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The twenty-first century has witnessed an explosion in research on animal migration, in large part due to a technological revolution in tracking and remote-sensing technologies, along with advances in genomics and integrative biology. We now have access to unprecedented amounts of data on when, where, and how animals migrate across various continents and oceans. Among the important advancements, recent studies have uncovered a surprising level of variation in migratory trajectories at the species and population levels with implications for both speciation and the conservation of migratory populations. At the organismal level, studies linking molecular and physiological mechanisms to traits that support migration have revealed a remarkable amount of seasonal flexibility in many migratory animals. Advancements in the theory for why animals migrate have resulted in promising new directions for empirical studies. We provide an overview of the current state of knowledge and promising future avenues of study.

Bio-loggers are widely used for studying the movement and behavior of animals. However, some sensors provide more data than is practical to store given experiment or bio-logger design constraints. One approach for overcoming this limitation is to utilize data collection strategies, such as non-continuous recording or data summarization that may record data more efficiently, but need to be validated for correctness. In this paper we address two fundamental questions—how can researchers determine suitable parameters and behaviors for bio-logger sensors, and how do they validate their choices? We present a methodology that uses software-based simulation of bio-loggers to validate various data collection strategies using recorded data and synchronized, annotated video. The use of simulation allows for fast and repeatable tests, which facilitates the validation of data collection methods as well as the configuration of bio-loggers in preparation for experiments. We demonstrate this methodology using accelerometer loggers for recording the activity of the small songbird Junco hyemalis hyemalis.

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 differ-entiation 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 infer-ence 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., Funding was provided by grants CGL-2011-25866 and CGL-2015-66381 from Spain’s Ministerio de Ciencia e Innovación to B.M., and USA National Science Foundation IOS-1257527 to T.J.G.

Migratory bird populations frequently consist of individuals that overwinter variable distances from the breeding site. Seasonal changes in photoperiod, which varies with latitude, underlie seasonal changes in singing frequency in birds. Therefore, migratory populations that consist of individuals that overwinter at different latitudes with large overwintering ranges could experience within‐population variation in seasonal production of song. To test the influence of overwintering latitude on intrapopulation variance in song production in the spring, we subjected two groups of Eastern Song Sparrows (Melospiza melodia melodia) from the same partially migratory breeding population to different photoperiodic schedules associated with a 1,300‐km difference in overwintering location. One group remained on the natural photoperiodic schedule of the breeding site (resident group) while the other group experienced a nonbreeding photoperiod that mimicked a southern migration in the fall followed by a northern migration back to the breeding site in the spring (migratory group). We compared song output between the two groups in three different stages (nonbreeding, prebreeding, and breeding). Little singing occurred during nonbreeding stage sample dates (20 November, 6 December) for the resident group, and no singing occurred for the migrant group. During the prebreeding stage (27 January, 7 February), significantly more singing occurred in the resident group than in the migrant group. During the breeding stage (21 March, 4 April), after a simulated migration for the migrants, song output was similar in both groups. These results suggest that within‐population variation in wintering latitude may contribute to variation in seasonal changes in singing behavior, which may covary with readiness to breed. Studies utilizing confirmed migrants and residents, rather than merely simulated migrants and residents, are also needed to better understand these processes., Migratory bird populations often consist of individuals that overwinter at different distances from a common breeding site. In the laboratory, we compared singing behavior between two groups of birds (one “migratory” and one “resident”) that we subjected to natural photoperiods of Tampa, Florida, and Bloomington, Indiana, respectively. We found that the residents sang more during the prebreeding stage, but after a simulated spring migration, song output in the two groups was the same.

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.

As society confronts a multitude of wicked problems without clear solutions, transdisciplinary research institutes have the opportunity to meet the increasingly important challenge to foster research capable of addressing such problems—that is, cross-disciplinary and societally relevant research. There is a growing body of literature on how to conduct effective interdisciplinary, transdisciplinary, and team-based research, but there is less work that evaluates (1) the lessons learned, pitfalls, and successes involved in creating and maintaining transdisciplinary institutes that support this research and (2) how early-career researchers are shaped by and shape such institutes. In this commentary, we share insights and critical questions germane for those involved in the formation of, or participation in (especially as early-career, non-tenure-track researchers), transdisciplinary institutes. From our perspective as part of a unique cohort of research fellows developed as part of a new transdisciplinary institute at Indiana University, we explore facilitators and barriers to our ability to support the institute’s mission. Topics addressed include tensions between research and implementation, rapidly achieving collaborative research, and community building, especially in the context of nurturing an institute with temporary employees as a key component. We reflect on what our experiences as part of such an institute mean for our career pathways, especially in the context of current academic structures and incentives. Our insights are in the context of an environmental-focused institute, but the issues raised are likely relevant to transdisciplinary institutes formed around a wide range of other themes or topics, especially those seeking to learn from the experiences of the first few years of an institute.

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., A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.

Individuals and populations time annual events such as migration and reproduction to match favorable times in their environment. Physiological preparations for reproduction rely on predictive cues such as day length to accurately time reproduction. In birds, preparation typically begins with light reception by the hypothalamus, which initiates multiple central and peripheral responses. We studied two closely related populations of a songbird, the dark-eyed junco, that live in a common winter environment but diverge in their timing of reproduction as spring approaches. One population is resident and initiates reproduction earlier than the other, which migrates northward prior to reproducing. We caught resident and migrant juncos from the field during early spring and collected hypothalamic and pituitary tissues. We used isobaric tandem mass tag (TMT) labeling to identify differentially expressed proteins (DEPs) as possible regulators of the seasonal divergence in reproductive timing. We found 3038 unique proteins expressed in the hypothalamus and pituitary proteome, among which we identified 75 DEPs. These were associated with hormones, neurotransmitter secretion, transport, neuropeptide synthesis, prohormone synthesis, neurogenesis, GnRH synthesis, release and stability, food intake, locomotion, and social behavior. Some of these proteins were associated with early breeding in resident juncos, and others were associated with increased food intake, fat metabolism, locomotor activity and phenology in migratory juncos. Our results provide new insight into the neuroendocrine regulation of the timing of reproduction and migration. This study provides the first evidence of a relationship between functional protein variation in the neuroendocrine tissues and seasonal divergence in reproductive timing.

In Supplementary Table 1 of this Article, 23 samples (B10K-DU-029-32, B10K-DU-029-33, B10K-DU-029-36 to B10K-DU-029-44, B10K-DU- 029-46, B10K-DU-029-47, B10K-DU-029-49 to B10K-DU-029-53, B10K-DU- 029-75 to B10K-DU-029-77, B10K-DU-029-80, and B10K-DU-030-03; styled in boldface in the revised table) were assigned to the incorrect institution. Supplementary Table 1 has been amended to reflect the correct source institution for these samples, and associated data (tissue, museum ID/source specimen ID, site, state/province, latitude, longitude, date collected and sex) have been updated accordingly. The original table is provided as Supplementary Information to this Amendment, and the original Article has been corrected online.

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.

Understanding how populations adapt to constantly changing environments requires approaches drawn from integrative and evolutionary biology as well as population ecology. Timing of reproduction and migration reflect seasonal pulses in resources, are driven by day length, and are also responsive to environmental cues that change with climate. Researchers focusing on birds have discovered accelerated breeding, reductions in migration, and extensive variation in perception, transduction, and response to the environment. We consider situations in which individuals experience the same environment but differ in the timing of the annual cycle. Such scenarios provide exceptional opportunities to study mechanisms related to among-population differences in timing (allochrony) and distribution (sympatry–allopatry–heteropatry), which have the potential either to enhance or reduce population divergence and biodiversity.

Ongoing changes to global weather patterns and human modifications of the environment have altered the breeding and non-breeding ranges of migratory species, the timing of their migrations, and even whether they continue to migrate at all. Animal movements are arguably one of the most difficult behaviours to study, particularly in smaller birds that migrate tens to thousands of kilometres seasonally, often moving hundreds of kilometres each day. The recent miniaturization of tracking and logging devices has led to a radical transformation in our understanding of avian migratory behaviour and migratory connectivity. While advances in technology have altered the way researchers study migratory behaviour in the field, advances in techniques related to the study of physiological and genetic mechanisms underlying migratory behaviour have rarely been integrated into field studies of tracking. To predict the capacity of migrants to adjust to a changing planet, it is essential that we combine avian migration data with physiological and genetic measurements taken at key time points prior to, during and after migration.

Spatial and temporal fluctuations in resource availability have led to the evolution of varied migration patterns. In order to appropriately time movements in relation to resources, environmental cues are used to provide proximate information for timing and the endocrine system serves to integrate these external cues and behavioral and physiological responses. Yet, the regulatory mechanisms underlying migratory timing have rarely been compared across a broad range of migratory patterns. First, we offer an updated nomenclature of migration using a mechanistic perspective to clarify terminology describing migratory types in relation to ecology, behavior and endocrinology. We divide migratory patterns into three types: obligate, nomadic, and fugitive. Obligate migration is characterized by regular and directed annual movements between locations, most commonly for breeding and overwintering, where resources are predictable and sufficient. Nomadic migrations occur less predictably than do obligate migrations as animals make use of potentially rich but ephemeral resources that occur unpredictably in space or time. Fugitive migrations move animals away from an area in response to severe disruption of environmental conditions and occur as part of an emergency life history stage. We also consider partially migratory populations, which include a mix of sedentary and migratory individuals; the movement patterns of partial migrants are expected to fall into one of the three types above. For these various forms of migration, we review our understanding of the environmental cues and endocrine mechanisms that underlie the expression of a migratory state. Several common hormonal mechanisms exist across the varied migratory forms, but there are also important areas where further investigations are needed in order to gain broad insight into the origin of movements and the diversity of migratory patterns. We propose that taking a comparative approach across the migratory types that considers endocrine mechanisms will advance a new understanding of migration biology.

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 non-significant 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. This article is protected by copyright. All rights reserved.

Scientific Reports 6: Article number: 34207; published online: 26 September 2016; updated: 09 December 2016

Every year, billions of wild diurnal songbirds migrate at night. To do so, they shift their daily rhythm from diurnality to nocturnality. In captivity this is observed as a gradual transition of daytime activity developing into nocturnal activity, but how wild birds prepare their daily rhythms for migration remains largely unknown. Using an automated radio-telemetry system, we compared activity patterns of free-living migrant and resident European blackbirds (Turdus merula) in a partially migratory population during the pre-migratory season. We found that activity patterns between migrant and resident birds did not differ during day and night. Migrants did not change their daily rhythm in a progressive manner as has been observed in captivity, but instead abruptly became active during the night of departure. The rapid shift in rhythmicity might be more common across migratory songbird species, but may not have been observed before in wild animals due to a lack of technology.

Every year, billions of wild diurnal songbirds migrate at night. To do so, they shift their daily rhythm from diurnality to nocturnality. In captivity this is observed as a gradual transition of daytime activity developing into nocturnal activity, but how wild birds prepare their daily rhythms for migration remains largely unknown. Using an automated radio-telemetry system, we compared activity patterns of free-living migrant and resident European blackbirds (Turdus merula) in a partially migratory population during the pre-migratory season. We found that activity patterns between migrant and resident birds did not differ during day and night. Migrants did not change their daily rhythm in a progressive manner as has been observed in captivity, but instead abruptly became active during the night of departure. The rapid shift in rhythmicity might be more common across migratory songbird species, but may not have been observed before in wild animals due to a lack of technology.

Stable isotope ratios of hydrogen (δD) and carbon (δ13C) in feathers collected from Painted Buntings ( Passerina ciris (L., 1758)) breeding in the midwestern United States revealed a surprising degree of variation in δD, as well as a clear bimodal signal in δ13C in the innermost primary feather. Because this population does not molt on the breeding grounds, we reasoned that these observations could be due (i) to birds migrating to two (or possibly more) distinct molting areas or (ii) to differences in the timing of molt (as opposed to molt location) relative to arrival at the stopover site. To evaluate these hypotheses, we collected feathers at a molting location in northwestern Mexico, which revealed patterns similar to those from the birds in the US (favoring the second hypothesis above). We suspect that some birds arrive at stopover sites and begin molting before their body tissues equilibrate to the new isoscape so that the first feathers grown represent a blend of materials from the breeding and stopover locations. Other birds may delay molt after arriving at the molting site, allowing them to equilibrate with the local isoscape and produce feathers with isotope signatures of the molting location.

Summary 1. 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.

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.

The potential reproductive rate (PRR, the rate at which each sex could reproduce if given unlimited mates) has proven to be a useful tool in predicting the direction and strength of sexual selection. We conducted a 2-month study of the PRR in the polyandrous gulf pipefish, Syngnathus scovelli, a year-round breeder. In this sex-role reversed species, the female transfers eggs to a male's brood pouch during mating and thus renders him unavailable to mate for 2 weeks. We predicted females would have a higher PRR than males and that the rates in both sexes would change over successive breeding bouts in relationship to previous reproductive output. Females did have a higher overall PRR than males for the entire study period. However, PRR was not constant across individual breeding bouts. For each sex, the PRRs from the first and third bouts of mating were significantly higher than the PRR of second mating bout. Our results are consistent with individuals making trade-offs between current and future reproductive investment. We also discuss how ovarian morphology may contribute to elevated female PRR in this species. To our knowledge, this is the first study of PRR in a North American pipefish.

Comparative equilibration has been proposed as a methodological approach for determining the hydrogen isotopic composition (δD) of non-exchangeable hydrogen in complex organic materials, from feathers to blood and soils. This method depends on using homogenized standards that have been previously calibrated for their δD values of non-exchangeable H, that are compositionally similar to unknown samples, and that span an appropriate isotopic range. Currently no certified organic reference materials with exchangeable H exist, and so isotope laboratories have been required to develop provisional internal calibration standards, such as the keratin standards currently used in animal migration studies. Unfortunately, the isotope ratios of some samples fall outside the range of keratin standards currently used for comparative equilibration. Here we tested a set of five homogenized keratin powders as well as feathers from Painted Buntings and Dark-eyed Juncos to determine the effects of extrapolating comparative equilibration normalization equations outside the isotopic range of keratin standards. We found that (1) comparative equilibration gave precise results within the range of the calibration standards; (2) linear extrapolation of normalization equations produced accurate δD results to ∼40‰ outside the range of the keratins standards used (−187 to −108); and (3) for both homogenized keratin powders and heterogeneous unknown samples there was no difference in variance between samples within and outside the range of keratin standards. This suggested that comparative equilibration is a robust and practical method for determining the δD of complex organic matrices, although caution is required for samples that fall far outside the calibration range. Copyright © 2009 John Wiley & Sons, Ltd.

Migratory vertebrates adjust their movements in response to environmental change. Throughout their migrations, they gather information, integrate environmental and internal state data, and make decisions about the timing and orientation of migratory movements. Understanding this class of animal decision-making has both basic and applied interest because migratory animals face unique challenges adjusting to anthropogenic environmental changes worldwide. Evolved changes in decision mechanisms necessarily lag behind environmental changes, as their evolution is driven by the consequences of resulting actions, and this raises the possibility of major mismatches between behaviour and environmental circumstances when the latter change faster than the pace of natural selection. Yet, migration-decision systems have the capacity for considerable flexibility at the phenotypic level. Distinguishing the evolution of fixed genetic changes from changes that can occur in individual phenotypes often requires a better understanding of the mechanisms underlying organismal response. We reflect on such issues, hoping to engender new thinking about the special difficulties that long-distance migrants face in times of rapid environmental change. We focus on three key aspects: (1) We distinguish between variations in migratory paths forced upon the migrants by overwhelming environmental changes and those that arise from individual "strategic" variation in decision-making. (2) We examine how the availability and reliability of information about environmental quality determines optimal cue choice and cue-response, highlighting how changes in the correlations between cues and environmental parameters can lead to detrimental departure timing and negative fitness consequences on the breeding grounds. (3) We highlight how adjustments of individual migration strategies can be made by changes in the decision-making machinery during development, dramatically increasing the rate at which migratory strategies can adjust to environmental change.

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.

Variations in the geometry of the external flight apparatus of birds are beneficial for different behaviors. Long-distance flight is less costly with more pointed wings and shorter tails; however these traits decrease maneuverability at low speeds. Selection has led to interspecific differences in these and other flight apparatuses in relation to migration distance. If these principles are general, how are the external flight apparatus within a partially migratory bird species shaped in which individuals either migrate or stay at their breeding grounds? We resolved this question by comparing the wing pointedness and tail length (relative to wing length) of migrant and resident European blackbirds (Turdus merula) breeding in the same population. We predicted that migrant blackbirds would have more pointed wings and shorter tails than residents. Contrary to our predictions, there were no differences between migrants and residents in either measure. Our results indicate that morphological differences between migrants and residents in this partially migratory population may be constrained.

Comparative equilibration has been proposed as a methodological approach for determining the hydrogen isotopic composition (deltaD) of non-exchangeable hydrogen in complex organic materials, from feathers to blood and soils. This method depends on using homogenized standards that have been previously calibrated for their deltaD values of non-exchangeable H, that are compositionally similar to unknown samples, and that span an appropriate isotopic range. Currently no certified organic reference materials with exchangeable H exist, and so isotope laboratories have been required to develop provisional internal calibration standards, such as the keratin standards currently used in animal migration studies. Unfortunately, the isotope ratios of some samples fall outside the range of keratin standards currently used for comparative equilibration. Here we tested a set of five homogenized keratin powders as well as feathers from Painted Buntings and Dark-eyed Juncos to determine the effects of extrapolating comparative equilibration normalization equations outside the isotopic range of keratin standards. We found that (1) comparative equilibration gave precise results within the range of the calibration standards; (2) linear extrapolation of normalization equations produced accurate deltaD results to approximately 40 per thousand outside the range of the keratins standards used (-187 to -108); and (3) for both homogenized keratin powders and heterogeneous unknown samples there was no difference in variance between samples within and outside the range of keratin standards. This suggested that comparative equilibration is a robust and practical method for determining the deltaD of complex organic matrices, although caution is required for samples that fall far outside the calibration range.