Structural genomic variation and migratory behavior in a wild songbird.

Structural variants (SVs) are a major source of genetic variation; and descriptions in natural populations and connections with phenotypic traits are beginning to accumulate in the literature. We integrated advances in genomic sequencing and animal tracking to begin filling this knowledge gap in the Eurasian blackcap. Specifically, we (a) characterized the genome-wide distribution, frequency, and overall fitness effects of SVs using haplotype-resolved assemblies for 79 birds, and (b) used these SVs to study the genetics of seasonal migration. We detected >15 K SVs. Many SVs overlapped repetitive regions and exhibited evidence of purifying selection suggesting they have overall deleterious effects on fitness. We used estimates of genomic differentiation to identify SVs exhibiting evidence of selection in blackcaps with different migratory strategies. Insertions and deletions dominated the SVs we identified and were associated with genes that are either directly (e.g., regulatory motifs that maintain circadian rhythms) or indirectly (e.g., through immune response) related to migration. We also broke migration down into individual traits (direction, distance, and timing) using existing tracking data and tested if genetic variation at the SVs we identified could account for phenotypic variation at these traits. This was only the case for 1 trait-direction-and 1 specific SV (a deletion on chromosome 27) accounted for much of this variation. Our results highlight the evolutionary importance of SVs in natural populations and provide insight into the genetic basis of seasonal migration.

Space weather disrupts nocturnal bird migration.

Space weather, including solar storms, can impact Earth by disturbing the geomagnetic field. Despite the known dependence of birds and other animals on geomagnetic cues for successful seasonal migrations, the potential effects of space weather on organisms that use Earth's magnetic field for navigation have received little study. We tested whether space weather geomagnetic disturbances are associated with disruptions to bird migration at a macroecological scale. We leveraged long-term radar data to characterize the nightly migration dynamics of the nocturnally migrating North American avifauna over 22 y. We then used concurrent magnetometer data to develop a local magnetic disturbance index associated with each radar station (ΔBmax), facilitating spatiotemporally explicit analyses of the relationship between migration and geomagnetic disturbance. After controlling for effects of atmospheric weather and spatiotemporal patterns, we found a 9 to 17% decrease in migration intensity in both spring and fall during severe space weather events. During fall migration, we also found evidence for decreases in effort flying against the wind, which may represent a depression of active navigation such that birds drift more with the wind during geomagnetic disturbances. Effort flying against the wind in the fall was most reduced under both overcast conditions and high geomagnetic disturbance, suggesting that a combination of obscured celestial cues and magnetic disturbance may disrupt navigation. Collectively, our results provide evidence for community-wide avifaunal responses to geomagnetic disturbances driven by space weather during nocturnal migration.

Lower survival of hybrid grosbeaks, but not towhees, suggests a molt divide disfavors hybrids.

Although avian hybrid zones in the Great Plains have been studied for almost 70 years, we know surprisingly little about the fitness costs to hybrids that keep these zones narrow. We compare age ratios in grosbeaks (Pheucticus ludovicianus and P. melanocephalus) and towhees (Pipilo erythropthalums and P. maculatus), two species pairs that differ in their life histories and molt schedules, to evaluate survival between hybrids and parentals. We then contrast molt and migratory divides as possible sources of selection against hybrids. Hybrid grosbeaks had 27%-33% lower survival relative to their parentals, whereas hybrid towhees had survival rates similar to parentals. Age ratio data for hybrid grosbeaks suggest high mortality in older birds, as expected if selection operates after the first year of life. This pattern is consistent with parental species of grosbeaks having contrasting molt schedules relative to migration, suggesting high mortality costs to hybrids driven by molt biology, which are expressed later in life. Contrasts in molt schedules are absent in towhees. While migratory divides may exist for towhees and grosbeaks, the low adult survival of hybrid grosbeaks suggest that molt may be an important and underappreciated source of selection maintaining this and other narrow avian hybrid zones.

Six decades of North American bird banding records reveal plasticity in migration phenology.

The timing of avian migration has evolved to exploit critical seasonal resources, yet plasticity within phenological responses may allow adjustments to interannual resource phenology. The diversity of migratory species and changes in underlying resources in response to climate change make it challenging to generalize these relationships. We use bird banding records during spring and fall migration from across North America to examine macroscale phenological responses to interannual fluctuations in temperature and long-term annual trends in phenology. In total, we examine 19 species of North American wood warblers (family Parulidae), summarizing migration timing from 2,826,588 banded birds from 1961 to 2018 across 46 sites during spring and 124 sites during fall. During spring, warmer spring temperatures at banding locations translated to earlier median passage dates for 16 of 19 species, with an average 0.65-day advancement in median passage for every 1°C increase in temperature, ranging from 0.25 to 1.26 days °C-1 . During the fall, relationships were considerably weaker, with only 3 of 19 species showing a relationship with temperature. In those three cases, later departure dates were associated with warmer fall periods. Projecting these trends forward under climate scenarios of temperature change, we forecast continued spring advancements under shared socioeconomic pathways from 2041 to 2060 and 2081 to 2100 and more muted and variable shifts for fall. These results demonstrate the capacity of long-distance migrants to respond to interannual fluctuations in temperatures, at least during the spring, and showcase the potential of North American bird banding data understanding phenological trends across a wide diversity of avian species.

Avoidance of different durations, colours and intensities of artificial light by adult seabirds.

There is increasing evidence for impacts of light pollution on the physiology and behaviour of wild animals. Nocturnally active Procellariiform seabirds are often found grounded in areas polluted by light and struggle to take to the air again without human intervention. Hence, understanding their responses to different wavelengths and intensities of light is urgently needed to inform mitigation measures. Here, we demonstrate how different light characteristics can affect the nocturnal flight of Manx shearwaters Puffinus puffinus by experimentally introducing lights at a colony subject to low levels of light pollution due to passing ships and coastal developments. The density of birds in flight above the colony was measured using a thermal imaging camera. We compared number of flying shearwaters under dark conditions and in response to an artificially introduced light, and observed fewer birds in flight during 'light-on' periods, suggesting that adult shearwaters were repelled by the light. This effect was stronger with higher light intensity, increasing duration of 'light-on' periods and with green and blue compared to red light. Thus, we recommend lower light intensity, red colour, and shorter duration of 'light-on' periods as mitigation measures to reduce the effects of light at breeding colonies and in their vicinity.

Drivers of fatal bird collisions in an urban center.

Millions of nocturnally migrating birds die each year from collisions with built structures, especially brightly illuminated buildings and communication towers. Reducing this source of mortality requires knowledge of important behavioral, meteorological, and anthropogenic factors, yet we lack an understanding of the interacting roles of migration, artificial lighting, and weather conditions in causing fatal bird collisions. Using two decades of collision surveys and concurrent weather and migration measures, we model numbers of collisions occurring at a large urban building in Chicago. We find that the magnitude of nocturnal bird migration, building light output, and wind conditions are the most important predictors of fatal collisions. The greatest mortality occurred when the building was brightly lit during large nocturnal migration events and when winds concentrated birds along the Chicago lakeshore. We estimate that halving lighted window area decreases collision counts by 11× in spring and 6× in fall. Bird mortality could be reduced by ∼60% at this site by decreasing lighted window area to minimum levels historically recorded. Our study provides strong support for a relationship between nocturnal migration magnitude and urban bird mortality, mediated by light pollution and local atmospheric conditions. Although our research focuses on a single site, our findings have global implications for reducing or eliminating a critically important cause of bird mortality.

Near-term ecological forecasting for dynamic aeroconservation of migratory birds.

Near-term ecological forecasting has the potential to mitigate negative impacts of human modifications on wildlife by directing efficient action through relevant and timely predictions. We used the U.S. avian migration system to highlight ecological forecasting applications for aeroconservation. We used millions of observations from 143 weather surveillance radars to construct and evaluate a migration forecasting system for nocturnal bird migration over the contiguous United States. We identified the number of nights of mitigation required to reduce the risk of aerial hazards to 50% of avian migrants passing a given area in spring and autumn based on dynamic forecasts of migration activity. We also investigated an alternative approach, that is, employing a fixed conservation strategy based on time windows that historically capture 50% of migratory passage. In practice, during both spring and autumn, dynamic forecasts required fewer action nights compared with fixed window selection at all locations (spring: mean of 7.3 more alert days; fall: mean of 12.8 more alert days). This pattern resulted in part from the pulsed nature of bird migration captured in the radar data, where the majority (54.3%) of birds move on 10% of a migration season's nights. Our results highlight the benefits of near-term ecological forecasting and the potential advantages of dynamic mitigation strategies over static ones, especially in the face of increasing risks to migrating birds from light pollution, wind energy infrastructure, and collisions with structures.

La estimación ecológica a corto plazo tiene el potencial para mitigar los impactos negativos de las modificaciones humanas sobre la fauna al dirigir las acciones eficientes mediante predicciones relevantes y oportunas. Usamos el sistema de migración de aves de Estados Unidos para resaltar las aplicaciones de la estimación ecológica para la aeroconservación. Usamos millones de observaciones tomadas de 143 radares de vigilancia climática para construir y evaluar un sistema de estimaciones migratorias para la migración de aves nocturnas en los Estados Unidos contiguos. Identificamos el número de noches de mitigación requeridas para reducir el riesgo de peligros aéreos para el 50% de las aves migratorias que pasan por un área específica en la primavera y en el otoño con base en las estimaciones dinámicas de la actividad migratoria. También investigamos una estrategia alternativa: el uso de una estrategia fija de conservación basada en las ventanas temporales que históricamente han capturado el 50% del pasaje migratorio. En la práctica, durante la primavera y el otoño, las estimaciones dinámicas requirieron menos noches de acción en comparación con la selección de ventana fija en todas las localidades (primavera: promedio de 7.3 más días de alerta; otoño: promedio de 12.8 más días de alerta). Este patrón resultó en parte por la naturaleza pulsada de las migraciones aviarias capturadas en los datos del radar, en los cuales la mayoría de las aves (54.3%) se mueven durante el 10% de las noches durante la temporada migratoria. Nuestros resultados resaltan los beneficios que tienen las estimaciones ecológicas a corto plazo en comparación con las estáticas, especialmente de frente a los riesgos crecientes que encaran las aves migratorias por la contaminación lumínica, la infraestructura de energía eólica y las colisiones con las estructuras.

Human activity shapes the wintering ecology of a migratory bird.

Human behavior profoundly affects the natural world. Migratory birds are particularly susceptible to adverse effects of human activities because the global networks of ecosystems on which birds rely are undergoing rapid change. In spite of these challenges, the blackcap (Sylvia atricapilla) is a thriving migratory species. Its recent establishment of high-latitude wintering areas in Britain and Ireland has been linked to climate change and backyard bird feeding, exemplifying the interaction between human activity and migrant ecology. To understand how anthropogenic influences shape avian movements and ecology, we marked 623 wintering blackcaps at 59 sites across Britain and Ireland and compiled a dataset of 9929 encounters. We investigated visitation behavior at garden feeding sites, inter-annual site fidelity, and movements within and across seasons. We analyzed migration tracks from 25 geolocators fitted to a subset of individuals to understand how garden behavior may impact subsequent migration and breeding. We found that blackcaps wintering in Britain and Ireland showed high site fidelity and low transience among wintering sites, in contrast to the itinerant movements characteristic of blackcaps wintering in their traditional winter range. First-winter birds showed lower site fidelity and a greater likelihood of transience than adults. Adults that frequented gardens had better body condition, smaller fat stores, longer bills, and rounder wingtips. However, blackcaps did not exclusively feed in gardens; visits were linked to harsher weather. Individuals generally stayed at garden sites until immediately before spring departure. Our results suggest that supplementary feeding is modifying blackcap winter ecology and driving morphological evolution. Supplemental feeding may have multifaceted benefits on winter survival, and these positive effects may carry over to migration and subsequent breeding. Overall, the high individual variability in blackcap movement and foraging ecology, and the flexibility it imparts, may have allowed this species to flourish during rapid environmental change.

Individual variability and versatility in an eco-evolutionary model of avian migration.

Seasonal migration is a complex and variable behaviour with the potential to promote reproductive isolation. In Eurasian blackcaps (Sylvia atricapilla), a migratory divide in central Europe separating populations with southwest (SW) and southeast (SE) autumn routes may facilitate isolation, and individuals using new wintering areas in Britain show divergence from Mediterranean winterers. We tracked 100 blackcaps in the wild to characterize these strategies. Blackcaps to the west and east of the divide used predominantly SW and SE directions, respectively, but close to the contact zone many individuals took intermediate (S) routes. At 14.0° E, we documented a sharp transition from SW to SE migratory directions across only 27 (10-86) km, implying a strong selection gradient across the divide. Blackcaps wintering in Britain took northwesterly migration routes from continental European breeding grounds. They originated from a surprisingly extensive area, spanning 2000 km of the breeding range. British winterers bred in sympatry with SW-bound migrants but arrived 9.8 days earlier on the breeding grounds, suggesting some potential for assortative mating by timing. Overall, our data reveal complex variation in songbird migration and suggest that selection can maintain variation in migration direction across short distances while enabling the spread of a novel strategy across a wide range.

The Genomic Landscape of Divergence Across the Speciation Continuum in Island-Colonising Silvereyes (Zosterops lateralis).

Inferring the evolutionary dynamics at play during the process of speciation by analyzing the genomic landscape of divergence is a major pursuit in population genomics. However, empirical assessments of genomic landscapes under varying evolutionary scenarios that are known a priori are few, thereby limiting our ability to achieve this goal. Here we combine RAD-sequencing and individual-based simulations to evaluate the genomic landscape of divergence in the silvereye (Zosterops lateralis). Using pairwise comparisons that differ in divergence timeframe and the presence or absence of gene flow, we document how genomic patterns accumulate along the speciation continuum. In contrast to previous predictions, our results provide limited support for the idea that divergence accumulates around loci under divergent selection or that genomic islands widen with time. While a small number of genomic islands were found in populations diverging with and without gene flow, in few cases were SNPs putatively under selection tightly associated with genomic islands. The transition from localized to genome-wide levels of divergence was captured using individual-based simulations that considered only neutral processes. Our results challenge the ubiquity of existing verbal models that explain the accumulation of genomic differences across the speciation continuum and instead support the idea that divergence both within and outside of genomic islands is important during the speciation process.

Evolutionary Response to Climate Change in Migratory Pied Flycatchers.

Climate change is rapidly advancing spring phenology [1-3] but at different rates in different species [1, 4]. Whether these advances are solely driven by phenotypic plasticity [2, 5] or also involve evolution is hotly debated (e.g., [5-7]). In some species, including avian long-distance migrants, plastic responses to early springs may be constrained by inherited circannual timing programs [8, 9], making evolutionary adjustment the only viable mechanism for keeping pace with shifting phenology [5, 10]. This constraint may be contributing to population declines in migratory species [5, 10-12]. To test whether a migrant's timing program has evolved [10, 12], we replicated an experimental study of the annual cycle of long-distance migratory pied flycatchers (Ficedula hypoleuca) after 21 years of warming. Flycatchers are a model for studying constrained ecological responses to climate change [6, 10, 12, 13]. We show that the phase of the flycatcher circannual clock controlling spring moult, migration, and reproductive timing advanced by 9 days. A nearby wild population mirrored these changes, concurrently advancing egg-laying by 11 days. Furthermore, the time window during which wild flycatcher reproductive timing was most sensitive to ambient temperature advanced by 0.8 days year-1. These results support a role of phenotypic evolution [14] in changing spring phenology [15, 16]. We suggest that the timing programs of long-distance migratory birds may have greater adaptive potential than previously thought, leaving some scope for evolutionary rescue in a changing climate.

Holding steady: Little change in intensity or timing of bird migration over the Gulf of Mexico.

Quantifying the timing and intensity of migratory movements is imperative for understanding impacts of changing landscapes and climates on migratory bird populations. Billions of birds migrate in the Western Hemisphere, but accurately estimating the population size of one migratory species, let alone hundreds, presents numerous obstacles. Here, we quantify the timing, intensity, and distribution of bird migration through one of the largest migration corridors in the Western Hemisphere, the Gulf of Mexico (the Gulf). We further assess whether there have been changes in migration timing or intensity through the Gulf. To achieve this, we integrate citizen science (eBird) observations with 21 years of weather surveillance radar data (1995-2015). We predicted no change in migration timing and a decline in migration intensity across the time series. We estimate that an average of 2.1 billion birds pass through this region each spring en route to Nearctic breeding grounds. Annually, half of these individuals pass through the region in just 18 days, between April 19 and May 7. The western region of the Gulf showed a mean rate of passage 5.4 times higher than the central and eastern regions. We did not detect an overall change in the annual numbers of migrants (2007-2015) or the annual timing of peak migration (1995-2015). However, we found that the earliest seasonal movements through the region occurred significantly earlier over time (1.6 days decade-1 ). Additionally, body mass and migration distance explained the magnitude of phenological changes, with the most rapid advances occurring with an assemblage of larger-bodied shorter-distance migrants. Our results provide baseline information that can be used to advance our understanding of the developing implications of climate change, urbanization, and energy development for migratory bird populations in North America.

Aeroecology of a solar eclipse.

Light cues elicit strong responses from nearly all forms of life, perhaps most notably as circadian rhythms entrained by periods of daylight and darkness. Atypical periods of darkness, like solar eclipses, provide rare opportunities to study biological responses to light cues. By using a continental scale radar network, we investigated responses of flying animals to the total solar eclipse of 21 August 2017. We quantified the number of biological targets in the atmosphere at 143 weather radar stations across the continental United States to investigate whether the decrease in light and temperature at an atypical time would initiate a response like that observed at sunset, when activity in the atmosphere usually increases. Overall, biological activity decreased in the period leading to totality, followed by a short low-altitude spike of biological activity during totality in some radars. This pattern suggests that cues associated with the eclipse were insufficient to initiate nocturnal activity comparable to that occurring at sunset but sufficient to suppress diurnal activity.

Comparative analysis examining patterns of genomic differentiation across multiple episodes of population divergence in birds.

Heterogeneous patterns of genomic differentiation are commonly documented between closely related populations and there is considerable interest in identifying factors that contribute to their formation. These factors could include genomic features (e.g., areas of low recombination) that promote processes like linked selection (positive or purifying selection that affects linked neutral sites) at specific genomic regions. Examinations of repeatable patterns of differentiation across population pairs can provide insight into the role of these factors. Birds are well suited for this work, as genome structure is conserved across this group. Accordingly, we reestimated relative (FST ) and absolute (dXY ) differentiation between eight sister pairs of birds that span a broad taxonomic range using a common pipeline. Across pairs, there were modest but significant correlations in window-based estimates of differentiation (up to 3% of variation explained for FST and 26% for dXY ), supporting a role for processes at conserved genomic features in generating heterogeneous patterns of differentiation; processes specific to each episode of population divergence likely explain the remaining variation. The role genomic features play was reinforced by linear models identifying several genomic variables (e.g., gene densities) as significant predictors of FST and dXY repeatability. FST repeatability was higher among pairs that were further along the speciation continuum (i.e., more reproductively isolated) providing further insight into how genomic differentiation changes with population divergence; early stages of speciation may be dominated by positive selection that is different between pairs but becomes integrated with processes acting according to shared genomic features as speciation proceeds.

A continental system for forecasting bird migration.

Billions of animals cross the globe each year during seasonal migrations, but efforts to monitor them are hampered by the unpredictability of their movements. We developed a bird migration forecast system at a continental scale by leveraging 23 years of spring observations to identify associations between atmospheric conditions and bird migration intensity. Our models explained up to 81% of variation in migration intensity across the United States at altitudes of 0 to 3000 meters, and performance remained high in forecasting events 1 to 7 days in advance (62 to 76% of variation was explained). Avian migratory movements across the United States likely exceed 500 million individuals per night during peak passage. Bird migration forecasts will reduce collisions with buildings, airplanes, and wind turbines; inform a variety of monitoring efforts; and engage the public.

Navigating north: how body mass and winds shape avian flight behaviours across a North American migratory flyway.

The migratory patterns of birds have been the focus of ecologists for millennia. What behavioural traits underlie these remarkably consistent movements? Addressing this question is central to advancing our understanding of migratory flight strategies and requires the integration of information across levels of biological organisation, e.g. species to communities. Here, we combine species-specific observations from the eBird citizen-science database with observations aggregated from weather surveillance radars during spring migration in central North America. Our results confirm a core prediction of migration theory at an unprecedented national scale: body mass predicts variation in flight strategies across latitudes, with larger-bodied species flying faster and compensating more for wind drift. We also find evidence that migrants travelling northward earlier in the spring increasingly compensate for wind drift at higher latitudes. This integration of information across biological scales provides new insight into patterns and determinants of broad-scale flight strategies of migratory birds.

High-intensity urban light installation dramatically alters nocturnal bird migration.

Billions of nocturnally migrating birds move through increasingly photopolluted skies, relying on cues for navigation and orientation that artificial light at night (ALAN) can impair. However, no studies have quantified avian responses to powerful ground-based light sources in urban areas. We studied effects of ALAN on migrating birds by monitoring the beams of the National September 11 Memorial & Museum's "Tribute in Light" in New York, quantifying behavioral responses with radar and acoustic sensors and modeling disorientation and attraction with simulations. This single light source induced significant behavioral alterations in birds, even in good visibility conditions, in this heavily photopolluted environment, and to altitudes up to 4 km. We estimate that the installation influenced ≈1.1 million birds during our study period of 7 d over 7 y. When the installation was illuminated, birds aggregated in high densities, decreased flight speeds, followed circular flight paths, and vocalized frequently. Simulations revealed a high probability of disorientation and subsequent attraction for nearby birds, and bird densities near the installation exceeded magnitudes 20 times greater than surrounding baseline densities during each year's observations. However, behavioral disruptions disappeared when lights were extinguished, suggesting that selective removal of light during nights with substantial bird migration is a viable strategy for minimizing potentially fatal interactions among ALAN, structures, and birds. Our results also highlight the value of additional studies describing behavioral patterns of nocturnally migrating birds in powerful lights in urban areas as well as conservation implications for such lighting installations.

Correlated patterns of genetic diversity and differentiation across an avian family.

Comparative studies of closely related taxa can provide insights into the evolutionary forces that shape genome evolution and the prevalence of convergent molecular evolution. We investigated patterns of genetic diversity and differentiation in stonechats (genus Saxicola), a widely distributed avian species complex with phenotypic variation in plumage, morphology and migratory behaviour, to ask whether similar genomic regions have become differentiated in independent, but closely related, taxa. We used whole-genome pooled sequencing of 262 individuals from five taxa and found that levels of genetic diversity and divergence are strongly correlated among different stonechat taxa. We then asked whether these patterns remain correlated at deeper evolutionary scales and found that homologous genomic regions have become differentiated in stonechats and the closely related Ficedula flycatchers. Such correlation across a range of evolutionary divergence and among phylogenetically independent comparisons suggests that similar processes may be driving the differentiation of these independently evolving lineages, which in turn may be the result of intrinsic properties of particular genomic regions (e.g. areas of low recombination). Consequently, studies employing genome scans to search for areas important for reproductive isolation or adaptation should account for corresponding regions of differentiation, as these regions may not necessarily represent speciation islands or evidence of local adaptation.

Where in the air? Aerial habitat use of nocturnally migrating birds.

The lower atmosphere (i.e. aerosphere) is critical habitat for migrant birds. This habitat is vast and little is known about the spatio-temporal patterns of distribution and abundance of migrants in it. Increased human encroachment into the aerosphere makes understanding where and when migratory birds use this airspace a key to reducing human-wildlife conflicts. We use weather surveillance radar to describe large-scale height distributions of nocturnally migrating birds and interpret these distributions as aggregate habitat selection behaviours of individual birds. As such, we detail wind cues that influence selection of flight heights. Using six radars in the eastern USA during the spring (2013-2015) and autumn (2013 and 2014), we found migrants tended to adjust their heights according to favourable wind profit. We found that migrants' flight altitudes correlated most closely with the altitude of maximum wind profit; however, absolute differences in flight heights and height of maximum wind profit were large. Migrants tended to fly slightly higher at inland sites compared with coastal sites during spring, but not during autumn. Migration activity was greater at coastal sites during autumn, but not during spring. This characterization of bird migration represents a critical advance in our understanding of migrant distributions in flight and a new window into habitat selection behaviours.