Determinants of spring migration departure dates in a New World sparrow: Weather variables reign supreme.

Numerous factors influence the timing of spring migration in birds, yet the relative importance of intrinsic and extrinsic variables on migration initiation remains unclear. To test for interactions among weather, migration distance, parasitism, and physiology in determining spring departure date, we used the Dark-eyed Junco (Junco hyemalis) as a model migratory species known to harbor diverse and common haemosporidian parasites. Prior to spring migration departure from their wintering grounds in Indiana, USA, we quantified the intrinsic variables of fat, body condition (i.e., mass ~ tarsus residuals), physiological stress (i.e., ratio of heterophils to lymphocytes), cellular immunity (i.e., leukocyte composition and total count), migration distance (i.e., distance to the breeding grounds) using stable isotopes of hydrogen from feathers, and haemosporidian parasite intensity. We then attached nanotags to determine the timing of spring migration departure date using the Motus Wildlife Tracking System. We used additive Cox proportional hazard mixed models to test how risk of spring migratory departure was predicted by the combined intrinsic measures, along with meteorological predictors on the evening of departure (i.e., average wind speed and direction, relative humidity, and temperature). Model comparisons found that the best predictor of spring departure date was average nightly wind direction and a principal component combining relative humidity and temperature. Juncos were more likely to depart for spring migration on nights with largely southwestern winds and on warmer and drier evenings (relative to cooler and more humid evenings). Our results indicate that weather conditions at take-off are more critical to departure decisions than the measured physiological and parasitism variables.

Novel Rickettsia spp. in two common overwintering North American songbirds.

American robins and dark-eyed juncos migrate across North America and have been found to be competent hosts for some bacterial and viral pathogens, but their contributions to arthropod-borne diseases more broadly remain poorly characterized. Here, we sampled robins and juncos in multiple sites across North America for arthropod-borne bacterial pathogens of public health significance. We identified two novel Rickettsia spp. in one wintering migrant per bird species related to bellii, transitional, and spotted rickettsiae fever groups. Stable isotope analyses of feathers suggested spring migration of these common songbirds could disperse these novel rickettsiae hundreds-to-thousands of kilometers to host breeding grounds. Further work is needed to characterize zoonotic potential of these rickettsiae and host reservoir competence.

Plasticity in female timing may explain earlier breeding in a North American songbird.

Many species have shifted their breeding phenology in response to climate change. Identifying the magnitude of phenological shifts and whether climate-mediated selection drives these shifts is key for determining species' resilience to climate change. Birds are a strong model for studying phenological shifts due to numerous long-term research studies; however, generalities pertaining to drivers of phenological shifts will emerge only as we add study species that differ in life history and geography. We investigated 32 years of reproductive timing in a non-migratory population of dark-eyed juncos Junco hyemalis. We predicted that plasticity in reproductive timing would allow females to breed earlier in warmer springs. We also predicted that selection would favour earlier breeding and asked whether the temperatures throughout the breeding season would predict the strength of selection. To test these predictions, we examined temporal changes in the annual median date for reproductive onset (i.e. first egg date) and we used a sliding window analysis to identify spring temperatures driving these patterns. Next, we explored plasticity in reproductive timing and asked whether selection favoured earlier breeding. Lastly, we used a sliding window analysis to identify the time during the breeding season that temperature was most associated with selection favouring earlier breeding. First egg dates occurred earlier over time and strongly covaried with April temperatures. Furthermore, individual females that bred in at least 3 years typically bred earlier in warmer Aprils, exhibiting plastic responses to April temperature. We also found significant overall selection favouring earlier breeding (i.e. higher relative fitness with earlier first egg dates) and variation in selection for earlier breeding over time. However, temperature across diverse climatic windows did not predict the strength of selection. Our findings provide further evidence for the role of phenotypic plasticity in shifting phenology in response to earlier springs. We also provide evidence for the role of selection favouring earlier breeding, regardless of temperature, thus setting the stage for adaptive changes in female breeding phenology. We suggest for multi-brooded birds that advancing first egg dates likely increase the length of the breeding season, and therefore, reproductive success.

A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird.

The dark-eyed junco (Junco hyemalis) is one of the most common passerines of North America, and has served as a model organism in studies related to ecophysiology, behavior, and evolutionary biology for over a century. It is composed of at least 6 distinct, geographically structured forms of recent evolutionary origin, presenting remarkable variation in phenotypic traits, migratory behavior, and habitat. Here, we report a high-quality genome assembly and annotation of the dark-eyed junco generated using a combination of shotgun libraries and proximity ligation Chicago and Dovetail Hi-C libraries. The final assembly is ∼1.03 Gb in size, with 98.3% of the sequence located in 30 full or nearly full chromosome scaffolds, and with a N50/L50 of 71.3 Mb/5 scaffolds. We identified 19,026 functional genes combining gene prediction and similarity approaches, of which 15,967 were associated to GO terms. The genome assembly and the set of annotated genes yielded 95.4% and 96.2% completeness scores, respectively when compared with the BUSCO avian dataset. This new assembly for J. hyemalis provides a valuable resource for genome evolution analysis, and for identifying functional genes involved in adaptive processes and speciation.

Rapid evolutionary divergence of a songbird population following recent colonization of an urban area.

Colonization of a novel environment by a few individuals can lead to rapid evolutionary change, yet there is scarce evidence of the relative contributions of neutral and selective factors in promoting divergence during the early stages of colonization. Here we explore the role of neutral and selective forces in the divergence of a unique urban population of the dark-eyed junco (Junco hyemalis), which became established on the campus of the University of California at San Diego (UCSD) in the early 1980s. Previous studies based on microsatellite loci documented significant genetic differentiation of the urban population as well as divergence in phenotypic traits relative to nearby montane populations, yet the geographical origin of the colonization and the contributing factors remained uncertain. Our genome-wide single nucleotide polymorphism data set confirmed the marked genetic differentiation of the UCSD population, and we identified the coastal subspecies pinosus from central California as its sister group instead of the neighbouring mountain population. Demographic inference recovered a separation from pinosus as recent as 20-32 generations ago after a strong bottleneck, suggesting a role for drift in genetic differentiation. However, we also found significant associations between habitat variables and genome-wide variants linked to functional genes, some of which have been reported as potentially adaptive in birds inhabiting modified environments. These results suggest that the interplay between founder events and selection may result in rapid shifts in neutral and adaptive loci across the genome, and reveal the UCSD junco population as a case of contemporary evolutionary divergence in an anthropogenic environment.

Experimentally elevated testosterone shortens telomeres across years in a free-living songbird.

Reproductive investment often comes at a cost to longevity, but the mechanisms that underlie these long-term effects are not well understood. In male vertebrates, elevated testosterone has been shown to increase reproductive success, but simultaneously to decrease survival. One factor that may contribute to or serve as a biomarker of these long-term effects of testosterone on longevity is telomeres, which are often positively related to lifespan and have been shown to shorten in response to reproduction. In this longitudinal study, we measured the effects of experimentally elevated testosterone on telomere shortening in free-living, male dark-eyed juncos (Junco hyemalis carolinensis), a system in which the experimental elevation of testosterone has previously been shown to increase reproductive success and reduce survival. We found a small, significant effect of testosterone treatment on telomeres, with testosterone-treated males exhibiting significantly greater telomere shortening with age than controls. These results are consistent with the hypothesis that increased telomere shortening may be a long-term cost of elevated testosterone exposure. As both testosterone and telomeres are conserved physiological mechanisms, our results suggest that their interaction may apply broadly to the long-term costs of reproduction in male vertebrates.

Urban birdsongs: higher minimum song frequency of an urban colonist persists in a common garden experiment.

Environmental changes caused by urbanization and noise pollution can have profound effects on acoustic communication. Many organisms use higher sound frequencies in urban environments with low-frequency noise, but the developmental and evolutionary mechanisms underlying these shifts are generally unknown. We used a common garden experiment to ask whether changes in minimum song frequency observed 30 years after a songbird colonized an urban environment are a consequence of behavioural flexibility. We captured male juvenile dark-eyed juncos, Junco hyemalis thurberi, from two populations (urban and mountain) soon after they reached independence (aged 25-40 days), raised them in identical indoor aviaries and studied their songs at an age of 3 years. We found that the large population difference in minimum frequency observed in the field persisted undiminished in the common garden despite the absence of noise. We also found some song sharing between the common garden and natal field populations, indicating that early song memorization before capture could contribute to the persistent song differences in adulthood. These results are the first to show that frequency shifts in urban birdsong are maintained in the absence of noise by genetic evolution and/or early life experiences.

Reactivation of latent infections with migration shapes population-level disease dynamics.

Annual migration is common across animal taxa and can dramatically shape the spatial and temporal patterns of infectious disease. Although migration can decrease infection prevalence in some contexts, these energetically costly long-distance movements can also have immunosuppressive effects that may interact with transmission processes in complex ways. Here, we develop a mechanistic model for the reactivation of latent infections driven by physiological changes or energetic costs associated with migration (i.e. 'migratory relapse') and its effects on disease dynamics. We determine conditions under which migratory relapse can amplify or reduce infection prevalence across pathogen and host traits (e.g. infectious periods, virulence, overwinter survival, timing of relapse) and transmission phenologies. We show that relapse at either the start or end of migration can dramatically increase prevalence across the annual cycle and may be crucial for maintaining pathogens with low transmissibility and short infectious periods in migratory populations. Conversely, relapse at the start of migration can reduce the prevalence of highly virulent pathogens by amplifying culling of infected hosts during costly migration, especially for highly transmissible pathogens and those transmitted during migration or the breeding season. Our study provides a mechanistic foundation for understanding the spatio-temporal patterns of relapsing infections in migratory hosts, with implications for zoonotic surveillance and understanding how infection patterns will respond to shifts in migratory propensity associated with environmental change. Further, our work suggests incorporating within-host processes into population-level models of pathogen transmission may be crucial for reconciling the range of migration-infection relationships observed across migratory species.

Artificial light at night amplifies seasonal relapse of haemosporidian parasites in a widespread songbird.

Urban habitats can shape interactions between hosts and parasites by altering not only exposure rates but also within-host processes. Artificial light at night (ALAN) is common in urban environments, and chronic exposure can impair host immunity in ways that may increase infection. However, studies of causal links between this stressor, immunity, and infection dynamics are rare, particularly in migratory animals. Here, we experimentally tested how ALAN affects cellular immunity and haemosporidian parasite intensity across the annual cycle of migrant and resident subspecies of the dark-eyed junco (Junco hyemalis). We monitored an experimental group exposed to light at night and a control group under natural light/dark cycles as they passed through short days simulating early spring to longer days simulating the breeding season, followed by autumn migration. Using generalized additive mixed models, we show that ALAN increased inflammation, and leucocyte counts were greatest in early spring and autumn. At the start of the experiment, few birds had active infections based on microscopy, but PCR revealed many birds had chronic infections. ALAN increased parasitaemia across the annual cycle, with strong peaks in spring and autumn that were largely absent in control birds. As birds were kept in indoor aviaries to prevent vector exposure, this increased parasitaemia indicates relapse of chronic infection during costly life-history stages (i.e. reproduction). Although the immunological and parasitological time series were in phase for control birds, cross-correlation analyses also revealed ALAN desynchronized leucocyte profiles and parasitaemia, which could suggest a general exaggerated inflammatory response. Our study shows how a common anthropogenic influence can shape within-host processes to affect infection dynamics.

What Do Ecology, Evolution, and Behavior Have in Common? The Organism in the Middle.

Biologists who publish in The American Naturalist are drawn to its unifying mission of covering research in the fields of ecology, evolution, behavior, and integrative biology. Presented here is one scientist's attempt to straddle these fields by focusing on a single organism. It is also an account of how time spent in the field stimulates a naturalist to wonder "why did that animal just do that?" and how research is guided by chance and intention interacting with the scientific literature and the people one meets along the way. With respect to the science, the examples come from bird migration, hormones and their connection to phenotypic integration, sexual and natural selection, and urban ecology. They also come from research on the impact of environmental change on the timing of reproduction and the potential for allochrony in migratory species to influence population divergence.

Migrant and resident female songbirds differ in gonadal response to upstream stimulation during seasonal sympatry.

Timing of seasonal reproduction is driven by environmental cues acting on the hypothalamic-pituitary-gonadal (HPG) axis. Groups of individuals, or populations, of the same species can exhibit different phenology despite facing similar environmental cues or living in the same habitat (i.e., seasonal sympatry). The mechanisms giving rise to population-level differences in reproductive timing are not fully understood, particularly for females. We studied the dark-eyed junco, a songbird with migratory and sedentary (i.e., resident) populations that live in overlapping distributions during winter. In early spring, residents initiate breeding and associated behaviors, including territory establishment and formation of pair bonds, while migrants prepare to depart for their breeding grounds. We tested whether migrant and resident hormonal response to upstream hormonal stimulation differed during this time period. We collected blood from free-living females in early spring, and challenged them with repeated gonadotropin-releasing hormone (GnRH) injections to measure testosterone (T) response. We predicted that if migrants are less sensitive to upstream stimulation than residents, then they would exhibit lower response to the repeated GnRH challenges in migrants. We found that migrant and resident females both responded to an initial challenge by elevating T, but residents responded more robustly, indicating that the ovary plays a role in population-level differences in reproductive timing. We also found that migrants and residents attenuated their response to repeated challenges, and did not differ from one another in final T levels. We speculate that the explanation for the generally reduced T response after repeated GnRH injections need not be the same for migrants and residents, but possible explanations include suppression of upstream stimulation owing to negative feedback after the initial injection oraromatization of T to estradiol between sampling time points. We suggest that future studies experimentally explore how the ovarian response to upstream stimulation changes during the transition to reproduction.

Seasonally sympatric songbirds that differ in migratory strategy also differ in neuroendocrine measures.

Seasonally breeding animals initiate gonadal recrudescence when mechanisms that suppress reproduction give way to mechanisms that stimulate it. However, knowledge of mechanistic changes in hormonal regulation during this transition is limited. Further, most studies of reproductive timing have focused on males, despite the critical role of females in determining breeding phenology. Closely related populations that live in the same environment but differ in reproductive timing provide an opportunity to examine differences in mechanisms during the transition from the pre-reproductive to reproductive state. We studied closely related migrant and resident populations of dark-eyed juncos (Junco hyemalis) that reside in the same environment in spring but differ in breeding phenology. Residents initiate breeding earlier than migrants, which do not breed until after they have migrated. To directly study differences in the hypothalamic mechanisms of reproduction, we captured 16 migrant and 13 resident females from the field on March 25-April 11. We quantified expression of mRNA transcripts and show that resident females had higher abundance of gonadotropin-releasing hormone transcripts than migrant females, indicating greater reproductive development in resident than migrant females living in the same environment. We also found higher transcript abundance of estrogen receptor and androgen receptor in migrant than resident females, suggesting that negative feedback may delay reproductive development in migrant females until after they migrate. These differences in hypothalamic mechanisms may help to explain differences in reproductive timing in populations that differ in migratory strategy.

Experimental evidence that symbiotic bacteria produce chemical cues in a songbird.

Symbiotic microbes that inhabit animal scent glands can produce volatile compounds used as chemical signals by the host animal. Though several studies have demonstrated correlations between scent gland bacterial community structure and host animal odour profiles, none have systematically demonstrated a causal relationship. In birds, volatile compounds in preen oil secreted by the uropygial gland serve as chemical cues and signals. Here, we tested whether manipulating the uropygial gland microbial community affects chemical profiles in the dark-eyed junco (Junco hyemalis). We found an effect of antibiotic treatment targeting the uropygial gland on both bacterial and volatile profiles. In a second experiment, we cultured bacteria from junco preen oil, and found that all of the cultivars produced at least one volatile compound common in junco preen oil, and that most cultivars produced multiple preen oil volatiles. In both experiments, we identified experimentally generated patterns in specific volatile compounds previously shown to predict junco reproductive success. Together, our data provide experimental support for the hypothesis that symbiotic bacteria produce behaviourally relevant volatile compounds within avian chemical cues and signals.

Density-dependent fitness, not dispersal movements, drives temporal variation in spatial genetic structure in dark-eyed juncos (Junco hyemalis).

Some studies have found that dispersal rates and distances increase with density, indicating that density-dependent dispersal likely affects spatial genetic structure. In an 11-year mark-recapture study on a passerine, the dark-eyed junco, we tested whether density affected dispersal distance and/or fine-scale spatial genetic structure. Contrary to expectations, we found no effect of predispersal density on dispersal distance or the proportion of locally produced juveniles returning to the population from which they hatched. However, even though density did not affect dispersal distance or natal return rates, we found that density still did affect spatial genetic structure. We found significant positive spatial genetic structure at low densities of (postdispersal) adults but not at high densities. In years with high postdispersal (adult) densities that also had high predispersal (juvenile) densities in the previous year, we found negative spatial genetic structure, indicating high levels of dispersal. We found that density also affected fitness of recruits, and fitness of immigrants, potentially linking these population parameters with the spatial genetic structure detected. Immigrants and recruits rarely nested in low postdispersal density years. In contrast, in years with high postdispersal density, recruits were common and immigrants had equal success to local birds, so novel genotypes diluted the gene pool and effectively eliminated positive spatial genetic structure. In relation to fine-scale spatial genetic structure, fitness of immigrants and new recruits is poorly understood compared to dispersal movements, but we conclude that it can have implications for the spatial distribution of genotypes in populations.

Changes in processes downstream of the hypothalamus are associated with seasonal follicle development in a songbird, the dark-eyed junco (Junco hyemalis).

Mechanisms related to seasonal reproductive timing in vertebrates have received far more study in males than in females, despite the fact that female timing decisions dictate when rearing of offspring will occur. Production and release of gonadotropin-releasing hormone (GnRH) by the hypothalamus stimulates the pituitary to secrete gonadotropins, initiating the beginning stages of gonadal recrudescence and production of the sex steroids, testosterone and estradiol, which are necessary to prime the liver for secretion of yolk precursors in breeding female birds. While stimulation by the hypothalamus can occur during the pre-breeding period, egg development itself is likely regulated downstream of the hypothalamus. We used GnRH challenges to examine variation in breeding-stage-specific patterns of pituitary and ovarian responsiveness in free-living female dark-eyed juncos (Junco hyemalis) and also examined the ovary and liver for variation in mRNA expression of candidate genes. Baseline LH levels increased during the transition from pre-breeding to egg-development, however no significant difference was observed in post-GnRH injection levels for LH or sex steroids (testosterone and estradiol). Interestingly, a stage by time-point interaction was observed, with post-GnRH LH levels increasing over baseline during the pre-breeding stage, but not during the egg-development stage. We observed a decrease in liver mRNA expression of estradiol receptor-alpha, and glucocorticoid and mineralocorticoid receptors and a decrease in glucocorticoid receptor expression levels in the ovary. A decline in FSH receptor expression across stages was also observed in the ovary. Combined, our data suggest seasonal variation in female's sensitivity to signals of HPG activity and energetic or stress signals. These data provide additional insight into the physiological mechanisms regulating onset of clutch initiation.

Early-breeding females experience greater telomere loss.

Annual reproductive success is often highest in individuals that initiate breeding early, yet relatively few individuals start breeding during this apparently optimal time. This suggests that individuals, particularly females who ultimately dictate when offspring are born, incur costs by initiating reproduction early in the season. We hypothesized that increases in the ageing rate of somatic cells may be one such cost. Telomeres, the repetitive DNA sequences on the ends of chromosomes, may be good proxies of biological wear and tear as they shorten with age and in response to stress. Using historical data from a long-term study population of dark-eyed juncos (Junco hyemalis), we found that telomere loss between years was greater in earlier breeding females, regardless of chronological age. There was no relationship between telomere loss and the annual number of eggs laid or chicks that reached independence. However, telomere loss was greater when temperatures were cooler, and cooler temperatures generally occur early in the season. This suggests that environmental conditions could be the primary cause of accelerated telomere loss in early breeders.

Seasonally sympatric but allochronic: differential expression of hypothalamic genes in a songbird during gonadal development.

Allochrony, the mismatch of reproductive schedules, is one mechanism that can mediate sympatric speciation and diversification. In songbirds, the transition into breeding condition and gonadal growth is regulated by the hypothalamic-pituitary-gonadal (HPG) axis at multiple levels. We investigated whether the difference in reproductive timing between two seasonally sympatric subspecies of dark-eyed juncos (Junco hyemalis) was related to gene expression along the HPG axis. During the sympatric pre-breeding stage, we measured hypothalamic and testicular mRNA expression of candidate genes via qPCR in captive male juncos. For hypothalamic mRNA, we found our earlier breeding subspecies had increased expression of gonadotropin-releasing hormone (GnRH) and decreased expression of androgen receptor, oestrogen receptor alpha and mineralocorticoid receptor (MR). Subspecies did not differ in expression of hypothalamic gonadotropin-inhibitory hormone (GnIH) and glucocorticoid receptor (GR). While our earlier breeding subspecies had higher mRNA expression of testicular GR, subspecies did not differ in testicular luteinizing hormone receptor, follicle-stimulating hormone receptor or MR mRNA expression levels. Our findings indicate increased GnRH production and decreased hypothalamic sensitivity to sex steroid negative feedback as factors promoting differences in the timing of gonadal recrudescence between recently diverged populations. Differential gene expression along the HPG axis may facilitate species diversification under seasonal sympatry.

Differential gene regulation underlies variation in melanic plumage coloration in the dark-eyed junco (Junco hyemalis).

Colour plays a prominent role in species recognition; therefore, understanding the proximate basis of pigmentation can provide insight into reproductive isolation and speciation. Colour differences between taxa may be the result of regulatory differences or be caused by mutations in coding regions of the expressed genes. To investigate these two alternatives, we studied the pigment composition and the genetic basis of coloration in two divergent dark-eyed junco (Junco hyemalis) subspecies, the slate-coloured and Oregon juncos, which have evolved marked differences in plumage coloration since the Last Glacial Maximum. We used HPLC and light microscopy to investigate pigment composition and deposition in feathers from four body areas. We then used RNA-seq to compare the relative roles of differential gene expression in developing feathers and sequence divergence in transcribed loci under common-garden conditions. Junco feathers differed in eumelanin and pheomelanin content and distribution. Within subspecies, in lighter feathers melanin synthesis genes were downregulated (including PMEL, TYR, TYRP1, OCA2 and MLANA), and ASIP was upregulated. Feathers from different body regions also showed differential expression of HOX and WNT genes. Feathers from the same body regions that differed in colour between the two subspecies showed differential expression of ASIP and three other genes (MFSD12, KCNJ13 and HAND2) associated with pigmentation in other taxa. Sequence variation in the expressed genes was not related to colour differences. Our findings support the hypothesis that differential regulation of a few genes can account for marked differences in coloration, a mechanism that may facilitate the rapid phenotypic diversification of juncos.

Sedentary songbirds maintain higher prevalence of haemosporidian parasite infections than migratory conspecifics during seasonal sympatry.

Long-distance migrations influence the physiology, behavior, and fitness of migratory animals throughout their annual cycles, and fundamentally alter their interactions with parasites. Several hypotheses relating migratory behavior to the likelihood of parasitism have entered the literature, making conflicting, testable predictions. To assess how migratory behavior of hosts is associated with parasitism, we compared haemosporidian parasite infections between two closely related populations of a common North American sparrow, the dark-eyed junco, that co-occur in shared habitats during the non-breeding season. One population is sedentary and winters and breeds in the Appalachian Mountains. The other population is migratory and is found in seasonal sympatry with the sedentary population from October through April, but then flies (≥ 900 km) northwards to breed. The populations were sampled in the wild on the shared montane habitat at the beginning of winter and again after confining them in a captive common environment until the spring. We found significantly higher prevalence of haemosporidian parasite infections in the sedentary population. Among infected juncos, we found no difference in parasite densities (parasitemias) between the sedentary and migrant populations and no evidence for winter dormancy of the parasites. Our results suggest that long-distance migration may reduce the prevalence of parasite infections at the population level. Our results are inconsistent with the migratory exposure hypothesis, which posits that long-distance migration increases exposure of hosts to diverse parasites, and with the migratory susceptibility hypothesis, which posits that trade-offs between immune function and migration increase host susceptibility to parasites. However, our results are consistent with the migratory culling hypothesis, which posits that heavily infected animals are less likely to survive long-distance migration, and with the migratory escape hypothesis, which posits that long-distance migration allows host populations to seasonally escape areas of high infection risk.