Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

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Summary1. Tracking return migrations in songbirds has been impossible until recently when miniaturization of light-level loggers enabled observation of the first complete round trip. Although geolocators are extensively used on animals at sea, little is known about how accurate geolocators are for tracking terrestrial or forest-dwelling migrants. 2. To test the accuracy of geolocators for tracking migratory songbirds living in forested habitat, we calibrated geolocators to a source population located in central Europe and collected location estimates based on the source population calibration from stationary geolocators deployed over an 800 km NE to SW gradient in Western Europe. Additionally, we fit non-migratory songbirds (European blackbirds, Turdus merula) with geolocators for 12 months to compare known locations of individuals with locations estimated by geolocators. 3. We found an average error ±95% CI of 201 ± 43 km in latitude for stationary geolocators in forest habitat. Longitude error was considerably lower (12 ± 03 km). The most accurate geolocator was on average 23 km off target, the worst was on average 390 km off. 4. The winter latitude estimate error for geolocators deployed on sedentary birds was on average (±95% CI) 143 ± 62 km when geolocators were calibrated during the breeding season and 132 ± 75 km when they were calibrated during the winter. Longitude error for geolocators deployed on birds was on average (±95% CI) 50 ± 34 km. 5. Although we found error most likely due to seasonal changes in habitat and behaviour, our results indicate that geolocators can be used to reliably track long-distance forest-dwelling migrants. We also found that the low degree of error for longitude estimates attained from geolocators makes this technology suitable for identifying relatively short-distance movements in longitude.

Reproductive allochrony presents a potential barrier to gene flow and is common in seasonally sympatric migratory and sedentary birds. Mechanisms mediating reproductive allochrony can influence population divergence and the capacity of populations to respond to environmental change. We asked whether reproductive allochrony in seasonally sympatric birds results from a difference in response to supplementary or photoperiodic cues and whether the response varies in relation to the distance separating breeding and wintering locations as measured by stable isotopes. We held seasonally sympatric migratory and sedentary male dark-eyed juncos (Junco hyemalis) in a common garden in early spring under simulated natural changes in photoperiod and made measurements of reproductive and migratory physiology. On the same dates and photoperiods, sedentary juncos had higher testosterone (initial and gonadotropin-releasing hormone induced), more developed cloacal protuberances, and larger testes than migrants. In contrast, migratory juncos had larger fat reserves (fuel for migration). We found a negative relationship between testis mass and feather hydrogen isotope ratios, indicating that testis growth was more delayed in migrants making longer migrations. We conclude that reproductive allochrony in seasonally sympatric migratory and sedentary birds can result from a differential response to photoperiodic cues in a common garden, and as a result, gene flow between migrants and residents may be reduced by photoperiodic control of reproductive development. Further, earlier breeding in response to future climate change may currently be constrained by differential response to photoperiodic cues.

Summary 1.Partial migration occurs when a breeding population consists of seasonal migrants and year-round residents. Although it is common among birds, the basis of individual movement decisions within partially migratory populations is still unresolved. 2. Over 4 years, we used state of the art tracking techniques, a combination of geolocators and radio transmitters, to follow individual European blackbirds Turdus merula year round from a partially migratory population to determine individual strategies and departure and arrival dates. The individual-based tracking combined with measures of energetic and hormonal (corticosterone) state enabled us to distinguish between obligate and facultative migration and to test several classical hypotheses of partial migration: the 'Arrival Time'-, 'Dominance'-and 'Thermal Tolerance'-hypotheses. 3. Two distinct periods of departures from the breeding grounds were observed during the study; one in early autumn, and another during the midst of winter. Although blackbirds that migrated in autumn were never observed overwintering within 300 km of the study site, four individuals that departed in the winter were observed within 40 km. Females were significantly more likely to migrate in autumn than males but there was no difference in the age or body size of migrants and non migrants in autumn. Just prior to autumn migration, migrants had higher fat scores than non migrants and tended to have higher concentrations of baseline corticosterone, but similar concentrations of triglycerides. Unlike autumn migrants, we found no difference between the tendencies of males versus females to depart in winter, nor did we find any difference in body size or age of individuals that departed in the winter. 4. Autumn migration was sex biased and resembled obligate migration. Our results provide strong support for the 'Arrival Time' hypothesis for partial migration in the autumn. We found no clear support for the 'Dominance' or 'Thermal Tolerance' hypotheses. By tracking individuals year round, we were able to identify a second period of departures. Overall, these results suggest the co-occurrence of obligate autumn migrants, winter movements and sedentary individuals within a single population.

Seasonal migration is a widespread phenomenon, which is found in many different lineages of animals. This spectacular behaviour allows animals to avoid seasonally adverse environmental conditions to exploit more favourable habitats. Migration has been intensively studied in birds, which display astonishing variation in migration strategies, thus providing a powerful system for studying the ecological and evolutionary processes that shape migratory behaviour. Despite intensive research, the genetic basis of migration remains largely unknown. Here, we used state-of-the-art radio-tracking technology to characterize the migratory behaviour of a partially migratory population of European blackbirds (Turdus merula) in southern Germany. We compared gene expression of resident and migrant individuals using high-throughput transcriptomics in blood samples. Analyses of sequence variation revealed a nonsignificant genetic structure between blackbirds differing by their migratory phenotype. We detected only four differentially expressed genes between migrants and residents, which might be associated with hyperphagia, moulting and enhanced DNA replication and transcription. The most pronounced changes in gene expression occurred between migratory birds depending on when, in relation to their date of departure, blood was collected. Overall, the differentially expressed genes detected in this analysis may play crucial roles in determining the decision to migrate, or in controlling the physiological processes required for the onset of migration. These results provide new insights into, and testable hypotheses for, the molecular mechanisms controlling the migratory phenotype and its underlying physiological mechanisms in blackbirds and other migratory bird species.

In an era of climate change, understanding the genetic and physiological mechanisms underlying flexibility in phenology and life history has gained greater importance. These mechanisms can be elucidated by comparing closely related populations that differ in key behavioural and physiological traits such as migration and timing of reproduction. We compared gene expression in two recently diverged dark-eyed Junco (Junco hyemalis) subspecies that live in seasonal sympatry during winter and early spring, but that differ in behaviour and physiology, despite exposure to identical environmental cues. We identified 547 genes differentially expressed in blood and pectoral muscle. Genes involved in lipid transport and metabolism were highly expressed in migrant juncos, while genes involved in reproductive processes were highly expressed in resident breeders. Seasonal differences in gene expression in closely related populations residing in the same environment provide significant insights into mechanisms underlying variation in phenology and life history, and have potential implications for the role of seasonal timing differences in gene flow and reproductive isolation.

Billions of animals migrate between breeding and non-breeding areas worldwide. Partial migration, where both migrants and residents coexist within a population, occurs in most animal taxa, including fish, insects, birds and mammals. Partial migration has been hypothesised to be the most common form of migration and to be an evolutionary precursor to full migration. Despite extensive theoretical models about partial migration and its potential to provide insight into the ecology and evolution of migration, the physiological mechanisms that shape partial migration remain poorly understood. Here, we review current knowledge on how physiological processes mediate the causes and consequences of avian partial migration, and how they may help us understand why some individuals migrate and others remain resident. When information from birds is missing, we highlight examples from other taxa. In particular, we focus on temperature regulation, metabolic rate, immune function, oxidative stress, telomeres, and neuroendocrine and endocrine systems. We argue that these traits provide physiological pathways that regulate the ecological and behavioural causes and/or consequences of partial migration, and may provide insight into the mechanistic basis of wintering decisions. They may, thus, also help us to explain why individuals switch strategies among winters. We also highlight current gaps in our knowledge and suggest promising future research opportunities. A deeper understanding of the physiological mechanisms mediating the causes and consequences of partial migration will not only provide novel insights into the ecology and evolution of migration in general, but will also be vital to precisely modelling population trends and predicting range shifts under global change. Keywords Ecophysiology • Ecoimmunology • Hormones • Metabolism • Movement ecology • Avian life history Zusammenfassung Weltweit ziehen Milliarden von Vögeln zwischen Brut-und Überwinterungsgebieten. Eine der häufigsten Zugformen ist Teilzug. Bei Teilzug gibt es innerhalb einer Population sowohl Zugvögel als auch Standvögel. Diese Form des Zuges gibt es in fast allen Tiergruppen, von Fischen über Insekten und Vögel bis hin zu Säugetieren. Teilzug ist möglicherwiese die evolutionäre Frühform von vollständigem Zug. Obwohl es viele theoretische Modelle über Teilzug gibt und Teilzug das Potential hat uns viele Einblicke in die Ökologie und Evolution von Zugverhalten zu geben, sind die physiologischen Mechanismen die Teilzug regulieren weitgehend unbekannt. In dieser Literaturübersicht fassen wir das derzeitige Wissen wie physiologische Prozesse die Ursachen und Folgen von Teilzug regulieren zusammen. Wir zeigen auf wie ein Verständnis der physiologischen Prozesse uns dabei helfen kann zu verstehen warum manche Individuen ziehen und andere Standvögel sind. Unsere Literaturübersicht fokussiert sich auf Wissen an Vögeln, aber wenn solches Wissen nicht vorhanden ist, greifen wir auf Beispiele von anderen Tiergruppen zurück. Wir fokussieren uns auf die folgenden physiol...