A chromosome-level reference genome and pangenome for barn swallow population genomics

Insights into the evolution of non-model organisms are limited by the lack of reference genomes of high accuracy, completeness, and contiguity. Here, we present a chromosome-level, karyotype-validated reference genome and pangenome for the barn swallow (Hirundo rustica). We complement these resources with a reference-free multialignment of the reference genome with other bird genomes and with the most comprehensive catalog of genetic markers for the barn swallow. We identify potentially conserved and accelerated genes using the multialignment and estimate genome-wide linkage disequilibrium using the catalog. We use the pangenome to infer core and accessory genes and to detect variants using it as a reference. Overall, these resources will foster population genomics studies in the barn swallow, enable detection of candidate genes in comparative genomics studies, and help reduce bias toward a single reference genome.

Individual quality and phenology mediate the effect of radioactive contamination on body temperature in Chernobyl barn swallows

Anthropogenic stressors, such as radioactive contaminants released from the Chernobyl and Fukushima Daiichi accidents, deteriorate ecological and evolutionary processes, as evidence for damaging effects of radioactive contamination on wildlife is accumulating. Yet little is known about physiological traits of animals inhabiting contaminated areas, and how those are affected by individual quality and phenology. We investigated variation in body temperature of wild barn swallows, Hirundo rustica, exposed to radioactive contamination from the Chernobyl accident in Ukraine and Belarus. We tested whether exposure to variable levels of radioactive contamination modified core body temperature of birds, and whether individual and phenological characteristics modulated radiosensitivity of body temperature. We showed that barn swallow body temperature varied with exposure to environmental radioactive contamination and that individual characteristics and phenology affected radioactive exposure. Increased radiosensitivity and up-regulation of body temperature were detected in birds of low body condition, high risk of capture, and in animals captured late during the day but early during the season. These results highlight the complex ways that the body temperature of a wild bird is impacted by exposure to increased radioactive contamination in natural habitats. By impacting body temperature, increased radioactive contamination may compromise energetic balance, jeopardize responsiveness to global warming, and increase risk of overheating.

Migration, pathogens and the avian microbiome: A comparative study in sympatric migrants and residents

Animals generally benefit from their gastrointestinal microbiome, but the factors that influence the composition and dynamics of their microbiota remain poorly understood. Studies of nonmodel host species can illuminate how microbiota and their hosts interact in natural environments. We investigated the role of migratory behaviour in shaping the gut microbiota of free-ranging barn swallows (Hirundo rustica) by studying co-occurring migrant and resident subspecies sampled during the autumn migration at a migratory bottleneck. We found that within-host microbial richness (α-diversity) was similar between migrant and resident microbial communities. In contrast, we found that microbial communities (β-diversity) were significantly different between groups regarding both microbes present and their relative abundances. Compositional differences were found for 36 bacterial genera, with 27 exhibiting greater abundance in migrants and nine exhibiting greater abundance in residents. There was heightened abundance of Mycoplasma spp. and Corynebacterium spp. in migrants, a pattern shared by other studies of migratory species. Screens for key regional pathogens revealed that neither residents nor migrants carried avian influenza viruses and Newcastle disease virus, suggesting that the status of these diseases did not underlie observed differences in microbiome composition. Furthermore, the prevalence and abundance of Salmonella spp., as determined from microbiome data and cultural assays, were both low and similar across the groups. Overall, our results indicate that microbial composition differs between migratory and resident barn swallows, even when they are conspecific and sympatrically occurring. Differences in host origins (breeding sites) may result in microbial community divergence, and varied behaviours throughout the annual cycle (e.g., migration) could further differentiate compositional structure as it relates to functional needs.

Heterochiasmy and Sexual Dimorphism: The Case of the Barn Swallow (Hirundo rustica, Hirundinidae, Aves)

Heterochiasmy, a sex-based difference in recombination rate, has been detected in many species of animals and plants. Several hypotheses about evolutionary causes of heterochiasmy were proposed. However, there is a shortage of empirical data. In this paper, we compared recombination related traits in females and males of the barn swallow Hirundo rustica (Linnaeus, 1758), the species under strong sexual selection, with those in the pale martin Riparia diluta (Sharpe and Wyatt, 1893), a related and ecologically similar species with the same karyotype (2N = 78), but without obvious sexual dimorphism. Recombination traits were examined in pachytene chromosome spreads prepared from spermatocytes and oocytes. Synaptonemal complexes and mature recombination nodules were visualized with antibodies to SYCP3 and MLH1 proteins, correspondingly. Recombination rate was significantly higher (p = 0.0001) in barn swallow females (55.6 ± 6.3 recombination nodules per autosomal genome), caused by the higher number of nodules at the macrochromosomes, than in males (49.0 ± 4.5). They also showed more even distribution of recombination nodules along the macrochromosomes. At the same time, in the pale martin, sexual differences in recombination rate and distributions were rather small. We speculate that an elevated recombination rate in the female barn swallows might have evolved as a compensatory reaction to runaway sexual selection in males.

Selection on multiple sexual signals in two Central and Eastern European populations of the barn swallow

Variation in intensity and targets of sexual selection on multiple traits has been suggested to play a major role in promoting phenotypic differentiation between populations, although the divergence in selection may depend on year, local conditions or age. In this study, we quantified sexual selection for two putative sexual signals across two Central and East European barn swallow (Hirundo rustica rustica) populations from Czech Republic and Romania over multiple years. We then related these differences in selection to variation in sexual characters among barn swallow populations. Our results show that tail length and ventral coloration vary between populations, sexes, and age classes (first-time breeders vs. experienced birds). We found that selection on tail length was stronger in first-time breeders than in experienced birds and in males than in females in the Romanian population, while these differences between age groups and sexes were weak in Czech birds. We suggest that the populational difference in selection on tail length might be related to the differences in breeding conditions. Our results show that ventral coloration is darker (i.e., has lower brightness) in the Romanian than in the Czech population, and in experienced birds and males compared with first-time breeders and females, respectively. The sexual difference in ventral coloration may suggest sexual selection on this trait, which is supported by the significant directional selection of ventral coloration in first-time breeding males on laying date. However, after controlling for the confounding effect of wing length and tarsus length, the partial directional selection gradient on this trait turned nonsignificant, suggesting that the advantage of dark ventral coloration in early breeding birds is determined by the correlated traits of body size. These findings show that ventral coloration may be advantageous over the breeding season, but the underlying mechanism of this relationship is not clarified.

Feather steroid hormone concentrations in relation to age, sex, and molting time in a long-distance migratory passerine

In birds, concentrations of testosterone (T) and corticosterone (Cort) are closely connected with many morphological, behavioral, and other physiological traits, including reproduction, metabolism, immunity, and fitness. The direction of the effect of these hormones on above-mentioned traits, and the potential feedback between hormones are in general unclear; in addition, knowledge on how age and sex can affect T and Cort concentrations is still inconsistent. Our study used a novel method to analyze testosterone and corticosterone in feathers (Tf, Cortf) based on the precolumn chemical derivatization of hormones before liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Unlike previously used methods (RIA, EIA), our analytical procedure allows simultaneous analysis of both hormones from small amounts of feathers (4-25 mg) and, thus, overcomes the problem of insufficient detection limits. We applied this method to reveal associations between Tf and Cortf hormone concentrations and feather growth, age, and sex in feathers grown during the postbreeding (flanks) and prebreeding (tails) periods in barn swallows (Hirundo rustica). There was neither a correlation between prebreeding and postbreeding Tf, nor between prebreeding and postbreeding Cortf. Tail Cortf concentrations were negatively associated with tail feather growth rates. Feather hormone concentrations were correlated in the prebreeding period, negatively in males but positively in females. Both Cortf and Tf were higher in young birds compared to older ones, indicating either an age-related decrease in hormone concentrations within individuals, or the selective disappearance of individuals with high steroid concentrations. Males and females did not differ in Cortf, but Tf concentrations were higher in males than females, particularly during the prebreeding period. In this study, we provide an effective method for analyzing hormones in feathers in an ecological context, especially in situations when the total amount of feathers available for the analysis is limited.

Intestinal parasites among migrant barn swallows (Hirundo rustica) in the central region of Mazandaran Province, Northern Iran

Aim:

Swallows are a family of migratory birds found worldwide except Antarctica. Annually, a number of species of swallows migrate to Iran. As they make their nests close to human living places, this may be a potential risk for public health. Conversely, no study has been conducted on intestinal parasitic infections of these birds so far. Therefore, the objective of this study was to determine the prevalence of intestinal parasites in migratory swallows (Hirundo rustica) in the central region of Mazandaran Province, Northern Iran.

Materials and Methods:

In this cross-sectional study, 205 feces samples from two districts (Sari and Qaemshahr) in the central region of Mazandaran were randomly collected during the summer and spring sessions of 2016-2017. The collected samples were examined using the routine direct fecal examination and formalin-ethyl acetate concentration. In addition, the samples were examined by cold acid-fast staining method to detect possible Cryptosporidium oocysts.

Results:

The results of this study indicated that 38 samples (18.5%) were infected with intestinal parasites. Among the helminthic parasites, eight genera and species were identified as follows: Ascaridia galli, Syngamus trachea, Raillietina, Toxocara spp., Choanotaenia, Taenia spp., Ascaridia spp., and Moniezia spp. In addition, among protozoan parasites, only the Coccidia spp. oocysts were identified.

Conclusion:

Our findings showed a relatively high prevalence of parasitic infections in migratory barn swallows in Mazandaran Province. Given the presence of zoonotic parasites in the samples, further investigations are needed to identify all parasites fauna, particularly zoonotic species among swallows in the region.

Recapture probability, flight morphology, and microorganisms

Microorganisms on and within organisms are ubiquitous and interactions with their hosts range from mutualistic over commensal, to pathogenic. We hypothesized that microorganisms might affect the ability of barn swallows Hirundo rustica to escape from potential predators, with positive associations between the abundance of microorganisms and escape ability implying mutualistic effects, while negative associations would imply antagonistic effects. We quantified escape behavior as the ability to avoid capture in a mist net and hence as a small number of recaptures. Because recapture probability may also depend on timing of reproduction and reproductive success, we also tested whether the association between recapture and microorganisms was mediated by an association between recapture and life history. We found intermediate to strong positive relationships between recapture probability and abundance of Bacillus megaterium, but not abundance of other bacteria or fungi. The abundance of B. megaterium was associated with an advance in laying date and an increase in reproductive success. However, these effects were independent of the number of recaptures. This interpretation is supported by the fact that there was no direct correlation between laying date and reproductive success on one hand and the number of recaptures on the other. These findings have implications not only for predator-prey interactions, but also for capture-mark-recapture analyses of vital rates such as survival and dispersal.

[Intestinal Microbiota in Migrating Barn Swallows around Osaka]

 Migratory birds are considered as vectors of infectious diseases, owing to their potential for transmitting pathogens over large distances. The populations of barn swallow (Hirundo rustica) migrate from Southeast Asia to the Japanese mainland during spring and migrate back to Southeast Asia during autumn. This migratory population is estimated to comprise approximately hundreds to thousands of individuals per year. However, to date, not much is known about the gastrointestinal microbiota of the barn swallow. In this study, we characterized the fecal bacterial community in barn swallow. Using 16S rRNA gene metagenomic sequencing analysis, we examined the presence and composition of potentially pathogenic bacteria in the fecal samples, which were collected during spring season from Osaka. The number (±S.D.) of total bacteria was approximately 2.1(±3.4)×10⁸ per gram of feces. In most samples, the bacterial community composition was dominated by families, such as Enterobacteriaceae, Pseudomonadaceae, Mycoplasmataceae, Enterococcaceae, Streptococcaceae, and Alcaligenaceae. However, no relationship was found between the bacterial community composition and geographical area in the fecal samples. Potentially pathogenic bacteria were detected at the rate of >0.1%, which included Pseudomonas spp., Escherichia/Shigella spp., Enterobacter spp., Yersinia spp., Mycoplasma spp., Enterococcus spp., Achromobacter spp., and Serratia spp. Our results suggested that barn swallow is instrumental in the transmission of these genera over large distances.

Temporal Stability and the Effect of Transgenerational Transfer on Fecal Microbiota Structure in a Long Distance Migratory Bird

Animal bodies are inhabited by a taxonomically and functionally diverse community of symbiotic and commensal microorganisms. From an ecological and evolutionary perspective, inter-individual variation in host-associated microbiota contributes to physiological and immune system variation. As such, host-associated microbiota may be considered an integral part of the host’s phenotype, serving as a substrate for natural selection. This assumes that host-associated microbiota exhibits high temporal stability, however, and that its composition is shaped by trans-generational transfer or heritable host-associated microbiota modulators encoded by the host genome. Although this concept is widely accepted, its crucial assumptions have rarely been tested in wild vertebrate populations. We performed 16S rRNA metabarcoding on an extensive set of fecal microbiota (FM) samples from an insectivorous, long-distance migratory bird, the barn swallow (Hirundo rustica). Our data revealed clear differences in FM among juveniles and adults as regards taxonomic and functional composition, diversity and co-occurrence network complexity. Multiple FM samples from the same juvenile or adult collected within single breeding seasons exhibited higher similarity than expected by chance, as did adult FM samples over two consecutive years. Despite low effect sizes for FM stability over time at the community level, we identified an adult FM subset with relative abundances exhibiting significant temporal consistency, possibly inducing long-term effects on the host phenotype. Our data also indicate a slight maternal (but not paternal) effect on FM composition in social offspring, though this is unlikely to persist into adulthood. We discuss our findings in the context of both evolution and ecology of microbiota vs. host interactions and barn swallow biology.

An experimental analysis of the heritability of variation in glucocorticoid concentrations in a wild avian population

Glucocorticoid hormones (CORT) are predicted to promote adaptation to variable environments, yet little is known about the potential for CORT secretion patterns to respond to selection in free-living populations. We assessed the heritable variation underlying differences in hormonal phenotypes using a cross-foster experimental design with nestling North American barn swallows (Hirundo rustica erythrogaster). Using a bivariate animal model, we partitioned variance in baseline and stress-induced CORT concentrations into their additive genetic and rearing environment components and estimated their genetic correlation. Both baseline and stress-induced CORT were heritable with heritability of 0.152 and 0.343, respectively. We found that the variation in baseline CORT was best explained by rearing environment, whereas the variation in stress-induced CORT was contributed to by a combination of genetic and environmental factors. Further, we did not detect a genetic correlation between these two hormonal traits. Although rearing environment appears to play an important role in the secretion of both types of CORT, our results suggest that stress-induced CORT levels are underlain by greater additive genetic variance compared with baseline CORT levels. Accordingly, we infer that the glucocorticoid response to stress has a greater potential for evolutionary change in response to selection compared with baseline glucocorticoid secretion patterns.

Quantitative genetics of plumage color: lifetime effects of early nest environment on a colorful sexual signal

Phenotypic differences among individuals are often linked to differential survival and mating success. Quantifying the relative influence of genetic and environmental variation on phenotype allows evolutionary biologists to make predictions about the potential for a given trait to respond to selection and various aspects of environmental variation. In particular, the environment individuals experience during early development can have lasting effects on phenotype later in life. Here, we used a natural full-sib/half-sib design as well as within-individual longitudinal analyses to examine genetic and various environmental influences on plumage color. We find that variation in melanin-based plumage color - a trait known to influence mating success in adult North American barn swallows (Hirundo rustica erythrogaster) - is influenced by both genetics and aspects of the developmental environment, including variation due to the maternal phenotype and the nest environment. Within individuals, nestling color is predictive of adult color. Accordingly, these early environmental influences are relevant to the sexually selected plumage color variation in adults. Early environmental conditions appear to have important lifelong implications for individual reproductive performance through sexual signal development in barn swallows. Our results indicate that feather color variation conveys information about developmental conditions and maternal care alleles to potential mates in North American barn swallows. Melanin-based colors are used for sexual signaling in many organisms, and our study suggests that these signals may be more sensitive to environmental variation than previously thought.