data from the blood of wild house sparrows Passer domesticus, we found that only rare classical MHC-I alleles were highly expressed, while common classical MHC-I alleles were lowly expressed or not expressed. Moreover, highly expressed rare classical MHC-I alleles had more positively selected sites, indicating exposure to stronger PMBS, compared with lowly expressed classical alleles. As predicted, the level of expression was unrelated to allele frequency in the monomorphic non-classical MHC-I alleles. Going beyond previous studies, we offer a fine-scale view of selection on classical MHC-I genes in a wild population by revealing differences in the strength of PMBS according to allele frequency and expression level.

Seasonal changes in bird communities on poultry farms and house sparrow-wild bird contacts revealed by camera trapping.

Wild birds are considered reservoirs of poultry pathogens although transmission routes have not been conclusively established. Here we use camera trapping to study wild bird communities on commercial layer and red-legged partridge farms over a one-year timeframe. We also analyze direct and indirect interactions of other bird species with the house sparrow (Passer domesticus), a potential bridge host. We conducted camera trapping events between January 2018 and October 2019, in two caged layer farms, one free-range layer farm, and two red-legged partridge farms in South-Central Spain. We observed wild bird visits on all types of farms, with the significantly highest occurrence on red-legged partridge farms where food and water are more easily accessible, followed by commercial caged layer farms, and free-range chicken farms. The house sparrow (Passer domesticus) followed by spotless starlings (Sturnus unicolor) was the most encountered species on all farms, with the highest frequency in caged layer farms. On partridge farms, the house sparrow accounted for 58% of the wild bird detections, while on the free-range chicken farm, it made up 11% of the detections. Notably, the breeding season, when food and water are scarce in Mediterranean climates, saw the highest number of wild bird visits to the farms. Our findings confirm that the house sparrow, is in direct and indirect contact with layers and red-legged partridges and other wild birds independent of the type of farm. Contacts between house sparrows and other bird species were most frequent during the breeding season followed by the spring migration period. The species most frequently involved in interactions with the house sparrow belonged to the order Passeriformes. The study provides a comparative description of the composition and seasonal variations of bird communities in different types of layer/ poultry farms in Southern Spain i.e. a Mediterranean climate. It confirms the effectiveness of biosecurity measures that restrict access to feed and water. Additionally, it underscores the importance of synanthropic species, particularly the house sparrow, as potential bridge vector of avian pathogens.

The impact of parental and developmental stress on DNA methylation in the avian hypothalamic-pituitary-adrenal axis.

The hypothalamic-pituitary-adrenal (HPA) axis coordinates an organism's response to environmental stress. The responsiveness and sensitivity of an offspring's stress response may be shaped not only by stressors encountered in their early post-natal environment but also by stressors in their parent's environment. Yet, few studies have considered how stressors encountered in both of these early life environments may function together to impact the developing HPA axis. Here, we manipulated stressors in the parental and post-natal environments in a population of house sparrows (Passer domesticus) to assess their impact on changes in DNA methylation (and corresponding gene expression) in a suite of genes within the HPA axis. We found that nestlings that experienced early life stress across both life-history periods had higher DNA methylation in a critical HPA axis gene, the glucocorticoid receptor (NR3C1). In addition, we found that the life-history stage when stress was encountered impacted some genes (HSD11B1, NR3C1 and NR3C2) differently. We also found evidence for the mitigation of parental stress by post-natal stress (in HSD11B1 and NR3C2). Finally, by assessing DNA methylation in both the brain and blood, we were able to evaluate cross-tissue patterns. While some differentially methylated regions were tissue-specific, we found cross-tissue changes in NR3C2 and NR3C1, suggesting that blood is a suitable tissue for assessing DNA methylation as a biomarker of early life stress. Our results provide a crucial first step in understanding the mechanisms by which early life stress in different life-history periods contributes to changes in the epigenome of the HPA axis.

Lead exposure is related to higher infection rate with the gapeworm in Norwegian house sparrows (Passer domesticus)

Anthropogenic pollution is identified as an important threat to bird and other wildlife populations. Many metals and toxic elements, along with poly- and perfluoroalkyl substances (PFASs) are known to induce immunomodulation and have previously been linked to increased pathogen prevalence and infectious disease severity. In this study, the house sparrow (Passer domesticus) was investigated at the coast of Helgeland in northern Norway. This population is commonly infected with the parasitic nematode “gapeworm” (Syngamus trachea), with a prevalence of 40–60 % during summer months. Gapeworm induces severe respiratory disease in birds and has been previously demonstrated to decrease survival and reproductive success in wild house sparrows. The aim of this study was to investigate whether a higher exposure to pollution with PFASs, metals and other elements influences gapeworm infection in wild house sparrows. We conducted PFASs and elemental analysis on whole blood from 52 house sparrows from Helgeland, including analyses of highly toxic metals such as lead (Pb), mercury (Hg) and arsenic (As). In addition, we studied gapeworm infection load by counting the parasite eggs in faeces from each individual. We also studied the expression of microRNA 155 (miR155) as a key regulator in the immune system. Elevated blood concentrations of Pb were found to be associated with an increased prevalence of gapeworm infection in the house sparrow. The expression of miR155 in the plasma of the house sparrow was only weakly associated with Pb. In contrast, we found relatively low PFASs concentrations in the house sparrow blood (∑ PFASs 0.00048–354 μg/L) and PFASs were not associated to miR155 nor infection rate. The current study highlights the potential threat posed by Pb as an immunotoxic pollutant in small songbirds.

Comments on the paper “correlation does not imply causation: decline of House Sparrow overshadowed by electromagnetic radiation” by Nath et al.

Comments on the paper “correlation does not imply causation: decline of House Sparrow overshadowed by electromagnetic radiation” by Nath et al.

Dynamics оf Nesting Ornithofauna Structure оf Tiraspol City’s Resident Area

43 species of nesting birds were registered of Tiraspol City’s resident area in 1999–2019. The total density was about 1995,7–2361 pairs/km2 . House Sparrow, Rock Dove, Tree Sparrow and Common Swift were the dominants. Crested Lark, Willow Warbler and Wood Warbler disappeared from nesting ornithofauna of resident area. Common Kestrel, Common Woodpigeon, Eurasian Scops-owl, Robin, Blackbird, Song Thrush, Blue Tit and Eurasian Nuthatch for 20 years were appeared. A signifi cant increase in abundance was noted in populations of Rock Dove, Long-eared Owl, Common Swift, Eurasian Golden Oriole, Rook and Tree Sparrow. There was a decrease in the number in the populations of Chiffchaff, Northern Wheatear, Black Redstart, House Sparrow and Chaffi nch. The majority of birds nesting in the resident area belong to the Transpalearctic type of the fauna, to the desert-mountains landscape-genetic faunistic complex, to the sklerophilnai ecological group and phytophagan trophic group.

Investigating the effects of acute and chronic stress on DNA damage.

A hallmark of the vertebrate stress response is a rapid increase in glucocorticoids and catecholamines; however, this does not mean that these mediators are the best, or should be the only, metric measured when studying stress. Instead, it is becoming increasingly clear that assaying a suite of downstream metrics is necessary in stress physiology. One component of this suite could be assessing double-stranded DNA damage (dsDNA damage), which has recently been shown to increase in blood with both acute and chronic stress in house sparrows (Passer domesticus). To further understand the relationship between stress and dsDNA damage, we designed two experiments to address the following questions: (1) how does dsDNA damage with chronic stress vary across tissues? (2) does the increase in dsDNA damage during acute stress come from one arm of the stress response or both? We found that (1) dsDNA damage affects tissues differently during chronic stress and (2) the hypothalamic-pituitary-adrenal axis influences dsDNA damage with acute stress, but the sympathetic-adreno-medullary system does not. Surprisingly, our data are not explained by studies on changes in hormone receptor levels with chronic stress, so the underlying mechanism remains unclear.

The House Sparrows: Causes of Decline in Punjab, Ecological Importance & Proactive Steps

The House Sparrows: Causes of Decline in Punjab, Ecological Importance & Proactive Steps

Screening H3 Histone Acetylation in a Wild Bird, the House Sparrow (Passer Domesticus).

Epigenetic mechanisms are increasingly understood to have major impacts across ecology. However, one molecular epigenetic mechanism, DNA methylation, currently dominates the literature. A second mechanism, histone modification, is likely important to ecologically relevant phenotypes and thus warrants investigation, especially because molecular interplay between methylation and histone acetylation can strongly affect gene expression. There are a limited number of histone acetylation studies on non-model organisms, yet those that exist show that it can impact gene expression and phenotypic plasticity. Wild birds provide an excellent system to investigate histone acetylation, as free-living individuals must rapidly adjust to environmental change. Here, we screen histone acetylation in the house sparrow (Passer domesticus); we studied this species because DNA methylation was important in the spread of this bird globally. This species has one of the broadest geographic distributions in the world, and part of this success is related to the way that it uses methylation to regulate its gene expression. Here, we verify that a commercially available assay that was developed for mammals can be used in house sparrows. We detected high variance in histone acetylation among individuals in both liver and spleen tissue. Further, house sparrows with higher epigenetic potential in the Toll Like Receptor-4 (TLR-4) promoter (i.e., CpG content) had higher histone acetylation in liver. Also, there was a negative correlation between histone acetylation in spleen and TLR-4 expression. In addition to validating a method for measuring histone acetylation in wild songbirds, this study also shows that histone acetylation is related to epigenetic potential and gene expression, adding a new study option for ecological epigenetics.

House sparrows are heavier on organic and integrated-production farms than on conventional farms

The negative impact of conventional farming on avian biodiversity has been increasingly documented. However, the potential effects of different farming practices on bird populations' health remain unclear. We aimed to investigate whether different farming practices (organic, integrated production, conventional/intensive) have differential effects on the body mass - as a proxy for body condition - and biomarkers of oxidative stress in house sparrows (Passer domesticus), a model species strongly associated with human activities and still abundant in Switzerland. We captured a total of 681 birds in 19 organic farms, 20 integrated-production farms (labelled “IP-Suisse”) and 18 conventional farms, and measured bird body mass and tarsus length, as well as levels of malondialdehydes (MDA, a marker of oxidative damage to lipids), superoxide dismutase (SOD, a first-line antioxidant enzyme) activity, and the ratio of oxidized over reduced glutathione (GSSG/GSH, a marker of cellular oxidative stress) in blood and sperm as biomarkers of the systemic oxidative stress endured by birds. Our findings show that house sparrows living in integrated and organic farms were 2.39 % and 4.33 % heavier than birds living in conventional farms, but we did not find any difference in tarsus length, suggesting that birds were of similar size. In addition, we did not find any difference in oxidative stress markers across farming practices. Our results highlight the potential benefits of sustainable farming practices, such as organic and integrated farming, for bird populations and emphasize the need for mitigating the negative impact of agricultural intensification on biodiversity through practices that may enhance the birds’ health and thus lead to positive population dynamics.

A study of nests and nesting materials used by house sparrow across different habitat scale of Bhavnagar, Gujarat, India

This study investigates the nests and nest materials used by House Sparrows across various habitat scales in Bhavnagar, Gujarat, India. House Sparrows are adaptable to urban environments but have faced declines due to nesting site scarcity. Nest design, placement and materials influence predation risk and affect reproductive success. Artificial nest-boxes serve as crucial alternatives in urban areas. Overall, this research sheds light on House Sparrows’ adaptability for nesting, aiding conservation efforts and expanding our understanding of avian nesting dynamics.

Experimental investigation of the effect of tebuconazole on three biomarkers of innate immunity in the house sparrow (Passer domesticus).

Triazoles are among the most widely used fungicides in the world due to their efficacy against fungal crop diseases and their broad spectrum of action. Intensive use of triazoles has resulted in residual contamination in different compartments of agroecosystems and exposes non-target species to potential sublethal effects. Triazoles are known to be immunomodulators in medicine and therapeutic treatments, but very little data is available on their potential effect on immune parameters of non-target vertebrate species living in agroecosystems. In this study, we experimentally examined the impact of tebuconazole on three immune biomarkers (haemagglutination titre (HA), haemolysis titre (HL), and haptoglobin concentration (Hp)), as well as on the body condition of house sparrows (Passer domesticus). Our results suggest that tebuconazole had very little, if any, effect on the studied immune parameters. However, further studies are needed to better assess the effect of tebuconazole on bird immunity because (1) experimental individuals were kept under optimal conditions and the impact of tebuconazole on immunity may occur under suboptimal conditions, (2) only one concentration of tebuconazole was tested and its effect could be dose-dependent and (3) other complementary immunological biomarkers should be studied, given the complexity of the vertebrate immune system. Current knowledge on the potential effects of triazoles on the immunity of wild farmland vertebrates is still largely insufficient. Further physiological and immune studies should be conducted to better understand the effect of triazole fungicides on farmland birds.

Comparative Macro- and Micro-morphological Study on the Syrinx of Three Avian Species

This study aimed to explain and compare the anatomical, histological, histochemical & histomorphometric analyses of the syrinx in different species of birds. This study includes 21 healthy birds from geese (Anser Anser Domesticus), cattle egrets (Bublucus ibis) & house sparrows (Passer domesticus), seven from each species. Results: Anatomically, the syrinx of the three studied species was tracheobronchial type composed of 2 different cartilaginous groups arranged in three parts: Tracheo-Syringeal cartilage in (cranial, intermediate part (tympanum)) and broncho-syringeal cartilage; as well as the trachea's muscles were once thought to be the syrinx's extrinsic muscles. Histologically, the lamina epithelialis of the Tracheo-Syringeal part was represented by pseudostratified ciliated columnar epithelium in the three investigated species with goblet cells in geese, house sparrows and lack goblet cells in cattle egrets. The pessulus in all three investigated species was triangular and positioned at the tip of the tracheal bifurcation. The bulla of house sparrow was considered the intrinsic syringeal muscles and these muscles in sparrows are not only present in geese or cattle egrets.

Abundance, temporal variation, and microhabitat use of the house sparrow, Passer domesticus (Passeriformes: Passeridae), in urban and anthropogenic environments in Northeastern Brazil

Abundance, temporal variation, and microhabitat use of the house sparrow, Passer domesticus (Passeriformes: Passeridae), in urban and anthropogenic environments in Northeastern Brazil